Bioinformatics and Computational Biology articles

Time frame: 1 June 2025 - 30 May 2026

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Count: 2324

Article ‘Count’ for Bioinformatics and Computational Biology.

Journal Count
9
Quantum Dot Encoding for In-Solution Single-Molecule Biomarker Counting in Metastatic Prostate Cancer
Surfactant-Modified Magnetic Nanoparticles Enable Efficient and Cost-Effective Plasma Proteomics for Enhanced Biomarker Discovery
Multimodal DNA Nanostructure Barcodes for Single-Cell Protein Profiling and Tumor Subtyping
Lung Cancer Cell–Macrophage Interaction System for Signal Pathway-Based Logic Analysis and Drug Testing
Gemini SERS for Cross-Category Biomarker Detection and Early Warning of Sudden Cardiac Death in Acute Coronary Syndrome
Nanostraw Electroporation for Temporal RNA Sampling from Living 2D and 3D Cell Culture Systems
Integrated Error Correction to Enhance Efficiency of Digital Data Storage Based on DNA Nanostructures
Machine Learning-Enhanced Single-Particle Tracking for Rapid Screening of Tumor Immunomodulatory Drugs
Chromato-Kinetic Fingerprinting Enables Multiomic Digital Counting of Single Disease Biomarker Molecules
4
Adaptive Peroxynitrite Scavenging–Driven Synergistic Drug Release for Targeted and Efficient Theranostics in Ischemic Stroke
A Multiplexed and In Situ Self-Calibration Biosensor Integrated System for Metabolic Health Analysis in Human Urine
Peptide Sequencing With Single Acid Resolution Using a Sub-Nanometer Diameter Pore
Rapid Single‐Cell Proteomics Using Nanoconfined Enzyme Reactors on a Microscale Digital Microfluidics Platform
3
Engineered Development: Directed Morphogenesis of an Embryonic Heart Tube
MUTE‐Seq: An Ultrasensitive Method for Detecting Low‐Frequency Mutations in cfDNA With Engineered Advanced‐Fidelity FnCas9
Self‐Evolving Discovery of Carrier Biomaterials with Ultra‐Low Nonspecific Protein Adsorption for Single Cell Analysis
5
Plasma metabolites, dietary intakes, and breast cancer incidence: a prospective case-cohort study in NutriNet-Santé
Metabolome contribution to sex differences in the link between alcohol consumption and type 2 diabetes: a prospective analysis in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
Thiamine status in Belgian adults assessed by volumetric absorptive microsampling: a nation-wide cross-sectional survey
Comparing a diet-wide panel of biomarkers of food intake in whole blood and 24-hour urine and self-reported with known dietary intakes: randomized feeding trial of three 48-hour interventions
Impact of Comprehensive Lifestyle Interventions on Plasma Branched-Chain Amino Acid Concentrations: A Randomized Trial
1
Power and sample size calculations for testing the ratio of reproductive values in phylogenetic samples
71
Integrative genomics and single-cell CRISPRi screening dissect Alzheimer GWAS non-coding variants regulating TSPAN14
A phenome-wide association study of CNVs genotyped from genome sequencing read depth in the UK Biobank
A next-generation episignature for Kabuki syndrome enables fine mapping of the impact of KMT2D variants to inform precision medicine
Principled measures and estimates of trait polygenicity
Sensitivity of HiFi long-read genome sequencing for difficult-to-detect pathogenic variants when applied to real-world clinical laboratory samples
Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases
A flexible and unified framework for single- and multi-outcome Mendelian randomization using summary statistics
Putting polygenic scores in context: How intersectional factors affect relative and absolute genetic risk
PACells identifies phenotype-associated cell states from single-cell chromatin accessibility profiles
Neurodevelopmental copy-number variants increase risk of internalizing and cardiometabolic multimorbidity: Findings from the UK Biobank
Associations of genetic variants with gene expression factors reveal biological pathways underlying complex traits
Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies
Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants
Best practices for improving alignment and variant calling on human sex chromosomes
Genetics of skeletal proportions across two different populations
Inclusion bias affects common variant discovery and replication in a health-system linked biobank
MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes
Mind the gap: Characterizing bias due to population mismatch in two-sample Mendelian randomization
Higher eQTL power reveals signals that boost GWAS colocalization
Multiple-testing corrections in case-control studies using identity-by-descent segments
Validation and context-dependent effects of a prostate cancer polygenic risk score in the All of Us Research Program
Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver
Mendelian randomization linking metabolites with enzymes reveals pathway regulation and therapeutic avenues
AncientProxy: A catalog of ancient proxies for modern genetic variants
A gene-specific variance-control approach corrects polygenicity-driven inflation observed in transcriptome-wide association studies
LiMA: Robust inference of molecular mediation from summary statistics
Functional analysis of NPR2 variants supports the therapeutic rationale for CNP in short stature
The relationship between genotype- and phenotype-based estimates of genetic liability to psychiatric disorders, in practice and in theory
MIRAGE: A Bayesian statistical method for gene-level rare-variant analysis incorporating functional annotations
Genetic control of non-coding RNAs in the human brain and their implications for complex traits
Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits
Genetic regulation of the plasma proteome and its link to cardiometabolic disease in Greenlandic Inuit
A deep dive into statistical modeling of RNA splicing QTLs reveals variants that explain neurodegenerative disease
Using the ancestral recombination graph to study the history of rare variants in founder populations
Logica: A likelihood framework for cross-ancestry local genetic correlation estimation using summary statistics
A scalable framework for identifying allelic series from summary statistics
The utility of ultra-deep RNA sequencing in Mendelian disorder diagnostics
COMPADRE: Combined pedigree-aware distant relatedness estimation for improved pedigree reconstruction
Local ancestry-informed GWAS of warfarin dose requirement in African Americans identifies a CYP2C19 splicing QTL
Multiple-testing corrections in selection scans using identity-by-descent segments
Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits
Genetic architecture and analysis practices of circulating metabolites in the NHLBI Trans-Omics for Precision Medicine Program
Unveiling tissue heterogeneity through genomic interaction-encoded image representation of RNA-sequencing data
MosCoverY: A method to estimate mosaic loss of Y chromosome from sequencing coverage data
Combining evidence from human genetic and functional screens to identify pathways altering obesity and fat distribution
A semi-empirical Bayes approach for calibrating weak instrumental bias in sex-specific Mendelian randomization studies
Evaluating multi-ancestry genome-wide association methods: Statistical power, population structure, and practical implications
Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies
Estimating gene conversion rates from population data using multi-individual identity by descent
SPINK1-related chronic pancreatitis: A model that encapsulates the spectrum of variant effects, genetic complexity, and classificatory challenges
Leveraging functional annotations to map rare variants associated with Alzheimer disease with gruyere
The Causal Pivot: A structural approach to genetic heterogeneity and variant discovery in complex diseases
Estimation of demography and mutation rates from one million haploid genomes
Exploring the omnigenic architecture of selected complex traits
Sparse modeling of interactions enables fast detection of genome-wide epistasis in biobank-scale studies
Rare-variant association studies: When are aggregation tests more powerful than single-variant tests?
Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components
A genealogy-based approach for revealing ancestry-specific structures in admixed populations
A calcium-sensing receptor allelic series and underdiagnosis of genetically driven hypocalcemia
Efficient Mendelian randomization analysis with self-adaptive determination of sample structure and multiple pleiotropic effects
Haplotype analysis reveals pleiotropic disease associations in the HLA region
Leveraging local ancestry and cross-ancestry genetic architecture to improve genetic prediction of complex traits in admixed populations
Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets
Toward whole-genome inference of polygenic scores with fast and memory-efficient algorithms
TransferTWAS: A transfer learning framework for cross-tissue transcriptome-wide association study
Single-cell transcriptome-wide Mendelian randomization and colocalization analyses uncover cell-specific mechanisms in atherosclerotic cardiovascular disease
Applying multimodal AI to physiological waveforms improves genetic prediction of cardiovascular traits
CADET: Enhanced transcriptome-wide association analyses in admixed samples using eQTL summary data
Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples
Validating data from multiplex assays of variant effect: A CanVIG-UK national survey of NHS clinical scientists
Beyond predictive R2: Quantile regression and non-equivalence tests reveal complex relationships of traits and polygenic scores
1
Genetic Associations with Placental and Pregnancy Proteins in Maternal Serum Identify Biomarkers for Hypertension in Pregnancy
7
An Integrated Machine Learning and Genomic Framework for Precise Detection of Gastric Cancer
Leveraging Kappa-Lambda Signatures in a Multistage Machine Learning Pipeline for B-Cell Lymphoma Detection by Flow Cytometry
Single-cell triomics analysis of tumor cells infiltrating patient-derived breast cancer scaffolds
Interpreting Deep Learning-based Prediction of BRAF V600E Mutation using Diagnostic Whole Slide Images in Skin Cutaneous Melanoma
Cross-Modality Learning for Predicting IHC Biomarkers from H&E-Stained Whole-Slide Images
From Single-Cancer to Pan-cancer Prognosis: A Multi-modal Deep Learning Framework for Survival Analysis with Robust Generalization Capability
Cross-Species Functional Genomic Screens Identify Novel Therapeutic Targets in Malignant Peripheral Nerve Sheath Tumors
1
Novel Genetic Loci for Nontuberculous Mycobacterial Pulmonary Disease and Potential Protective Effect of Body Mass Index.
292
MS-Net: Multi-Similarity-Based Network Annotation for Untargeted Metabolomics
A Reproducible Multichannel Synchronous Rapid Phosphopeptide Enrichment Strategy Enabled by Anisotropic Porous Chitosan-Based Arrays
Determination from Nontargeted Metabolite Profiling Using Internal and External Standards
Ultrafast Postcolumn Microdroplet Derivatization of Nucleobases for Enhanced Online Detection, Characterization, and Quantification of Nucleic Acid Modifications Using LC-MS2
MS-MINT: An Open-Source Data Analysis Software for Large-Scale Metabolomics Studies
Pitfalls and Inherent Biases in Liquid Handling Robotics: Investigations in Automation for SI Traceable Measurements
Nuclear DNA-Gated Electrochemiluminescence Microscopy with Deep Learning for Single-Cell Apoptosis Profiling
Artificial Intelligence-Enhanced Electrogenerated Chemiluminescence Imaging for Single-Molecule Detection
ProteoIntegrator: A Scalable and Integrated Platform for Robust Multi-Source Proteomics Data Harmonization, Differential and Functional Analysis
Ribonucleotide-Modified Primer Overlapping Blocker Elongation (PROBE) Assay for Highly Specific Mutation Detection
Lipid Class Prediction from MS1 Data using Gaussian Graphical Models
WTop: A Wavelet-Driven Framework for Comprehensive Proteoform Characterization in Top-Down Mass Spectrometry
A Multidimensional Workflow for Comprehensive Xenometabolome Profiling by Integrating TIMS-PASEF with LC-HRMS and Biotransformation-Informed Suspect and Nontarget Screening
A Miniaturized, Automated Proteomic Sample Preparation Platform for High-Throughput Target Deconvolution of Natural Products
General Nuclear Magnetic Resonance Analysis Toolbox for Stats: A Comprehensive Module for Nuclear Magnetic Resonance-Based Chemometrics and Metabolomics
Hairpin-Mediated TMSDR-CHA Signal Conversion for Highly Specific Single-Base Discrimination of EGFR L858R Mutation
One-Pot Cascade Amplification Coupled with Lanthanide-Tagged ICP-MS for the Ultrasensitive Simultaneous Quantification of BCR-ABL Fusion Gene Subtypes
Real-Time Monitoring of Self-Repair in Single Bacteria after Photodamage by Synchronous Bioluminescence-Autofluorescence Imaging
Coupling Isotope-Coded Derivatization with Fragment-Imprinted Selective Recognition for Comprehensive Analysis of Temporal Dynamics in the Serum Neurotransmitters’ Metabolic Network by UHPLC-MS/MS
A Practical DNA Molecular Computing Platform for Identifying Expression Patterns of Multiple miRNAs Related to Diseases
Rapid Noninvasive Classification of Prostatic Disease Using Paper Spray Ionization Mass Spectrometry (PSI-MS)-Based Nontargeted Metabolomics
Single-Blood-Draw-Based Screening of Cancer Histotypes via Homologous Adhesion between Tumor Extracellular Vesicles and Bionic Microspheres
Circulating Tumor DNA Monitoring in Patients with Uveal Melanoma Using Mutation-Agnostic Multiplex Drop-Off ddPCR Assays
Simultaneous In-Depth Single-Cell Proteomic and Metabolomic Analysis
Simple, Fast, and Highly Efficient One- or Two-Step Proteomic Preparation Enables Deep Profiling of Microgram-Level FF and FFPE Tissues
Development of a Fluorescence Polarization Assay for p300/CBP and Its Application Using a Direct-to-Biology Approach
Best Practices in GC–MS and GC × GC–MS-Based Metabolomics and Volatile Analyses: An International Survey
Expanding the Analytical Toolbox for Extracellular Vesicle Biochemical Profiling: A Multiplatform Spectroscopic and Chromatographic Strategy
FiLM-Enhanced Biologically Informed Neural Networks for Multiclass Omics Analysis and Biomarker Discovery
FlashMRM: An Automated Platform for MRM Method Generation and Iterative Optimization Based on High-Resolution Spectra
METLIN 960 K: An Empirical Tandem Mass Spectrometry Data Resource
A Universal Framework for Blood Ionome Extraction and Intelligent Quality Control in 1H NMR Metabolomics
CASMDB: An Open-Source Database of Metabolite Annotation Data for 1D 1H NMR-Based Metabolomics
Rational Selection of Minimal Sensor Arrays for Analyte Fingerprinting
Label-Free High-Throughput Screening of CYP3A4 Inhibitors Using Acoustic Ejection Mass Spectrometry
Decoding the Oxylipin Chemical Space Using Ion Identity Molecular Networking
ValveCCI-seq: An Advanced Microfluidic Approach for Deciphering Cell–Cell Interactions
Automating Middle-Down Mass Spectrometry Analysis for Extensive Antibody Characterization
Multigated DNA Cascade Amplifier for Ultrasensitive Spatiotemporal Imaging of PLS3 mRNA at the Single-Cell Level for Early Detection of Breast Cancer Metastasis
scAClc: A Multi-Objective Adaptive Clustering Framework for Single-Cell Transcriptomics via Contrastive and Resolution-Aware Representation Learning
Rapid Analysis of NAD and Other Phosphorylated Metabolites in Complex Biological Samples by Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry
Efficient Transformation Product Identification and Structural Elucidation Using an Integrated Bottom-Up HRMS Workflow with Pyhrms and Transformapy
Achieving Effective Batch-to-Batch Error Correction through Suppression Correction and Dual MSTUS Normalization
A Prototype timsOmni Platform Enables Confident Annotation of the Key Hypervariable CDR3 Regions of IgG Immunoglobulins Using Low- and High-Energy Electron-Based Fragmentation
A Chemically Derivatized in Silico Mass Spectral Library for Fine-Structure Annotation of Phosphoinositides
Integrated Single-Cell Mass Spectrometry Imaging and Immunofluorescence Microscopy for Multimodal Characterization of Human Immune Cells
Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer
Automatic Blood Protein Enrichment by Magnetic-COF Polymers
Implementing Annotation Confidence Scoring in Untargeted Mass Spectrometry Workflows for Small Molecule Analysis
Artificial Intelligence-Based LC-OzESI-MRM for Isomer-Resolved Triacylglycerol Profiling by In-Source Ozonolysis
A Clinical Lipidomics Platform: Development and Validation of a High-Throughput LC-MS Assay for Cardiovascular Disease Risk Assessment
Automated Platform for Mass-Spectrometry-Based Multiomics Analysis from Small Volumes of Biofluids
Direct Infusion Acoustic Droplet Ejection Mass Spectrometry: Enabling High-Throughput Shotgun Lipidomics
High-Throughput Single-Cell Lipid Mass Cytometry for Rapid and Robust Screening of Rare Cells
Mapping Cell Metabolic States by Image-Enabled Gating Metabolomic Cytometry
Automated Online Direct mRNA Sequence Mapping Using Partial RNase T1 Digests
SIBioX: A Matrix Based Bioinformatics Analysis Tool Based on Swarm Intelligence Algorithm
Lessons Learned in Orbitrap MS-Based Isotope Ratio Analysis of Organic Acid Mixtures
A Biologically Informed Machine Learning Pipeline Uncovers Metabolic Features of Intestinal Barrier Dysfunction
Comparison of Liquid Chromatography- and Nano-Electrospray Ionization-Mass Spectrometry Approaches for Single-Cell Metabolomics
A Sugaromics Method for Combined Targeted and Untargeted Sugar Profiling: Fit-for-Purpose Validation of a Quantitative GC × GC-MS Approach
Protein-Corona-Based Nanomagnetic Enrichment Strategy for In-Depth Secretome Profiling of Lung Adenocarcinoma Organoids
Targeted and Nontargeted Detection and Quantitation of Arsenolipids in a Tuna Fish Reference Material (BCR-627) Using Reversed-Phase HPLC with High-Resolution Electrospray Mass Spectrometry and Inductively Coupled Plasma Mass Spectrometry
Untargeted Multiple Reaction Monitoring
Challenges and Good Practices in Preprocessing and Normalization of Untargeted DNA Adductomics Data in Exposomics Research
DNA Logic Gate-Integrated Peptide Nucleic Acid-Optical Fiber Sensor for Ultrasensitive Breast Cancer Exosome Profiling
SPIN: Inkjet-Driven Nanowell Workflow for Scalable and Sensitive Single-Cell Proteomics
Suppression Probe Enrichment for Highly Sensitive and Multiplexed Detection of RAS Mutations in Colorectal Cancer
A Proximal-Guaranteed Dual-Marker Electrochemiluminescence System for Accurate Identification of Colorectal Cancer Cell Subpopulations
Intrinsic N-Terminal Reactivity and Improved Analysis of DSSO-Carbamate and Carbamate-Based Cross-Linkers
Position-Specific Carbon Isotope Fingerprinting of Fluorinated Organics and Degradation Products
Resolving sn-Positional Isomers of Docosahexaenoic Acid-Bound Phospholipids in the Mouse Brain by Cyclic Ion Mobility Mass Spectrometry Imaging
Machine Learning-Enhanced Microfluidic Impedance Platform for Rare Cell Analysis
Ultra-High-Resolution MS1-Based Quantification with Chimeric Spectra Deconvolution Enables In-Depth Quantitative Proteomics and Application in Whole-Tissue Spatial Proteomics
Covalent Organic Framework with Acid Precipitation Enhances Microprotein Enrichment and Discovery of Ferroptosis-Associated Microproteins
Advancing Collision-Induced Affinity Selection Mass Spectrometry for Quantitative Ligand Analysis in Complex Mixtures
High Coverage Quantitative Lipidomic Analysis for Multiple Biological Matrices Using Ultrahigh-Performance Liquid-Chromatography and Tandem Mass Spectrometry
Measurable Feature Prediction for Estimating Chemical Space Coverage in LC–ESI–HRMS Nontargeted Analysis
LCMS-Net: Deep Learning for Raw High Resolution Mass Spectrometry Data Applied to Forensic Cause-of-Death Screening
SILICO-MS: Exploring Structural Lipidomic Alterations Using an Ionization-Coupled Ozonolysis Mass Spectrometry Strategy
MiProChip: A Scalable Microfluidic Platform for Multiplexed Single-Cell Proteomics via Isobaric Labeling
Pho-Tip: One-Pot Dephosphorylation for Rapid and Sensitive Analysis of DIA Phosphoproteomics Data
Automated High-Throughput Proteomics Sample Preparation Platform Using DNA Extraction Plate for Industrial Microorganisms
NMR Based Real-Time Analysis of Exometabolites Decodes the Mechanism of Action of Antibacterial Molecules, Nanoparticles, and Materials
Integrative Molecular Pattern Learning for Mental Disorders Via Dual-Effect Matrix-Enabled Multiomics Platform
Multidose Inline Size-Exclusion Chromatography–Flash Oxidation for Structural Analysis of Dynamic Protein–Ligand Interactions of Antithrombin III and Unfractionated Heparin
Soft-Chain-Induced Ultrahigh-Resolution Chiral Separation of Amino Acids via Bimetallic Immobilization in MALDI-TIMS-MS
Programmable Multiplexed Proteomics via Sequence-Encoded Mass Tagging
Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA
CellMate─A Deep Learning-Assisted Single-Cell Data Processing Platform
Single-Electrode High-Throughput 12-Well Array Electrochemiluminescence Imaging Sensor for Portable Parallel Dual-Color Analysis of Dual Breast Cancer Susceptibility Genes
Enzyme-Catalyzed Sulfo-Tagging Accelerates 3-OH Steroid-Targeted Submetabolome Profiling
Ultrasensitive Detection of Tissue Lipids at the Femtomole Scale Using Low-Microflow Targeted Lipidomics
Benchmarking Lysosome Enrichment Methods: A Guide for Research and Clinical Translation
Uncertainty-Aware Learning of Multiple Conditions as a Framework for Streamlined Retention Time Prediction to Accelerate Method Development
A Highly Sensitive and High-Throughput Quantitative HILIC-MS/MS Method for Systematic Profiling of RNA Modifications
Exploration of Semiconductor Chip-Based Single-Molecule Protein Sequencing for Identification of Hemoglobin Variants
Enhancing Proteoform Sequence Coverage Using Top-Down Mass Spectrometry with In-Source Fragmentation and Middle-Down Mass Spectrometry
Spectral Quality-Guided Optimization of Hybrid EAciD Fragmentation on the ZenoTOF 7600 System Enables Efficient Characterization of the Serum N-Glycoproteome
An All-in-Tip Accelerated Proteomics Platform for Large-Scale Cancer Screening
Trend-Aligner: A Retention Time Modeling-Based Feature Alignment Method for Untargeted LC–MS Data Analysis
IsoPS-DIA: Dual Functionality of Absolute Targeted Quantification and Global Proteome Profiling
Comprehensive Curation and Harmonization of Small-Molecule MS/MS Libraries in Spectraverse
Integrated GC-MS/MS Metabolomics in Cardiovascular Disease: Targeted Nitro-Oleic Acid Quantification Meets Untargeted Profiling
Construction of Non-Self-Ligating Blunt-End Adapters for Sequencing by Leveraging the Asymmetry of T4 DNA Ligase
Single Cell Quantification of Let-7a with an Electrophoresis-Assisted Tandem Signal Amplification Strategy based on Intracellular Catalytic Hairpin Assembly-Branched Hybridization Chain Reaction-MNAzyme
Quantitative Food Compounds Enable Dietary Ontology Referencing across 500 Foods and Human Plasma
Mass-Invariant Natural Log-Transformed Mass Spectra Enable Internal Calibration and De Novo Sequencing of Intact Proteins
mtDNApipe: A Pioneering Pipeline for High-Sensitivity Detection of Low-Frequency Mitochondrial DNA Mutations
Multiplexed Isotope-Coded Mass Spectrometry Footprinting Enables Broad Heteroatom-Residue Mapping and Uncovers Noncanonical Ligand-Binding Sites in Amyloidosis Proteins
Dual Protease-Mediated Proteolysis Coupled with Ultrafiltration for System-Level Profiling of Drug Targets and Conformational Dynamics
A Data-Driven Multifunctional Microfluidic Platform for in Vitro Safety Assessment of 5-Hydroxymethylfurfural
Temperature-Responsive Agarose-Based Digital Microfluidics: An In-Chip Sample Preparation To Mass Spectrometry Analysis for Trace Cells and Single-Cell Proteomics
13C-Isotope Tracing Structural Lipidomics for Resolving Phospholipid Metabolism Dynamics in Human Breast Cancer Cells
Profiling Glycoproteins Enriched by Multinanoparticle Protein Corona
A GC–MS Data Analysis Platform for Untargeted Metabolomics with Enhanced Coeluting Peak Resolution
Mapping C═C Positions in Branched Fatty Acid Esters of Hydroxy Fatty Acids by Oxygen Attachment Dissociation Mass Spectrometry Coupled with Chemical Labeling
Computer-Customized Design of Graphene Oxide Logic Circuit Catalytic Hairpin Assembly Linkage (CHA-Linkage) Enables Molecular-Level Identification of Cancer Cells
GNPS Feature-Based Molecular Networking as a Tool to Visualize Metabolic Toxicity from Drug–Drug Interactions: A Case Study with Methamphetamine and Ethanol
Signal Attrition in Whole Cell Cross-Linking Mass Spectrometry
Position-Specific Carbon Isotope Analysis of Glucose at Natural Isotope Abundance by Electrospray-Ionization Orbitrap Mass Spectrometry
Robust Workflow for Multiclass Host-Gut Microbial Cometabolite Quantitation in Human Stool via 3-Nitrophenylhydrazine Derivatization and LC-MS/MS: A Validated Analytical Platform for Translational Studies
Extreme Ultraviolet Photodissociation Decodes the Chain Modifications of Lipids
Chiral Derivatization Enables High-Resolution Ion Mobility Spectrometry of 30 Amino Acid Enantiomers
Local Sample Cohesion Normalization: Preserving Inherent Biological Heterogeneity in Metabolomics Data
DLQMA: A Deep Learning Framework for Qualitative and Quantitative NMR Analysis of Complex Hydrocarbon Mixtures
Coupling Liquid Chromatography to Orbitrap Isotope Ratio Mass Spectrometry: Overcoming Isotope Effects of Chromatography and Amount-Dependency by Peak Homogenization
Imaging of Protein Assemblies up to 231 kDa in Tissues with Nano-DESI Mass Spectrometry
AND-Gate Logic-Controlled Catalytic Hybridization Network for Robust Dual-Mode Fluorescence-Colorimetric Detection of Breast Cancer miRNAs
Epoxidation-Enhanced Charge-Switch Derivatization for Rapid Profiling of Monounsaturated Fatty Acid Isomers
Deep Learning-Assisted G4 Nanowire-Enhanced Carbon Dot Biosensor for Exosomal LncRNA Artificial Intelligence Diagnosis
VirMolAnalyte: An AI-Driven In Silico Metabolite Annotation Tool
Machine Learning-Driven Extracellular Vesicles Peptidomics Powers Precision Classification of Endometrial Cancer
NMR Spectral Alignment Utilizing a CryoEM Motion Correction Algorithm
Combining Retip Retention Time Prediction with High-Resolution Mass Spectrometry: A Systematic Analysis of Schisandra chinensis-Evodia Conducted for the First Time
Machine Learning-Assisted False Positive Detection in Metabolite Identification Workflows
A Streamlined Sequential Enrichment Strategy for Multi-PTM Profiling from Low Micrograms of Samples
A Deep Learning Model for Efficient Nontargeted Screening of New Psychoactive Substances with Benchtop Nuclear Magnetic Resonance Devices
HDSE-MS: Tandem Mass Spectrum Prediction for Small Molecules via Hierarchical Distance Structural Encoding
GPMassSimulator: A Graphormer-Based Method for Glycopeptide MS/MS Spectra Prediction
xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem
Analytical Considerations for the Development of Plate-Based Proteomics Platforms Using Isobaric Labeling
Deep-Learning Prediction of Protein Secondary Structure from Circular Dichroism Spectrum Using Three-Layer Image Recognition
Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions
On-Demand Submetabolome Profiling of Early Ferroptosis with Porous Polymeric Magnetic Chemoselective Probes
Resolution-Adaptive Binning Enhances Machine Learning Modeling by Interbatch and Multiplatform Orbitrap-Based Shotgun Mass Spectrometry Data Integration
Expanding Metabolome Coverage in LC–MS/MS Analysis through Hydralazine-Based Multifunctional Derivatization
Multidimensional Mass Spectral Similarity Algorithm: Discriminate Disaccharide and Flavonoid Isomers Coupled with Online Energy-Resolved Acquisition and Electron Activation Dissociation
Comprehensive Quantitative Profiling of Less Polar Lipids in Human Plasma Using Validated Reversed-Phase UHPSFC/MS/MS
Improving the Detection of Analyte Degeneracies in Untargeted Liquid Chromatography-Tandem Mass Spectrometry Data
IBT-16plex-Based Quantitative Proteomics at the Single-Cell Level: Enabling Protein Profiles toward the Single Cells from Mouse Spleen
The SIMPLIFY Protocol: A Monophasic Extraction System Suitable for Exposomics, Metabolomics, Lipidomics, and Proteomics Research
An Analytical Strategy for Reliable Metabolome Analysis of Clinical Leftover Sera Using Timed Aliquoting
Quantitative Assessment of the Target Engagement of a KRAS G12C Inhibitor in Formalin-Fixed Paraffin-Embedded Tumor Tissues Using Immunoaffinity Capture 2D-LC-MS/MS
Quantitative Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry
A Computational Integration Strategy Driven by Chemical Similarity Uncovers Comprehensive Metabolic Profiles of Small Bioactive Peptides via UHPLC-HRMS for Doping Control
Not One Method to Rule Them All: A Comparative Study of Chromatographic Platforms (RP-LC-, HILIC-, SFC-, and IC-HRMS) for Water Analysis
A Novel Ultrahigh-Resolution Y-Injection Multireflecting Time-of-Flight Mass Spectrometer for Bottom-Up Proteomics
A Simple and Flexible Strategy for Single-Cell Proteomic Analysis Based on Protein Immobilization and Digestion Tube Reactor
OpenSpec Enables Detecting Unexpected Modifications from Proteomics Data Generated by Orbitrap Astral Mass Spectrometer
SMART 2.0 Statistical Metabolomics Analysis: An R Tool 2.0
Trapped Ion Mobility Improves Annotation Accuracy in LC-HRMS Screening Applications for Exposomics
Postcolumn Infusion of Labeled Racemic Chiral Selector Enables LC-Chiral MS/MS
Disposable Carbon Screen-Printed Electrodes for On-Chip Protein Digestion: A Proteomic Approach Coupled to MALDI-TOF MS
Adaptive Modeling of Tandem Mass Spectrometry Data: Creation of the METLIN 960K MRM Database
prm-PASEF-Based Quantification and Isomeric Model for Extended Coverage of Human Plasma Lipidome in Parkinson’s Disease
A Detergent-Free Grinding Sample Preparation Method Dramatically Enhances PELSA for Mapping Integral Membrane Proteins–Ligand Interaction
High-Frequency Microfluidic Fractionation for Compound-Resolved Bioactivity-Based Metabolomics
Investigating a Systematic and Widespread Misidentification in the Metabolic Profiling Literature: Phenylacetylglutamine and Phenylacetylglycine Signal Misassignment in Proton NMR Spectra of Human and Rodent Urine
SERS-Based AND Logic Gate for Monitoring Signal Transduction of Specific Cancer Cells and Evaluating Antitumor Efficacy via Imaging of Membrane Protein Dimerization
Tailored SONAR-MSI: Converting SONAR-MS Data into Pseudoimages for Deep-Learning-Based Natural Products Analysis
MODAPro: Explainable Heterogeneous Networks with Variational Graph Autoencoder for Mining Disease-Specific Functional Molecules and Pathways from Omics Data
CRB-FCC: A Standardized Nontargeted Analysis for Formula Assignment and Structure Annotation
Selective Comprehensive Online NanoLCxCZE-MS Platform for Top-Down Proteoform Analysis
Characterization of Lipid Epi-Metabolites/Reactions as Diagnostic Biomarkers for Idiopathic Pulmonary Fibrosis by Lipidepifind
Serum Fingerprinting-Based Integrative Dual-Omics Machine Learning for Endometriosis-Associated Ovarian Cancer
High Dynamic Range Peptide Mass Spectrometry Using Segmented Precursor Ion Accumulation
Plug-and-Play Competitive Hairpin Conversion Module Enables Enzyme-Free High-Resolution Discrimination of Single Nucleotide Polymorphisms
Biochemometric 2D NMR-Based Heterocovariance Analysis: A Targeted Approach for Identifying Bioactive Compounds in Complex Mixtures
In-Capillary Chemoselective Tagging-Facilitated Direct nESI-MS Profiling of Carboxyl- and Carbonyl-Containing Metabolites in Urine
Development of a Real-Time Monitoring System for the Adherent Human Keratinocyte Metabolism by Live-Cell Metabolic NMR with Illumination
Challenging the Database: Day-of-Analysis Calibration and UF Modeling for Reliable RRF Use in Medical Device Chemical Characterization
Formic Acid Pretreatment Enhances Untargeted Serum and Plasma Metabolomics
Unsupervised Machine Learning for Differential Analysis in Proteomics
Antibody-Free Inline Dual-Retention Nano-WCX-μSPE-MS/MS for Quantification of Intact Parathyroid Hormone and Antagonistic Fragments in Clinical Serum
13-Plex DeAla Isobaric Reagents for High-Throughput Proteome Quantification
Plasma–Microdroplet Fusion for Online Post-Column Epoxidation: Toward Deep Lipidomics on Unmodified Mass Spectrometers
hxsparse: A Feature Extraction Algorithm for Hydrogen Exchange-Mass Spectrometry Based on a Linear Deuteration Model and LASSO Regularization
Transposase Acting on an RNA/DNA Hybrid in Strand-Specific Sequencing
High-Throughput Top-Down Proteomic Analysis of Picogram-Level Complex Samples Using Multisegment Spray-Capillary CE-MS
Integrated Classifier Based on Coacervates for Weighted Digital miRNA Classification
A Flexible End-to-End Automated Sample Preparation Workflow Enables Standardized and Scalable Bottom-up Proteomics
Online Determination of mRNA Poly(A) Tail Length and Content
DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion
An Automated Multi-Sample Digital LAMP Platform for Quantitative Detection of SDC2 Methylation in Colorectal Cancer
A Hit Prioritization Strategy for Compound Library Screening Using LiP-MS and Molecular Dynamics Simulations Applied to KRas G12D Inhibitors
UCL-MetIsoLib: A Public High-Resolution Tandem Mass Spectrometry Library for HILIC-Based Isomer-Resolved Profiling of Glycolysis, Central Carbon Metabolism, and Beyond in Urine, Plasma, Tissues, Cells, and Patient-Derived Organoids
Hollow Dodecahedral Nanocages for Reliable Multi-Level Differentiation of Urological Cancers through Non-Invasive Metabolic Fingerprinting
Enhanced Fingerprinting Strategy for Rapid and Accurate Quantitative Source and Contaminant Apportionment via Online SPE-UHPLC-QTOF-MS
rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data
A New Approach to Large Multiomics Data Integration
Chemical Tagging with Mass Spectrometry Analysis for Sensitive Determination of Carboxylic Enantiomers in Hepatic Fibrosis
Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition
CLAW-MRM: Comprehensive Lipidomics Automation Workflow for Multiple Reaction Monitoring Using Large Language Models
DNA Molecular Sieve-Assistant Autocatalytic Circuits for High-Precision Cell Discrimination through an Improved Cellular Spatial Resolution
A Chromatography-Guided Co-Fractionation Mass Spectrometry Strategy for Rapid Profiling of Drug-Perturbed Protein Complexes
An Antibody Cocktail-Based Immunoaffinity-LC-MS Method Enabled Ultra-Sensitive and Robust Quantification of Circulating Proinsulin Proteoforms and C-Peptide
Deep Structural Characterization of Protein-Bound Lipids via Native MS and Ultraviolet Photodissociation
AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching
A “Space-for-Time” Strategy Based on Single-Cell Dual-Isotope ICP-MS Analysis Enabling High-Throughput and Sensitive Quantification of miRNAs in Breast Cancer Cells for Therapeutic Assessment
QC4Metabolomics: Real-Time and Retrospective Quality Control of Metabolomics Data
Rapid MS-Based Single-Cell Analysis Assisted by Photochemical Derivatization in Living Cell Membranes Reveals Lipidomic Patterns with Located C═C Bonds
Reverse Spectral Search Reimagined: A Simple but Overlooked Solution for Chimeric Spectral Annotation
Exploring the Potential of Chemically Matched Fragments as Internal Standards for Quantitative SERS with Panobinostat
Proteomic Profiling of Urinary Large Extracellular Vesicles for the Diagnosis of Prostate Cancer
Determination of Double Bond Positions in Unsaturated Fatty Acids using Permanganate Oxidation and Tandem Mass Spectrometry of CuIICl+ Adducted Ions
Untargeted Discovery and Localization of Isomerized Residues in Neuropeptides
Metalloproteome Factory: From Crude Extract to Identification of Metalloproteins via 3-Dimensional HPLC-ICP-MS
mzrtsim: Raw Data Simulation for Reproducible Gas/Liquid Chromatography–Mass Spectrometry-Based Nontargeted Metabolomics Data Analysis
Online Coupling of Acoustic Droplet Levitation with Capillary Electrophoresis Mass Spectrometry Enables Midair Enrichment for Improved Proteomic Sensitivity
Machine Learning for Enhanced Identification Probability in RPLC/HRMS Nontargeted Workflows
Development of a Robust Platform for Infrared Ion Spectroscopy: A New Addition to the Analytical Toolkit for Enhanced Metabolite Structure Elucidation
High-Throughput Monoclonal Antibody Peptide Mapping Using 15-s HPLC Gradients Coupled with Cyclic Ion Mobility-Mass Spectrometry
Precise Discovery of Novel N-Terminal Proteoforms beyond the Limitations of Proteogenomics and De Novo Sequencing
A Meta-Learning Approach for Multicenter and Small-Data Single-Cell Image Analysis
AUTO-SP: Automated Sample Preparation for Analyzing Proteins and Protein Modifications
Quantification of Arginine-Rich Cyclic Cell-Penetrating Peptide–Lipid Conjugates Using a Surrogate Peptide Extracted by Phospholipase D Digestion and Trifluoroacetic Acid-Based UPLC-MS/MS Analysis
Determination of Methyl Group Positions in Long-Chain Aliphatic Methyl Ethers and Alcohols by Gas Chromatography/Orbitrap Mass Spectrometry
Toward the Development of a Novel Newborn Screening Modality: In-Depth Nontargeted Proteome Analysis of Dried Blood Spots with a Robotic Pipeline Using Low-Cost Iron Powders
Mass In Situ Hybridization Enables Mass Cytometry to Detect Telomere Length
Gas Phase Separation of Modified Peptides for Activity-Based Protein Profiling
Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset
Investigating Metabolic Pathways of Ankylosing Spondylitis via Compound Similarity Network-Assisted Metabolomics Analysis
NMR Reaction Monitoring Robust to Spectral Distortions
Charged Water Enables the Determination of Inherited Metabolic Diseases by Mass Spectrometry
Novel Equivalent Carbon Number Strategy for Large-Scale Lipidomics Data Analysis via Ultrahigh–Performance Liquid Chromatography–Orbitrap Astral Mass Spectrometry
Top-Down Proteomics for the Characterization and Quantification of Calreticulin Arginylation
Monitoring the Chemical Transformation and Detoxification Process of Aconitum Herbs during Processing by Maximum-Quantum Filter NMR Spectroscopy
SMART: An Approach for Accurate Formula Assignment in Spatially Resolved Metabolomics
Composite Fluorescence Encoding Technology Based on Tetrahedral DNA Framework for Logical Distinction and Multiplexed Recognition
High-Throughput Fluorescence-Guided Sequential Single-Cell MALDI-ICC Mass Spectrometry
Improving Spectral Similarity and Molecular Network Reliability through Noise Signal Filtering in MS/MS Spectra
An Integrated Strategy Using Predicted Spectral Library and Tandem Enrichment for Large-Scale Identification of Low-Abundance Proteins and Intact N-Glycopeptides in Human Plasma
Deep Mining of Novel Acylated Polyamines by Integrated Prior-Knowledge-Guided Prediction and Chemical Isotope Labeling-Based Metabolomics
Dual Enhancement of Protein Imaging in Complex Tissues Using HydroWash: A Sequential Washing and Hydrogel Conditioning Strategy for DESI-MS
Liquid Chromatographic and Mass Spectrometric Methods for Quantitative Proteomic Analysis from Single-Cell and Nanogram-Level Samples
Integrated Single-Cell Proteomic and Morphometric Analysis Reveals Heterogeneous Drug-Resistant Subpopulations
Evaluation of a New Chemical Label iBASA/i: A Comparison with Gold Standards
MAMSI: Integration of Multiassay Liquid Chromatography–Mass Spectrometry Metabolomics Data Using Multiview Machine Learning
Fast and Accurate Charge State Deconvolution of Protein Mass Spectra
Coupling Supercritical Fluid Chromatography with Internal Standard Corrected Quantitative NMR for Rapid and Accurate Purity Assessment
A New Comprehensive Platform for Profile-Mode-Based Untargeted Metabolomics for Efficient Data Mining to Improve Compound Extraction and Identification
Developing a Two-Dimensional Size-Exclusion Liquid Chromatography Platform for Isolating the High-Quality Extracellular Vesicles to Predict and Evaluate Metabolic Improvement Outcomes of Sleeve Gastrectomy
MS2MP: A Deep Learning Framework for Metabolic Pathway Prediction from MS/MS-Based Untargeted Metabolomics
Low-Cost Heating Modalities Allow the Detection of Biomarkers for Plant Infection Using Rapid Evaporative Ionization Mass Spectrometry (REIMS) That Are Pathogen Specific
General Screening and Multiple Dissociation Methods for Complementary LC–MS Analysis of Pesticides in Beverages: Potential and Pitfalls
Top-Down Proteomic Analysis of Limited Samples Using Porous Layer Open Tubular Columns and High-Field Asymmetric Ion Mobility Spectrometry Coupled to Mass Spectrometry
Longitudinal Fragment Profiles Based on Multi-Collision Energy Tandem Mass Spectra Improve the Accuracy of Metabolite Identification in Untargeted Metabolomics
Leveraging Complementary Ion Activation Methods with Proton Transfer Charge Reduction Reactions for Comprehensive Characterization of Monoclonal Antibody Heavy Chain Subunits
Identification of Isomeric Metabolites Using Cold Ion Spectroscopy Add-on to Orbitrap-Based Mass Spectrometer
An Integrated Platform for High-Throughput Extraction and Mass Spectrometry-Based Quantification of Cholesterol and Sphingosine
Multicolumn Two-Dimensional Liquid Chromatography Screening Platform for Stereopeptidomics and Application to Antimicrobial Peptide Polyene and Lipopeptide
HyperXtract: Strategic Platform for Optimizing High-Bandwidth Nanopore Data Extraction Performance
Ultrafast Measurement of Circulating Ceramides in Human Cohorts
Assessing the Impact of Measurement Precision on Metabolite Identification Probability in Multidimensional Mass Spectrometry-Based, Reference-Free Metabolomics
Improving Regions of Interest Multivariate Curve Resolution: Development of an Empirical Metric System through the Study of Passive Sampling Extracts of Wastewater in Antarctica
High-Throughput Screening of Amyloid Inhibitors via Covalent-Labeling Mass Spectrometry
CSU-MS2: A Contrastive Learning Framework for Cross-Modal Compound Identification from MS/MS Spectra to Molecular Structures
Native Top-Down Proteomics of Endogenous Protein Complexes Enabled by Online Two-Dimensional Liquid Chromatography
Quantitative Assessment of a Novel Device Designed for Patient-centric Sampling of Dried Plasma Using Targeted Proteomics
Overcoming Matrix Effects in Non-Target Screening: A Novel Strategy for Urban Runoff Analysis
Single-Cell Lipidomics by LC-MS Interlaboratory Study Reveals the Impact of X-ray Irradiation on a Pancreatic Cancer Cell Line and Its Bystanders
A Comprehensive and Ultrasensitive Isotope Calibration Method for Soil Amino Compounds Using Orbitrap Mass Spectrometry
Dual-Drive Platform Combining Biotransformation Prediction and Diagnostic Ion Cluster Reveals Novel Type B Trichothecenes in Wheat
Development of a Thiol–ene Microfluidic Chip for Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS)
On Selecting Robust Approaches for Learning Predictive Biomarkers in Metabolomics Data Sets
Shining Light on DNA Mutations through Machine Learning-Augmented Vibrational Spectroscopy
DuReS: An R Package for Denoising Experimental Tandem Mass Spectra and Metabolite Annotation
Quantitative Determination of Click-Reactive Antisense Oligonucleotide and Its Reactivity in Rat Brains by Hybridization LC-MS/MS to Support Pretargeted PET Imaging
Nanoflow Size Exclusion Chromatography–Native Mass Spectrometry of Intact Proteoforms and Protein Complexes
Ozonolysis Dissociation Kinetics for the Relative Quantification of Geometrical Phosphatidylcholine Isomers
Bottom-Up Structural Analysis for Natural Products by Identifying Fragment Ions Resulted from Gas Phase Collision-Induced C–C Bond Fission
PEG Precipitation Followed by Albumin Depletion for Plasma Proteomics Analysis
Direct Microplate Sampling Mass Spectrometry for High-Throughput Screening of Biocatalytic Activity
Integrative Analysis of Nontargeted LC-HRMS and High-Throughput Metabarcoding Data for Aquatic Environmental Studies Using Combined Multivariate Statistical Approaches
Differential Protein Precipitation-Based GalNAc-siRNA Sample Preparation with LC/MS Method Development Workflow in Plasma
Enhanced Structure-guided Molecular Networking Annotation Method for Untargeted Metabolomics Data from Orbitrap Astral Mass Spectrometer
TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification
Improvements in Glycoproteomics through Architecture Changes to the Orbitrap Tribrid MS Platform
Single-Cell Proteomics Using the One-Step Droplet-in-Oil Digestion Method Reveals Proteins Important for Male Meiotic Progression
Selecting the Right C18 Stationary Phase with Parallel Array Microfluidic Column Liquid Chromatography (palmLC)
Multiplexed Detection of Pancreatic-Specific Nucleic Acids and Protein Biomarkers Using a Logic Nanofluidic Platform
22
Expanding High‐Fidelity Multiplexing in Ultrasensitive Single‐Molecule Protein Detection via Proximity Barcoding
Tissue Heterogeneity-Driven Parallel Acquisition for High-Coverage MS/MS Imaging of Lipids
High-Throughput Single-Cell-Resolved Spatial Proteomics Enabled by an Ordered Colloidal Crystal Column
Proximity‐Induced Transfer of a Mass Tag Enables Direct Profiling of Active Matrix Metalloproteases
Single‐Injection Multi‐Omics Analysis by Direct Infusion Mass Spectrometry
An Amorphous Nanocomposite for Dual-Mode Metabolic Fingerprinting and Diagnosis of Adolescent Depressive Disorder
Digital Decoding of Multicomponent Protein Systems via Nanocavity‐Confined Single‐Molecule Raman Fingerprinting
Intact Proteoform Analysis by Capillary Electrophoresis–Mass Spectrometry. Are We There Yet?
Time-Resolved In-Cell Protein Interactions and Structural Dynamics via Rapid Buffer Online Exchange-Ion Mobility-Mass Spectrometry
Optimized In‐Solution and Gas‐Phase Chemistry Enables High‐Efficiency Interactome Mapping by DSBSO‐Based Cross‐Linking Mass Spectrometry
Intact Mass Profiling Reveals Phospho-Proteoforms of the Catenins (85–110 kDa) Regulated by Actomyosin Contractility
Total Biocatalytic Synthesis of Capsaicinoids Using Ferulic Acid: A Versatile Two-Step Strategy for Natural Product Diversification
Simultaneous Measurement of RNA Synthesis and Degradation Rates in Single Cells Unveils the Regulatory Mechanisms of Temporal RNA Dynamics
Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High‐Throughput PRM‐MS in an Inflammatory Bowel Disease Cohort
Bifunctional Probes Reveal the Rules of Intracellular Ether Lipid Transport
Quantum Chemistry Calculation‐Assisted Large‐Scale Collision Cross Section Prediction Empowers Derivatization‐Enhanced Multidimensional Metabolomics
Real‐Time Eco–AI, Electrophoresis‐Correlative Data‐Dependent Acquisition with AI‐Based Data Processing Broadens Access to Single‐Cell Mass Spectrometry Proteomics
Building a Bridge Between Ambient MS and LC‐MS by Non‐Exhaustive Microdesorption
ABC‐seq Expands Small RNAs Profiling with Successive Nucleic Acid Structure‐Differentiated Enzymatic Recognition
One‐Step Enrichment and Quantitative Analysis of In Vivo Protein Complexes via Dimethylpiperidine Cross‐Linker DPST
LC‐MS and High‐Throughput Data Processing Solutions for Lipid Metabolic Tracing Using Bioorthogonal Click Chemistry
Integrating Ambient Ionization Mass Spectrometry Imaging and Spatial Transcriptomics on the Same Cancer Tissues to Identify RNA–Metabolite Correlations
3
Blood Lactate as a Prognostic Biomarker for Survival and Weight Loss in Amyotrophic Lateral Sclerosis: An Exploratory–Validation Study
Polygenic Resistance to Blood Pressure Treatment and Stroke Risk: Insights from the All of Us Research Program
Clinical and Genetic Findings in a Chinese Cohort of Dentatorubral–Pallidoluysian Atrophy Patients
4
Gain of function NOTCH4 variants disrupt angiogenesis in systemic sclerosis
Genome-wide association studies reveal new insights into the genetic basis of IgG4-related disease in the Chinese Han population
Spatially informed phenotyping by cyclic-in-situ-hybridisation identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis
Integrative exome sequencing and machine learning identify MICB and interferon pathway genes as contributors to SSc risk
4
Higher Complement C4 Gene Copy Number Constitutes a Shared Genetic Risk Factor for Giant Cell Arteritis and IgA Vasculitis
A Multifaceted Interplay Among Hemophagocytosis, Interleukin‐18, and Type I Interferon Distinguishes Still Disease From Other Autoinflammatory Diseases
Identification of Novel Noncoding Genetic Variants of Serum Urate Using Whole‐Genome Sequencing in 7,339 Chinese Participants
Distinct effects of complement C4A and C4B copy number in Systemic Sclerosis serological and clinical subtypes
6
Multiomic study of cutaneous T-cell lymphoma reveals single-cell clonal evolution in progression and therapy resistance
A stem and progenitor cell–derived gene expression signature is prognostic for survival in myelofibrosis
Correlates and consequences of clonal hematopoiesis expansion rate: a 16-year longitudinal study of 6976 women
Reactivation of developmentally silenced globin genes through forced linear recruitment of remote enhancers
IPSS-M risk and specific sex-associated somatic mutations predict response to ESA therapy in LR-MDS: building a new score
Array Genotyping of Transfusion Relevant Blood Cell Antigens in 6946 Ancestrally Diverse Subjects
5
The NeuroBioBank whole-genome catalogue of human brain donors with central nervous system disorders
Repeat-associated ataxias in a German patient cohort analysed by targeted parallel long-read sequencing
Deep learning-based cell type profiles reveal signatures of Alzheimer’s disease resilience and resistance
Novel modelling approaches to elucidate the genetic architecture of resilience to Alzheimer’s disease
Selective vulnerability and resilience to Alzheimer's disease tauopathy as a function of genes and the connectome
7
The landscape of structural variation in pediatric cancer
IGSF11-VISTA is a critical and targetable immune checkpoint axis in diffuse midline glioma
Multiomic integration reveals tumoral heterogeneity of lipid dependence within lethal group 3 medulloblastoma
Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer
Protein-based classification reveals an immune-hot subtype in IDH mutant astrocytoma with worse prognosis
The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets
Gene context drift identifies drug targets to mitigate cancer treatment resistance
13
In Silico Reconstruction of Primary and Metastatic Tumor Architecture Using Geographic Information System–Augmented Spatial Transcriptomics
Integrative Multiomics and Drug Sensitivity Profiling Reveal Potential Biomarkers and Therapeutic Strategies in Pediatric Solid Tumors
Path2Omics Enhances Transcriptomic and Methylation Prediction Accuracy from Tumor Histopathology.
A Deep Learning Framework Integrating Tumor Microenvironmental Features Accurately Predicts Multiple Driver Gene Mutations in Lung Cancer Pathology Images.
BESTDR Enables Bayesian Quantification of Mechanism-Specific Drug Responses.
Modeling Early-Onset Cancer Kinetics Reveals Changes in Underlying Risk and the Impact of Population Screening.
Spatial Multi-omics Defines a Shared Tumor Infiltrative Signature at the Resection Margin in High-Grade Gliomas.
Tumor Suppressor Genes with Segmental Duplications Are Prone to Somatic Deletions and Structural Variations
Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm
Heterogeneous Driving Effects Guide Personalized Tumor Treatments Targeting N6-methyladenosine
From Harmony to Discord: Multicellular Coordination in Tissues and Its Rewiring in Cancer.
Integration of Germline and Somatic Variation Improves Chronic Lymphocytic Leukemia Risk Stratification
Combining Spatial Transcriptomics, Pseudotime, and Machine Learning Enables Discovery of Biomarkers for Prostate Cancer
39
Uncovering spatially resolved functional genomics with CRISPR screen sequencing
RegVelo: Gene-regulatory-informed dynamics of single cells
Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects
D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response
AI-predicted spatial transcriptomics unlocks breast cancer biomarkers from pathology
Multi-cohort proteogenomic analyses reveal genetic effects across the proteome and diseasome
Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles
The evolution of high-order genome architecture revealed from 1,000 species
Complete biosynthesis of nicotine
Advancing precision health discovery in a genetically diverse health system
Whole-body molecular and cellular mapping of the laboratory mouse
Four centuries of commercial whaling eroded 11,000 years of population stability in bowhead whales
Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis
CLIM-TIME identifies metastatic microenvironment modulators for T cell therapy response
Multimodal AI generates virtual population for tumor microenvironment modeling
An archaeal transcription factor bridges prokaryotic and eukaryotic regulatory paradigms
Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
Ancient RNA expression profiles from the extinct woolly mammoth
Genome sequences of extant and extinct gibbons reveal their phylogeny, demographic history, and conservation status
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
Evolution of Mycobacterium tuberculosis transcription regulation is associated with increased transmission and drug resistance
Single-cell nascent transcription reveals sparse genome usage and plasticity
Reference genome choice compromises population genetic analyses
The genetic history of the Southern Caucasus from the Bronze Age to the Early Middle Ages: 5,000 years of genetic continuity despite high mobility
HT SpaceM: A high-throughput and reproducible method for small-molecule single-cell metabolomics
Coalescing single-cell genomes and transcriptomes to decode breast cancer progression
A de novo-originated gene drives rose scent diversification
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience
Cancer immunology data engine reveals secreted AOAH as a potential immunotherapy
Human-specific gene expansions contribute to brain evolution
Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning
Functional assessment of all ATM SNVs using prime editing and deep learning
50,000 years of evolutionary history of India: Impact on health and disease variation
Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium
Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids
2
A generative AI framework unifies human multi-omics to model aging, metabolic health, and intervention response
Metabolic polygenic risk scores for prediction of obesity, type 2 diabetes, and related morbidities
1
SPTEdU-seq enables parallel optics-free newborn cell tracking and spatial total transcriptional dynamics in intact microenvironments
4
An endogenous enzyme-triggered multivariate-gated DNA nanosystem for high-fidelity tumour cell recognition
Protein–DNA interactions in disease and drug discovery
Site-specific protein lipoylation analysis via aldehyde-acetal probe labelling and reversible enrichment (DA-Lipo)
Beyond the known cuts: trypsin specificity in native proteins
7
Single-cell structural lipidomics using a miniature dual-LIT mass spectrometer
AI-enabled new sensing technology: colorimetric analysis of exosomes for precise diagnosis of breast cancer
Multi-region mapping of ligand binding and structural changes in the β-1 adrenergic receptor using carbene footprinting and mass spectrometry
A high-throughput N-glycan analysis strategy with targeted mass spectrometry (HTnGQs-target) for liver disease diagnosis
Prediction of enzyme function using an interpretable optimized ensemble learning framework
Framework for de novo sequencing of peptide mixtures via network analysis and two-dimensional tandem mass spectrometry
Transfer learning enables discovery of sub-micromolar antibacterials for ESKAPE pathogens from ultra-large chemical spaces
1
High-throughput Proteomics in Lymphangioleiomyomatosis: PMEL as a Diagnostic Biomarker, Construction of a Diagnosis Score and Evidence of Neutrophil Involvement.
3
Genome and Transcriptome-Wide Analyses Identify Multiple Candidate Genes and a Significant Polygenic Contribution in Bicuspid Aortic Valve.
GRSF1 Protects Against Heart Failure by Maintaining BCAA Homeostasis.
CD4+ Tregs Regulate Heart Growth and Regeneration Through MRG15/TIP60-Mediated Epigenomic Remodeling in Proliferating Cardiomyocytes
2
Utilizing Whole Genome Sequencing to Investigate a Coronavirus Disease 2019 Cluster Among Healthcare Workers in a Tertiary Care Facility in the Philippines: Insights and Implications for Infection Prevention and Control
Epidemiologic and Bacterial Factors Facilitating Long-Term Transmission of Multidrug-Resistant Tuberculosis in Shanghai, China
1
Obesity- and Lipid-Related Traits May Causally Contribute to Sepsis-Associated Acute Kidney Injury.
24
A transitional, early Cambrian species bridges radiodonts and upper stem-group euarthropods
Adaptive genomic divergence parallels migratory behavior in Atlantic bluefin tuna
Gene flow from the European wild apple and selection shaped the domesticated apple genome
Rapid and repeated evolution of myosin copy number in threespine stickleback
Paralog interference contributes to the preservation of genetic redundancy
Compound starch granule formation in grass seeds is associated with distinct temporal patterns of gene expression
Dispersal and isolation of the scaly-foot snail across abyssal insular habitats and through time
Discovery of additional ancient genome duplications in yeasts
Population structure and domestication history of the Javan banteng
A new fossil fish sheds light on the rapid evolution of early lungfishes
Extensive horizontal transfer of transposable elements shapes fungal mobilomes
Robust termite phylogenies built using transposable element composition and insertion events
An early East Asian lineage with unexpectedly low Denisovan ancestry
A pan-genome framework reveals structural variation and small RNA regulation underlying heterodichogamy in Pterocarya
Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes
Linear covariation between germline and somatic mutation rates across ciliates and mammals
Phylogenomics of enigmatic crustacean y-larvae reveals multiple origins of parasitism in barnacles
Whole-genome sequences provide insights into the formation and adaptation of human populations in the Himalayas
A new Cambrian stem-group echinoderm reveals the evolution of the anteroposterior axis
Shifts and critical periods in coral metabolism reveal energetic vulnerability during development
Population genomics of a sailing siphonophore reveals genetic structure in the open ocean
Independent evolutionary deterioration of the oxygen-transport system in Asian noodlefishes and Antarctic icefishes
Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes
4
Endothelial-zippering proceeds by sensing heartbeat-driven force through cadherin-6 during heart-vessel connection in zebrafish
Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo
A dual enhancer-attenuator element ensures transient Cdx2 expression during mouse posterior body formation
TBX3 advances the developmental chromatin landscape toward the hepatic fate
4
Plasma Metabolite Associations for Risk and Laboratory Measures of Type 2 Diabetes in a Large-Scale Finnish Prospective Cohort.
Genetic Predictors of Response to Oral Insulin for Type 1 Diabetes Prevention.
Integrative Metabolomics of Targeted and Non-Targeted Analyses in T2D Progression.
A Metabolomics Study of Cardiac Dysfunction in Hyperglycemia: Findings From the Atherosclerosis Risk in Communities (ARIC) Study and the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
3
Domestication-Admixed Atlantic Salmon (Salmo salar) Establish a Productive Population in the Wild
Gene Family Expansions Provide Molecular Flexibility Required for Context‐Dependent Species Interactions
Phylogenomic Evidence of Fire Regime Changes: The Case of a Resprouting Juniper
4
Urinary Bisphenol A Analogues and Metabolically Unhealthy Obesity in School-Age Children
The changing of the guard: Genetic lineage replacement as the hidden driver of pollution tolerance in Collembola
The synergistic association of environmental stressors with abdominal aortic calcification: An observational and integrated genetic analysis
Marine litter drives population expansion of Metridium senile (Cnidaria: Actiniaria): Genomic insights into dual-scale ecological drivers
12
Unveiling Redox-Active Quinones in Pyrogenic Carbon by Nontargeted Metabolomics and Dual Chemical Tagging
A Framework Integrating Single-Cell Metallomic Data in Health Effect Analysis via Quantile Features and Machine Learning
Homologous Gene Analysis Reveals ACR3 Expansion as a Key Driver of Arsenic Hyperaccumulation in Plants
Identifying Novel DNA Adducts in Amphipods and Developing Sample Preparation for Adductomics Using Dispersive Solid-Phase Extraction
Evolutionary Advantages of Multiple Arsenic Binding Sites in an ArsR Transcriptional Repressor
Chemically Labeled Exposome Analysis (CLEAN): A Strategy for Nontargeted Identification of Urinary Metabolites
Blood Sample Preparation for Human Chemical Exposomics: Insights from Large-Scale Applications
Quantitative Exposomics Targeting over 200 Toxicants and Key Biomarkers at the Picomolar Level
Streamlining Quantification and Data Harmonization of Polychlorinated Alkanes Using a Platform-Independent Workflow
Using Environmental Mixture Exposure-Triggered Biological Knowledge-Driven Machine Learning to Predict Early Pregnancy Loss
Structural Molecular Network for Nontargeted Screening and Prioritization of New Pollutants in Urban Wastewater
Novel Copper-Responsive Cell Subtypes in Oyster Gills: scRNA-Seq Uncovers Detoxification Strategy and Intraspecific Accumulation Variation
7
Genetic determinants of childhood blood pressure and heart rate in relation to adult health outcomes: the consortium of childhood blood pressure
Cardiac sarcoidosis: new insights beyond the granuloma using spatial proteomics
A polygenic risk score for peripheral artery disease and major adverse limb events
<atl>Automated patch clamp data improve variant classification and penetrance stratification for iSCN5A/i –Brugada syndrome</atl>
Preeclampsia, gestational hypertension, and cardiovascular disease risk: a genetic epidemiological study
Clonal haematopoiesis of indeterminate potential and mortality in coronary artery disease
Germline and somatic variants in DNMT3A and other clonal haematopoiesis of indeterminate potential genes contribute to pulmonary arterial hypertension
1
DNA/RNA-Based Next-Generation Sequencing Improves the Early Diagnosis and Management of Neoplastic Bile Duct Strictures: A 6-Year, Prospective, Multi-Institutional, Real-Time Study
11
DDX3X-mediated translation of structured cardiac mRNAs is essential for female heart development
Temporal loss of En1 during limb development causes distinct phenotypes
Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer
The eukaryotic homology search complex distorts donor DNA structure to probe for homology
α-Satellite RNA marks the perinucleolar compartment and represses ribosomal RNA expression in naive human embryonic stem cells
B-lineage commitment is dependent on a reversible epigenetic switch
MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis
A cell type-specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage
MYOD represses gene expression from non-E-box motifs
A genome-wide, CRISPR-based screen reveals new requirements for translation initiation and ubiquitination in driving adipogenic fate change
Restrictor slows RNAPII elongation to promote termination at noncoding RNA loci
106
Hash functions in nucleotide sequence analysis
Single-cell template strand sequencing reveals culture-induced chromosomal instability in a gibbon cell line
Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
Lignature provides a curated resource of ligand induced transcriptomic signatures for signaling inference
Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
Parallel analysis of replication timing, gene expression and copy number with PARTAGE
Minimizing reference bias with an imputed personalized reference
Automated interpretable artificial intelligence genomic prediction with AIGP
Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
Robust and efficient annotation of cell states through gene signature scoring
Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
Analysis of coding gene expression from small RNA sequencing
spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
A systems view on DNA damage response kinetics in Tetrahymena
scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
Autoencoders for genomic variation analysis
Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
Quantifying pathological progression from single-cell transcriptomic data with scPSS
Stable genome structures in living fossil fishes
Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
A spectral component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis
The SynMall resource for characterizing the functional impact of synonymous variation
Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
Integration of high-throughput proteomic data and complementary omics layers with PriOmics
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
Graph-based deep reinforcement learning for haplotype assembly with Ralphi
Unified integration of spatial transcriptomics across platforms with LLOKI
Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
Partitioned Multi-MUM finding for scalable pangenomics with MumemtoM
Predicted protein 3D structure provides essential insights into the genetic architecture underlying phenotypic diversity in maize
BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
Interpretable phenotype decoding from multicondition sequencing data with ALPINE
Iterative improvement of deep learning models using synthetic regulatory genomics
Epigenetic and evolutionary features of ape subterminal heterochromatin
PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
Recovering gene regulatory networks in single-cell multiomics data with PRISM-GRN
Optimal marker genes for c-separated cell types with SepSolve
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
Strong bias in long-read sequencing prevents assembly of iDrosophila melanogaster/i Y-linked genes
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
Long-read reconstruction of many diverse haplotypes with devider
Deep structural clustering reveals hidden systematic biases in RNA sequencing data
Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
Robust 16S rRNA classification based on a compressed LCA index
Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
Estimating the size of long tandem repeat expansions from short reads with ScatTR
Accurate detection of tandem repeats from error-prone sequences with EquiRep
High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
Pangenome-based genome inference using integer programming
Tree-based differential testing using inferential uncertainty for RNA-seq
Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
Multicondition and multimodal temporal profile inference during mouse embryonic development
FocalSV enables target region-based structural variant assembly and refinement using single-molecule long-read sequencing data
The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
Genotype imputation from low-coverage data for medical and population genetic analyses
The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
Genetic variation in recalcitrant repetitive regions of the iDrosophila melanogaster/i genome
CGC1, a new reference genome for Caenorhabditis elegans
A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
Accurate short-read alignment throughir/i-index-based pangenome indexing
Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
Highly accurate assembly polishing with DeepPolisher
QuadST identifies cell-cell interaction-changed genes in spatially resolved transcriptomics data
Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
Analytical validation of germline small variant detection using long-read HiFi genome sequencing
Contiguous and complete assemblies ofiBlastocystis/igut microbiome–associated protists reveal evolutionary diversification to host ecology
Exon nomenclature and classification of transcripts (ENACT) provides a systematic framework to annotate exon attributes
TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data
1
Fortunian archaeocyath sponges acquired biomineralization in the beginning of the Cambrian explosion
1
Multiomics combined with machine learning defines unique molecular subtypes of cholangiocarcinoma and identifies TNK1 as a therapeutic target.
3
Large-scale analysis of FMR1 CGG repeat length and risk of premature ovarian insufficiency in over 92 000 women
Identifying candidate genes for spermatogenic failure and predicting ICSI outcomes using single-cell RNA sequencing and protein–protein interaction networks
Stratifying IVF population endometria using a prognosis gradient independent of endometrial timing
3
Ultra-high-throughput IGH genotyping of 25 global populations reveals population-biased allelic diversity and homozygous V and D gene deletions
Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells
Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing
2
Estimating causal effects of C-reactive protein on disease and health outcomes using multivariable Mendelian randomization adjusting for heritable confounding
A Mendelian randomization study of the effect of body mass index on 52 causes of death among 125 000 Mexican adults with admixed ancestry
8
Butyrylcholinesterase as a potential biomarker of metabolic imbalances in Afro-descendant populations
Genetic determinants of BMI, diet, and fitness interact to partially explain anthropometric obesity traits but not the metabolic consequences of obesity in men and women
Metabolic remodeling and the modulatory role of vitamin D deficiency in African American children and adolescents with obesity
Genome-wide meta-analysis with 2,206,440 individuals identifies 322 novel risk loci for obesity
Plasma metabolites may inhibit childhood obesity by regulating ferroptosis through SMPD1 and SIRT3
Genetic regulation of exosome biogenesis pathway in human adipose and muscle tissue and association with obesity and insulin resistance
Genetic impact of central adiposity on systolic blood pressure in females: interaction and mediation by TG/HDL-C, HbA1c, and uric acid across BMI categories
Integrating genetic and transcriptomic data to identify genes underlying obesity risk loci
2
Recurrent Copy Number Variants and Psychiatric Outcomes in the Context of Polygenic Scores
Structure of the Genetic Risks for Psychiatric Disorders in Swedish Population-Based Registries.
1
Drug-Gene Interactions and Clinical Outcomes After Vascular Surgery in the Million Veteran Program
18
Glucose-6-phosphate dehydrogenase variants modify 3D genomic organization to suppress maladaptive gene expression and vascular disease
Constitutive activation of a hybrid two-component regulator reveals cross-regulation of polysaccharide utilization genes in Bacteroides
Histone H2B-associated proteins: the Arabidopsis nucleolin 1 binds H2B and facilitates nucleosome disassembly via RNA-dependent mechanism
An artificial intelligence optimized hepatic differentiation unveils NR5A2 and AP-1 transcriptional regulation in hepatic maturation
Kinase signaling in liver disease via clinical-trial-on-a-PamChip: A distinctive methodology for drug mechanisms and personalized medicine
Phosphoregulation of RAD51AP1 function in homology-directed repair
Nucleosome linker DNA methylation by DNMT3A/DNMT3B3 is controlled by nucleosome binding and multimerization of DNMT3 complexes on DNA
CtBP1/2 Oligomerization Promotes G9a-Mediated Transcriptional Repression
Depletion of individual dietary amino acids induce distinct metabolic and chromatin states
Ternary complexes in protein–DNA interactions: Kinetics and mechanisms
Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases
Distinct Mechanisms of Recognition of Phosphorylated RNAPII C-Terminal Domain by BRCT Repeats of the BRCA1–BARD1 Complex
HMGN1 and HMGN2 are recruited to acetylated and histone variant H2A.Z-containing nucleosomes to regulate chromatin state and transcription
Large-scale functional assessment of variants of the potassium channel Kir2.1: clinical and comparative insights
Transcriptome and chromatin accessibility divergence during differentiation of a bipotential progenitor cell population to erythroblasts and megakaryocytes
ATP hydrolysis-driven structural transitions within the S. cerevisiae Rad51 and Dmc1 nucleoprotein filaments
Leveraging RNA-seq deconvolution to improve complex in vitro model characterization
Elevated mevalonolactone from Ruminococcus torques contributes to metabolically unhealthy obesity development
2
Stage-specific transcriptomics of a leader cell reveals cell machineries driving collective invasion
Condensin II collaborates with cohesin to establish and maintain interphase chromosome territories
9
Association of genetic risk and physical activity with incident type 2 diabetes
Hypothalamic-pituitary deficiency after radiation in childhood cancer survivors is associated with rare variants in TNS2
Impaired arginine, citrulline, and glutamine metabolism in type 2 diabetes: insights from a stable isotope study
Biomarkers of Insulin Resistance and Their Performance as Predictors of Treatment Response in Overweight Adults
Multiplatform Molecular Testing as an Adjunct to Fine Needle Aspiration in the Evaluation of Pediatric Thyroid Nodules
Effects of Rare Coding Variants in Severe Early-Onset Obesity Genes in the Population-Based UK Biobank Study
Plasma Branched-Chain Amino Acid and Cardiovascular Disease Risk Factors: A Longitudinal Analysis of a Lifestyle Trial
Compartment-Specific Metabolic Alterations to Insulin Reflect Adiposity-Driven Variation and Predict Type 2 Diabetes
Genetic Risk and Transition Through Preclinical Stages of Type 1 Diabetes
7
Genome-wide variation in cell-free DNA end motif entropy predicts immunotherapy response in head and neck cancer
Deep biochemical phenotyping reveals prognostic value of rare genetic variants in adult kidney stone disease
Alcohol use disorder-associated gene FNDC4 alters glutamatergic and GABAergic neurogenesis in neural organoids
The hematopoietic stem cell MYB enhancer is essential and recurrently amplified during T-cell leukemogenesis
Defective Notch1 signaling in endothelial cells drives pathogenesis in a mouse model of Adams-Oliver Syndrome
The cell-type-specific genetic architecture of chronic pain in brain and dorsal root ganglia
Gene-environment interactions modulate the phenotypic severity in mouse models of congenital craniofacial syndromes
1
Molecular-Based Ecosystem to Improve Personalized Medicine in Chronic Myelomonocytic Leukemia.
3
Molecularly guided therapies for advanced primary liver cancers refractory to systemic treatment: Results from the 2025 French genomic medicine initiative
Genetic and non-genetic drivers of histological progression and regression in MASLD
Proteogenomic profiling predicts outcomes of adjuvant chemotherapy in extrahepatic cholangiocarcinoma
1
Molecular Epidemiology of iMycobacterium tuberculosis/i Across 3 Distinct Geographic Sites in South Africa
1
An allostatic load domain‐specific metabolic profile in young adults: The African‐PREDICT study
1
Development of Gene-Expression Panel Predictive of Local Recurrence, Metastasis, and Overall Survival in Intermediate to High-risk Cutaneous Squamous Cell Carcinoma: A Cohort Study
18
Solvent-Modulated Orthogonal Release from Covalent Organic Frameworks Enables Sequential Multiomics Enrichment
A Broadly Accessible Approach to Elucidate the Carbon–Carbon Double Bond Position in Unsaturated Lipids by a Post-column In-Line Photochemical Reaction and Mass Spectrometry
Time-Resolved Native Mass Spectrometry for Direct Measurement of Biomolecular Kinetics
In Vivo Metabolic Engineering of Bladder Cancer-Derived Extracellular Vesicles for Noninvasive Cancer Detection
Bifunctional Lipid–Protein Cross-linking Efficiency and Reaction Products
Ribosome Heterogeneity Revealed by Complex-Up Native Mass Spectrometry and Top-Down Proteomics
Unnatural Cytosine Analogs Potentiate a Customizable, Enzymatic Method for Integrated Epigenetic and Four-Base Genetic Sequencing
Chemical Proteomics Reveals Regulation of Bile Salt Hydrolases via Oxidative Post-translational Modifications
Integrated Native Mass Spectrometry Imaging of Soluble and Membrane Proteins
In-Source Photoderivatization-Enhanced Neurometabolic Profiling Deciphers Vascular Cognitive Impairment
Living Cell Surfacome Lysine Footprinting (LiFT) Captures Virus-Induced Conformational Dynamics and Uncovers Influenza A Virus Host Factors
Unlocking Zeptomolar Single-Molecule Detection by Synergizing Digital Microfluidics and Digital CRISPR
Programmable Cancer Subtype Evaluator via Multiply-Guaranteed Catalytic DNA Computing Circuit
NRPStransformer, an Accurate Adenylation Domain Specificity Prediction Algorithm for Genome Mining of Nonribosomal Peptides
Intersegment Transfer and the Dynamical Architecture of Fis Protein–DNA Multimer Complexes
A Chemoproteomic Approach for System-Wide and Site-Specific Uncovering of Functional Protein N-Glycosylation
Subcellular Analysis of Fatty Acid Metabolism Using Organelle-Selective Click Chemistry
One-Pot Multisubstrate Screening for Asymmetric Catalysis Enabled by sup19/supF NMR-Based Simultaneous Chiral Analysis
2
Genetic Testing in the Management of Adult CKD
Identification of Epigenetic Regulators of Vascular Calcification with a CRISPR-Based Screen.
2
Interaction of genetic and lifestyle risk scores on colorectal cancer risk across five racial and ethnic populations
Performance of multiple multi-cancer detection tests using a large independent reference set (Alliance A212102)
2
Statistical inference for cell type deconvolution
Root cause discovery via permutations and Cholesky decomposition
1
Nephrotic syndrome genomic discovery in the Mass General Brigham Biobank identifies monoallelic MEFV variants as a risk factor for focal segmental glomerulosclerosis
1
Toward a Liquid Biopsy: Greedy Approximation Algorithms for Active Sequential Hypothesis Testing
34
Chromatin architectures underlying plasmid-based assays for regulatory variant effects
Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich’s ataxia
Mutual antagonism between PRC1 condensates and SWI/SNF in chromatin regulation
Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption
Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells
Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes
Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription
Large-scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell-cycle and DNA repair regulation
Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle
The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2
Precise control of transcription condensates across S phase balances linker histone expression with DNA replication, ensuring genome stability
BRD2 bridges TFIID and MOF-H4K16ac-containing nucleosomes to promote transcriptional initiation
Delineating the copy-number substructure of metastatic tumors with CopyKit
Two CTCF motifs impede cohesin-mediated DNA loop extrusion
In vivo proteomic labeling reveals diverse proteomes for therapeutic targets
High-throughput capture of actively transcribed region-interacting sequences reveals an intricate promoter-centered regulatory network
Structure of the transcriptional co-activator SAGA complex, including the histone acetyltransferase module
A mechanism of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence
Cryo-EM reveals open and closed Asgard chromatin assemblies
Sequential verification of transcription by Integrator and Restrictor
Requirements for establishment and epigenetic stability of mammalian heterochromatin
The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain
A CDK11-dependent RNA polymerase II pause-checkpoint precedes CDK9-mediated transition to transcriptional elongation
Distinct specificity and functions of PRC2 subcomplexes in human stem cells and cardiac differentiation
Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex
Chromatin-dependent motif syntax defines differentiation trajectories
PALB2 and 53BP1 govern post-resection homologous recombination DNA repair
Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA
Chromatin architecture mapping by multiplex proximity tagging
Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation
Chip (Ldb1) is a putative cofactor of Zelda forming a functional bridge to CBP during zygotic genome activation
The nucleolar granular component mediates genome-nucleolus interactions and establishes their repressive chromatin states
FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate
BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability
25
Genetic investigation of the association between maternal dietary patterns and offspring ADHD
Protective TMEM106B-rs3173615 delays age at onset in GRN mutation carriers
Cell-type-specific genetic architecture reveals neuronal and immune contributions to neuropsychiatric disorders
Genetic overlap and shared risk loci between autism spectrum disorder and cardiometabolic traits
Ethanolamine as a potential biomarker and therapeutic target for depressive disorder
Convergent coexpression reveals shared biological mechanisms underlying common and rare variant risk in six neuropsychiatric disorders
Integrative GWAS identifies novel loci and genetic links between psychiatric and metabolic factors in anorexia nervosa
Molecular regulatory mechanisms of schizophrenia-associated functional non-coding variants
Identifying genetic contributions of 6q21 loci and PPAR pathway to antipsychotic-induced metabolic syndrome: a Sex-Stratified Multi-Omics study
Cross-ancestry genetic architecture reveals shared biological pathways of major psychiatric disorders
A large-scale DNA methylation study of alcohol use identified robust associations and cell-type specific insights
Powering the mind: deciphering the shared genetic architecture between mitochondrial DNA copy number and major psychiatric disorders
Genome-wide association study of delay discounting identifies 11 loci and reveals transdiagnostic associations across mental and physical health
Mendelian randomization facilitates identification of schizophrenia risk enhancer RNAs
Within- and between-family genetic effects on educational achievement vary across countries and ages
Genome-wide association studies of lifetime and frequency of cannabis use in 131,895 individuals
Genome-wide meta-analyses of cross substance use disorders in diverse populations
Identification of SENP7 and UTF1/VENTX as new loci influencing clustered protocadherin methylation across blood and brain using a genome-wide association study
Leveraging transdiagnostic genetic liability to psychiatric disorders to dissect clinical outcomes of anorexia nervosa
Genetic nurture effects in depressive and anxiety disorders and symptoms, and in related traits
Associations of polygenic risk scores for major depression and depression severity: an investigation of 105 623 individuals with 16 years follow-up
Genetically modeled GLP1R and GIPR agonism reduce binge drinking and alcohol-associated phenotypes: a multi-ancestry drug-target Mendelian randomization study
Polygenic scores for psychiatric traits mediate the impact of multigenerational history for depression on offspring psychopathology
Genomic risk prediction for depression in a large prospective study of older adults of European descent
Genome-wide association meta-analysis and rare copy number variant analysis of treatment-resistant depression
4
Single-Molecule Identification of Tea Polyphenols and Their Interactions with Metal Ions Using an Engineered Nanopore
Logic-Gate-Controlled Positive-Feedback DNAzyme Catalytic Circuit for One-Pot Detection of Dual miRNA
Automated High-Throughput Raman Spectral Framework for Cellular Differentiation Monitoring
Revealing Single-Amino Acid Recognition and Cleavage Dynamics Using Plasmonic Biosensors
77
Mechanism of age-related accumulation of mtDNA mutations in human blood
Distinct genetic architecture in the tails of complex traits
Genetic analysis of circulating metabolic traits in 619,372 individuals
Accelerating scientific discovery with Co-Scientist
Non-invasive profiling of the tumour microenvironment with spatial ecotypes
Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup
Pervasive and programmed nucleosome distortion on single chromatin fibres
Telomere-to-Telomere Assembly Using HERRO-Corrected Simplex Nanopore Reads
The evolutionary history and unique genetic diversity of Indigenous Americans
Chromosomal fusions trigger rediploidization of autopolyploid genomes
Transposable elements are driving rapid adaptation of Enterococcus faecium
Mapping convergent regulators of melanoma drug resistance by PerturbFate
Ancient DNA reveals pervasive directional selection across West Eurasia
Multiomics and deep learning dissect regulatory syntax in human development
Saturation editing of reveals distinct dominant and recessive disorders
Gene regulatory landscape dissected by single-cell four-omics sequencing
The 1000 Chinese Pangenome empowers medical and population genetics
A sorghum pangenome reference improves global crop trait discovery
The oldest articulated bony fish from the early Silurian period
Genome modelling and design across all domains of life with Evo 2
Largest Silurian fish illuminates the origin of osteichthyan characters
BCDX2–CX3 and DX2–CX3 complexes assemble and stabilize RAD51 filaments
Functional dissection of complex trait variants at single-nucleotide resolution
A disease model resource reveals core principles of tissue-specific cancer evolution
Single-cell and isoform-specific translational profiling of the mouse brain
Lasting Lower Rhine–Meuse forager ancestry shaped Bell Beaker expansion
Efficient near-telomere-to-telomere assembly of nanopore simplex reads
Phenome-wide analysis of copy number variants in 470,727 UK Biobank genomes
Regulatory grammar in human promoters uncovered by MPRA-based deep learning
Advancing regulatory variant effect prediction with AlphaGenome
A cross-population compendium of gene–environment interactions
Temporal tissue dynamics from a spatial snapshot
Biological insights into schizophrenia from ancestrally diverse populations
Insights into DNA repeat expansions among 900,000 biobank participants
Stress controls heterochromatin inheritance via histone H3 ubiquitylation
An expanded registry of candidate -regulatory elements
An integrated view of the structure and function of the human 4D nucleome
Causal modelling of gene effects from regulators to programs to traits
Mapping the genetic landscape across 14 psychiatric disorders
Tumour-reactive heterotypic CD8 T cell clusters from clinical samples
Estimation and mapping of the missing heritability of human phenotypes
Assessing phylogenetic confidence at pandemic scales
Specificity, length and luck drive gene rankings in association studies
Eight millennia of continuity of a previously unknown lineage in Argentina
Evidence for improved DNA repair in long-lived bowhead whale
The Taiwan Precision Medicine Initiative provides a cohort for large-scale studies
Population-specific polygenic risk scores for people of Han Chinese ancestry
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
A conserved H3K14ub-driven H3K9me3 for chromatin compartmentalization
Hotspots of human mutation point to clonal expansions in spermatogonia
Efficient and accurate search in petabase-scale sequence repositories
Sperm sequencing reveals extensive positive selection in the male germline
Somatic mutation and selection at population scale
The formation and propagation of human Robertsonian chromosomes
A haplotype-based evolutionary history of barley domestication
One mother for two species via obligate cross-species cloning in ants
Spatial joint profiling of DNA methylome and transcriptome in tissues
Multiple overlapping binding sites determine transcription factor occupancy
Single-cell transcriptomic and genomic changes in the ageing human brain
Thymic epithelial cells amplify epigenetic noise to promote immune tolerance
Elementary 3D organization of active and silenced E. coli genome
Clone copy number diversity is linked to survival in lung cancer
Establishment of chromatin architecture interplays with embryo hypertranscription
Parent-of-origin effects on complex traits in up to 236,781 individuals
Novel assembly of a head–trunk interface in the sister group of jawed vertebrates
Whole-genome sequencing of 490,640 UK Biobank participants
Mouse lemur cell atlas informs primate genes, physiology and disease
A molecular cell atlas of mouse lemur, an emerging model primate
Structural variation in 1,019 diverse humans based on long-read sequencing
Complex genetic variation in nearly complete human genomes
Pathology-oriented multiplexing enables integrative disease mapping
Ongoing genome doubling shapes evolvability and immunity in ovarian cancer
A haplotype-resolved pangenome of the barley wild relative
Cryptic variation fuels plant phenotypic change through hierarchical epistasis
Range extender mediates long-distance enhancer activity
In vivo mapping of mutagenesis sensitivity of human enhancers
Ancient DNA reveals a two-clanned matrilineal community in Neolithic China
35
Scoring gene importance by interpreting single-cell foundation models
Zero-shot de novo peptide sequencing with open posttranslational modification discovery
Widespread DNA off-targeting confounds RNA chromatin occupancy studies
TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects
Reference-free discovery with barcoded single-cell sequencing
Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2
Scalable homology detection with ERAST
Scalable single-cell total RNA sequencing unifies coding and noncoding transcriptomics
Single-molecule peptide sequencing through reverse translation of peptides into DNA
Sensitive detection of cancer antigens enabled by user-defined peptide libraries
Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM
Revealing a coherent cell-state landscape across single-cell datasets with CONCORD
Predicting small molecule–RNA interactions without RNA tertiary structures
Computational prediction of human genetic variants in the mouse genome
In vivo gene editing of human hematopoietic stem and progenitor cells using envelope-engineered virus-like particles
Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets
Mapping single-cell diploid chromatin fiber architectures using DAF-seq
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut
Multimodal learning enables chat-based exploration of single-cell data
KATMAP infers splicing factor activity and regulatory targets from knockdown data
Live imaging of late-stage preimplantation human embryos reveals de novo mitotic errors
Tissue and cellular spatiotemporal dynamics in colon aging
AlphaDIA enables DIA transfer learning for feature-free proteomics
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic
Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap
Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation
Shortcomings of silhouette in single-cell integration benchmarking
Predicting the translation efficiency of messenger RNA in mammalian cells
Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases
Translation efficiency covariation identifies conserved coordination patterns across cell types
Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state
Prime editor-based high-throughput screening reveals functional synonymous mutations in human cells
Identification of non-canonical peptides with moPepGen
Improving gene isoform quantification with miniQuant
16
Lipid-trap mass spectrometry identifies lipid–protein interactions in cells
Visualizing suborganellar lipid distribution using correlative light and electron microscopy
LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis
The interpretable multimodal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics
Two distinct chromatin modules regulate proinflammatory gene expression
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm
Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation
Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues
TemporalVAE: atlas-assisted temporal mapping of time-series single-cell transcriptomes during embryogenesis
CoCo-ST detects global and local biological structures in spatial transcriptomics datasets
CellNavi predicts genes directing cellular transitions by learning a gene graph-enhanced cell state manifold
Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin
RNA-binding proteins mediate the maturation of chromatin topology during differentiation
Systematic decoding of functional enhancer connectomes and risk variants in human glioma
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation
1
Quantitative profiling of lipid transport between organelles enabled by subcellular photocatalytic labelling
2
Hybridization mitigates climate change risk in mountainous birds
Polyploidization in diatoms accelerates adaptation to warming
695
Brieflow: an integrated computational pipeline for high-throughput analysis of optical pooled screening data
Multi-ancestry transcriptome-wide association studies uncover insights into breast cancer genetics and biology
Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding
Evaluating confounding in rare variant genome wide association studies
Large-scale analysis of temporal gene expression variation in peripheral blood
Primer PICKR: literature-mined scoring platform for robust RT–qPCR primers
GWAS of extended prescription analgesic use identifies genetic loci in chronic pain
Population-scale chemical response revealed by a barcoded yeast collection
Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE–DD ancestry
Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes
qChIP-MS reveals the local chromatin composition by label-free quantitative proteomics
Unveiling gene modules at Atlas scale through hierarchical clustering of single-cell data
Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation
Benchmarking genome choice in functional genomics analyses
Genome-wide meta-analysis identifies genetic drivers of bile acid metabolism in intrahepatic cholestasis of pregnancy
MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics
N-Orbit: towards a universal model and metric for comparing tissue microenvironments
PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling
Ecological and genomic signatures of the convergent evolution of planktivory in fossil and living reef fishes over deep time
DGAT: a dual-graph attention network for inferring spatial protein landscapes from transcriptomics
Co-occurring clonal hematopoiesis exhibits strong selection and high leukemia risk
Interpretable deep learning framework for mapping E3–substrate binding interfaces
omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomics
Integrated genomic analyses identify oncogenic pathway interplay in hepatocarcinogenesis defining specific molecular subtypes
Engineering yeast chromosomal telomeres with a bacteriophage system
Inferring stochastic dynamics by biophysical Neural ODE using single-cell transcriptomics
Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes
Decoding spatial transcriptomics across multicellular and subcellular resolutions
Nicotine biosynthesis is completed by cryptic activating glucosylation
Inherent MS-cleavability of diazirine photo-cross-links enables residue-level structural analysis
Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling
Learning the PTM code through a coarse-to-fine mechanism-aware framework
Interpretable modality-aware mapping of gene regulation in single-cell multiomics with scMAGCA
A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA
Two distinct SWI/SNF complexes direct chromatin-linked transcriptional programs in Toxoplasma
Dissecting epigenetic heterogeneity in single-cell DNA methylomes with a unified framework
Robust integration of single-cell datasets with imbalanced modality composition
Distinct roles of MCM2-7 subunits in replication licensing in human cells
Large-scale data-driven pre-trained DNA models enhance performance across diverse genomics tasks
Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial development
Multi-phase hybrid metabolomics framework identifies clinically applicable plasma signatures for early detection of gastric cancer
Local graph estimation with pathwise false discovery control
Heterogeneous endocrine cell composition defines human islet functional phenotypes
Critical evaluation of drug response prediction models with DrEval
Reticulate leaf venation in Pilea peperomioides is a Voronoi diagram
Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing
SAASI: Sampling Aware Ancestral State Inference
Global-scale population genetic analysis of Plasmodium falciparum identifies region-specific patterns of malaria parasite adaptation
Multi-omics integration predicts the incidence of 17 diseases in the UK Biobank
CLASHub is an integrated database and analytical platform for microRNA-target interactions
Tumors hijack immune-privileging regulons via distinct cell types to confer T cell desertion and immunotherapy resistance across various cancers
SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing
The incomplete dominance of gene expression controlled by Trans-eQTL hotspots contributes to heterosis in maize
Enhancer placement impacts transcriptional dynamics in Drosophila embryos
A versatile multi-components mixed model for bacterial-Genome Wide association studies
Extensive antagonistic variants across the human genome
CAPTAIN: a multimodal foundation model pretrained on co-assayed single-cell RNA and protein
Charting spatial ligand-target activity using Renoir
Multi-trait polygenic risk scores improve genomic prediction of atrial fibrillation across diverse ancestries
Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system
RegFormer: a single-cell foundation model powered by gene regulatory hierarchies
Rapid adaptive increase of amylase gene copy number in Indigenous Andeans
BiGER: Bayesian rank aggregation in genomics with extended ranking schemes
Genetic landscape of adult executive function reveals a cell-type-specific developmental origin
Population-based genome-wide association study of plasma complex lipid species
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration
Genome reshaping by Helitron transposons in Fusarium oxysporum TR4 affects secondary metabolism but not virulence
Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT
Functional impact of genetic background on variable expressivity in neurodevelopmental disorders
Admixture-informed polygenic risk reporting using the ePRS framework
Nuclear genetic modulation of tissue-specific mitochondrial RNA processing contributes to common disease risk
Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression
Spatial-aware detection of copy number alterations from spatial transcriptomics using SpaCNA
Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients
Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials
Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation
Dynamic partitioning of a critical elongation factor between LEC and SEC regulates cellular snRNA and proliferation-related mRNA transcription
Proteome-wide prediction of the functional impact of missense variants with ProteoCast
HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states
Early and late RNA eQTL are driven by different genetic mechanisms
Integrating common and rare variants improves polygenic risk prediction across diverse populations
Chromatin accessibility landscape and its association with heterosis in maize hybrids
Improving genomic prediction accuracy of complex traits by integrating massive types of functional annotation information
szKendall: spatial-structural-zero-aware dissimilarity measures for subtype discovery using single cell Hi-C data
TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls
Horizontal gene transfer and diploidy illuminate evolution and stress adaptation in oleaginous Scenedesmaceae (Chlorophyta)
Mapping glioblastoma’s isoform diversity using long-read single-cell analysis
Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq
Leveraging cell-type specificity and similarity improves single-cell eQTL fine-mapping
CellNiche represents cellular microenvironments in atlas-scale spatial omics data with contrastive learning
Longitudinal protein profiling of blood during childhood into early adulthood
Multivariate genetic analysis reveals three distinct pathological dimensions in musculoskeletal disorders
Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution
Igh nuclear speckle association promotes V(D)J recombination
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
Comprehensive assessment of transcriptome assembly quality using CATS
Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion
Conserved and divergent gene regulatory networks for crop drought resistance
UK BioCoin: swift trait-specific summary statistics regression for UK Biobank
SpatialCOC: an integrative framework for spatial continuous mapping and cross-omics correction in spatial multi-omics data
Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance
Comparison and optimization of cellular neighbor preference methods for quantitative tissue analysis
Histone diversity in the archaeal domain of life
Meta-encoder: a unified integration framework for multiple pathological foundation models in cancer detection
Global impact of germline structural variation on the cancer proteome
A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation
Hi-Compass: a depth-aware deep learning framework for predicting cell-type-specific 3D genome organization from single-cell to spatial resolution
Characterizing gene perturbations in single cells via network divergence analysis
An information content principle explains regulatory patterns of gene expression across human tissues
Assembling unmapped reads reveals hidden variation in South Asian genomes
Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication
RESCUE: recovery of unattributed expression patterns in spatial transcriptomics
Combining multiplexed assays of variant effect for enhanced BRCA2 variant classification
Improved tumor-only variant calling and mutation burden estimation with VarNet-T
The adaptive molecular landscape of reprogrammed telomeric sequences
Break-induced replication is enhanced by a phospho-activated RPA-binding module in Pol32
Genetic genealogy of the Piast dynasty and related European royal families
Scaling up Bayesian population phylogenomics through virtual dimension reduction
RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions
African-specific genetic loci determine iron status and risk of severe malaria and bacteremia in African children
Genetic architecture of lumbar spinal stenosis
CellLoop: Identifying single-cell 3D genome chromatin loops
Experimental assessment of AI-based interactome mapping
Collective behavior and memory states in flow networks with tunable bistability
Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function
An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation
Whole-proteome phage immunoprecipitation sequencing reveals germ cell tumor–specific immunosignature
MIC-Drop-seq: scalable single-cell phenotyping of mutant vertebrate embryos
The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos
Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling
The global phylogeography of rapidly expanding multidrug resistant Ural lineage 4.2 Mycobacterium tuberculosis
Cell neighborhood topology directs rare cell population identification
Determinants of chromosome-specific telomere lengths among 2573 All of Us participants
TONSL suppresses polymerase theta-dependent tandem duplications through chromatin-guided repair
TONSOKU prevents the formation of large tandem duplications and restrains ATR–WEE1 checkpoint activation
Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish
An integrated germline and somatic genomic model for coronary artery disease
Leveraging weighted embedding and Transformer architecture to improve phenotype prediction of complex traits for crops
A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators
Solubility based mechanistic profiling of combinatorial drug therapy
CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on transcription
Ancient DNA reveals 4000 years of grapevine diversity, viticulture and clonal propagation in France
LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis
Network model for alignment, stitching and slice-to-volume 3D reconstruction of large-scale spatially resolved slices
A single cluster of RNA Polymerase II molecules is stably associated with active genes
Transcriptional competence defines the heterochromatin nucleating potential of isolated MSR units
Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues
Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling
Origins and breadth of pairwise epistasis in an α-helix of β-lactamase TEM-1
Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex
Mapping the heritability of disease: a nationwide study
A blueprint for local and distal invasion programs in glioblastoma
Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics
FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis
Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome
Condensin accelerates long-range intra-chromosomal interactions
Illuminating cell states by a comprehensive and interpretable single cell foundation model
Extensive enhancer crosstalk controls activation during adipogenesis
Optimizing global genomic surveillance for early detection of emerging SARS-CoV-2 variants
An international multi-centre study to develop and validate federated learning-based prognostic models for anal cancer
DIS3 mutations enhance AID-driven translocations during B-cell activation, promoting transformation to multiple myeloma
EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles
Enzymatic colorimetric encoding-based digital medicine for pancreatic cancer diagnosis
mist: a hierarchical Bayesian framework for detecting differential DNA methylation dynamics in single-cell data
Exon inclusion signatures enable accurate estimation of splicing factor activity
Genetic alternative splicing regulation mapping of cartilage and synovium reveals tissue-specific mechanisms of joint-related traits
Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy
scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies
A paired sequence language model for protein-protein interaction modeling
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci
Regionalized regulation of actomyosin organization influences cardiomyocyte cell shape changes during chamber curvature formation
Long-read sequencing of families reveals increased germline and postzygotic mutation rates in repetitive DNA
Mechanisms of gene regulation by SRCAP and H2A.Z
An H3K14ub-H3K9me3 feedback circuit governs heterochromatin spreading and inheritance in fission yeast
DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning
Molecular basis for the inhibition of de novo DNA methylation by TCL1A
Linker histones consolidate heterogenous nucleosome fiber contacts by linking together multiple nucleosomes
Genetic variations interact with polybrominated diphenyl ether exposure to alter lipid homeostasis
Mitotic microhomology-mediated break-induced replication promotes chromoanasynthesis
Branched-chain α-keto acids impair glucose-stimulated insulin secretion in pancreatic β-cells under diabetes by reactivating the LDHA-lactate axis
Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform
HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps
Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis
The dynamic distribution of genetic tandem amplifications in a heteroresistant Escherichia coli population revealed by ultra-deep long read sequencing
Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner
Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions
Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape
Mistranslation suppresses mistranscription in eukaryotes
Context-specific regulatory genetic variation in dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis
iCLAP: an innovative method for integrable co-detection of low-abundance antigens with high-plex immunostaining
Rare coding variants in CHRNB3 associate with reduced daily cigarette smoking across ancestries
Nanopore-based massively parallel sensing for peptide profiling and protein identification
Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant
Shared Genetic Liability across Systems of Psychiatric and Physical Illness
High-throughput chemical proteomics workflow for profiling protein citrullination dynamics
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer
Spatial perturb-seq: single-cell functional genomics within intact tissue architecture
Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX
Genetic modifiers of -ε4-associated cognitive decline
SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling
Nonlinear genomic selection index accelerates multi-trait crop improvement
FATE-MAP predicts teratogenicity and human gastrulation failure modes by integrating deep learning and mechanistic modeling
Distinct genetic profiles influence body mass index between infancy and adolescence
Enhancing microbial metabolic capacity through high-energy electron beam-induced intense structural variations
Combining xQTL and genome-wide association studies from diverse populations improves druggable gene discovery
Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation
PanMETAI - a high performance tabular foundation model for accurate pancreatic cancer diagnosis via NMR metabolomics
eQTL in diseased colon tissue identifies potential target genes associated with IBD
OmiGA for ultra-efficient molecular quantitative trait loci mapping
genome analyses indicate introgression may drive local adaptation and herbicide resistance
Single-cell resolution of splicing regulation in peripheral blood mononuclear cells uncovers heterogeneity-driven mechanisms underlying human complex traits
KidneyGenAfrica multi-cohort Genome-wide association study and polygenic prediction of kidney function in 110,000 Africans
A catalogue of early diverged contemporary human genome variation reveals distinct Khoe-San populations
XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry
High-throughput multi-organ proteomics workflow for drug efficacy and toxicity analysis
MYC modulates TOP2A diffusion to promote substrate detection and activity
Partitioned polygenic scores show mechanistic heterogeneity in type 2 diabetes and hypertension comorbidity
A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis
Electrostatic properties of disordered regions control transcription factor search and pioneer activity
Cross ionization mode chemical similarity prediction between tandem mass spectra in metabolomics
Analysis of the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins using snFLARE-seq and mxFRIZNGRND
Radical footprinting in mammalian whole blood
Convergent extreme reductive evolution in ancient planthopper symbioses
Adgrg6/Gpr126 is required for compact wall integrity and establishing trabecular identity during cardiac trabeculation
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genomics of rafting crustaceans reveals adaptation to climate change in tropical oceans
scLong: a billion-parameter foundation model for capturing long-range gene context in single-cell transcriptomics
Protein-protein interactions are a major source of epistasis in genetic interaction networks
FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models
Integrative functional genomics analysis identifies pleiotropic genes for vascular diseases
Genomic consequences of residual recombination in a hybrid apomictic hickory complex
An experimentally-informed polymer model reveals high resolution organization of genomic loci
An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines
Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data
A multi-ancestry genetic reference for the Quebec population
Metabolic characterization of tumor-immune interactions by multiplexed immunofluorescence reveals spatial mechanisms of immunotherapy response in non-small cell lung carcinoma (NSCLC)
Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics
AI-based multiomics profiling reveals complementary omics contributions to personalized prediction of cardiovascular disease
DNA diamond formulates a decomposable composite letter constellation model for DNA data storage
Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle
Crowdsourced biodiversity monitoring fills gaps in global plant trait mapping
Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts
Dual promoter–enhancer activities reflect a unified regulatory logic
A versatile platform for sequential glyco-, phospho-, and proteomics with multi-PTMs integration
A comprehensive tandem repeat catalog of the human genome
An adaptive, continuous-learning framework for clinical decision-making from proteome-wide biofluid data
A proteogenomic atlas of 1032 brain metastases identifies molecular subtypes, immune landscapes, and therapeutic vulnerabilities
Three open questions in polygenic score portability
Comprehensive benchmarking single and multi ancestry polygenic score methods with the PGS-hub platform
Essential role of NONO-HOXA1-Wnt axis in cardiomyocyte differentiation
BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters
Epigenome-wide analysis identifies DNA methylation mediators of treatment-related cardiometabolic risk in survivors of childhood cancer
Automated mapping of DNA replication fork progression in human cells with ForkML
Improving polygenic score prediction for underrepresented groups through transfer learning
NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes
The role of low-complexity repeats in RNA–RNA interactions and a deep learning framework for duplex prediction
Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling
Cross-ancestry comparison of aptamer and antibody protein measures
ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning
Neural crest cell-derived DKK1 and NEDD4 modulate Wnt signalling in the second heart field to orchestrate outflow tract development
Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics
PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells
A dual context-aware basecaller for nanopore direct RNA sequencing
Preventing premature deaths through polygenic risk scores
The ratio of circulatory levels of sphingolipids to steroids predicts asthma exacerbations
Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing
Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder
The Knowledge Connector decision support system for multiomics-based precision oncology
Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN
TidyMass2: advancing LC-MS untargeted metabolomics through metabolite origin inference and metabolic feature-based functional module analysis
Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data
Genetic insights and mechanistic parallels in gestational diabetes mellitus and type 2 diabetes
HEXIM1 inter-monomer autoinhibition governs 7SK RNA binding specificity and P-TEFb inactivation
Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization
Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion
Genetic and non-genetic factors distinctly shape the variation of the immune response in cattle
Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility
The Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation
A scalable two-step genome editing strategy for generating full-length gene-humanized mice at diverse genomic loci
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA
Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing
Global solidarity in genomic surveillance improves early detection of acute respiratory virus threats
The biomedical landscape of genomic structural variation in the qatari population
Cross-species dissection of saline-related genes by genetically deciphering a euryhaline microalga sp
Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation
Temporal constraints on enhancer usage shape the regulation of limb gene transcription
Fine-mapping a genome-wide meta-analysis of 98,374 migraine cases identifies 181 sets of candidate causal variants
Rad51 determines pathway usage in post-replication repair
Functional implications of polygenic risk for schizophrenia in human neurons
A large-scale multi-ancestry genome-wide association study of chronic prostatitis/chronic pelvic pain syndrome in men
sCellST predicts single-cell gene expression from H& E images
Genomic dissection of the clonal background and global dissemination of hypervirulent CG23-KL57 lineage
Pulsed evolution shaped extant angiosperm pollen disparity
Multi-organ network of cardiometabolic disease-depression multimorbidity revealed by phenotypic and genetic analyses of MR images
Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications
DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations
Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies
Deep learning guided design of protease substrates
VACmap: an accurate long-read aligner for unraveling complex genomic rearrangements
Tuning evolvability via plasmid copy number and regulatory architecture
Generating crossmodal gene expression from cancer histopathology improves multimodal AI predictions
CellScope: high-performance cell atlas workflow with tree-structured representation
The Health for Life in Singapore (HELIOS) Study: delivering precision medicine research for Asian populations
Multi-omic relay velocity modeling uncovers dynamic chromatin-transcription regulation across cell states
Leveraging genomic and transcriptomic data of diverse ancestry to uncover mechanisms of psychiatric risk in the adult and developing brain
Plasma protein profiling predicts cancer in patients with non-specific symptoms
ALFA-K: Local adaptive mapping of karyotype fitness landscapes
Population structure reverses selection of variants with proportionally scaled birth and death rates
Genetic Insights into Head-to-Body Ratios Via Deep Learning-Based Image Segmentation and Implications for Common Diseases
Proteomic signatures of smoking and their associations with risk of incident diseases and mortality in diverse populations
Structure of the Methanosarcina mazei Mtr complex bound to the oxygen-stress responsive small protein MtrI
Mapping rare protein-coding variants on multi-organ imaging traits
Large-scale drug sensitivity, gene dependency, and proteogenomic analyses of telomere maintenance mechanisms in cancer cells
Prostate cancer cells converge to an inflammatory-like state upon metastatic dissemination
Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data
Distinct immune cell dynamics associated with immune-related adverse events during combined chemoradiation and immune checkpoint inhibitor therapy
Cross-platform clinical proteomics using the Charité open standard for plasma proteomics (OSPP)
Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass
Mapping cis- and trans-regulatory target genes of human-specific deletions
Recombination junctions from antibody isotype switching classify immune and DNA repair dysfunction
Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA
Circulating causal protein networks linked to future risk of myocardial infarction
Analysis genome of Pseudotaxus chienii reveals insights into the origin and evolution of taxane biosynthesis
Chromosome-level assembly and analysis of three hydroxy fatty acid-producing Physaria species
Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis
Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework
Widespread naturally variable human exons aid genetic interpretation
Accurate imputation of pathway-specific gene expression in spatial transcriptomics with PASTA
Genome-wide screen reveals dependence of break induced replication on several distinct checkpoints
omprehensive discovery of m6A sites in the human transcriptome at single-molecule resolution
scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase
Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma
Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement
A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry
Complex genetic effects linked to plasma protein abundance in the UK Biobank
Single-array measurements reveal non-uniform, mosaic-like chemosensory arrays in bacteria
Identification of a deep-branching lineage of algae using environmental plastid genomes
Flexible read-aware genotype imputation from sequence using biobank sized reference panels
Evaluating transportability of in vitro cellular models to in vivo human phenotypes using gene perturbation data
FastCCC: a permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies
Cost-effective non-additive GWAS across 2329 diseases in 500,349 individuals
Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody
A multimodal knowledge-enhanced whole-slide pathology foundation model
Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions
Genetic profiling of the circulating proteome in common diseases suggests causal proteins and improves risk prediction
Biologically-informed integration of drug representations for breast cancer treatment using deep learning
Generalizable morphological profiling of cells by interpretable unsupervised learning
Cohesin forms fountains at active enhancers in C. elegans
Co-expression-wide association studies link genetically regulated interactions with complex traits
CellMentor: cell-type aware dimensionality reduction for single-cell RNA-sequencing data
scDrugMap: benchmarking large foundation models for drug response prediction
CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoire
Co-condensation between transcription factor and cBAF selectively modulates chromatin remodeling and gene expression
RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing
Repurposing clinically safe drugs for DNA repair pathway choice in CRISPR genome editing and synthetic lethality
Patient-derived colon epithelial organoids reveal lipid-related metabolic dysfunction in pediatric ulcerative colitis
SIDISH integrates single-cell and bulk transcriptomics to identify high-risk cells and guide precision therapeutics through in silico perturbation
The genetic architecture of brainstem structures
Transformer-based deep learning enhances discovery in migraine GWAS
Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor
Airqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping
The bHLH transcription factor PIL1 orchestrates starch synthesis in key cereal crops
Inherent instability of simple DNA repeats shapes an evolutionarily stable distribution of repeat lengths
CiFi: accurate long-read chromosome conformation capture with low-input requirements
Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits
Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications
Proteome-wide association study of prostate cancer risk across populations
PITX2 dosage-dependent changes in pacemaker cell state underlie sinus node dysfunction and atrial arrhythmias
Inducible chromosomal rearrangement reveals nonlinear polygenic dosage effects in driving aneuploid yeast traits
Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome
Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation
Near complete assembly of Drosophila melanogaster Canton S strain genome
Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual
MetaboLM: a metabolomic language model for multi-disease early prediction and risk stratification
RAD51 D-loop structures reveal the mechanism of eukaryotic RAD51-mediated strand exchange
Acquisition of ampliconic sequences marks a selfish mouse -haplotype
Deciphering gene redundancy in prokaryotic genomes provides evolutionary insights for pathogenicity and its roles in clinical infections
Insights into natural neocentromere evolution from a cattle T2T X chromosome
Impact of common variants on brain gene expression from RNA to protein to schizophrenia risk
Benchmarking DNA foundation models for genomic and genetic tasks
Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance
Expanding the utility of variant effect predictions with phenotype-specific models
Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays
A deep learning-based multiscale integration of spatial omics with tumor morphology
Compressed sensing expands the multiplexity of imaging mass cytometry
Human plasma proteomic profile of clonal hematopoiesis
Multimodal single cell analyses reveal gene networks of planarian stem cell differentiation
Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology
Recessive variants in the intergenic locus cause monogenic kidney disease responsive to anti-proteinuric treatment
Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes
Transcription start sites experience a high influx of heritable variants fueled by early development
AI-augmented intraoperative decision-making workflows in diffuse midline glioma biopsy using cryosection pathology
Genetics and context for precision health in Greater Boston
Integrating axis quantitative trait loci looks beyond cell types and offers insights into brain-related traits
scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization
3D spatial organization of heterogeneous + progenitors in the zebrafish heart field pre-patterns cardiovascular development
Integrated spatial proteomic analysis of breast cancer heterogeneity unravels cancer cell phenotypic plasticity
Targeted sequencing and iterative assembly of near-complete genomes
Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals key associations with AD pathology
Explainable AI unravels sepsis heterogeneity via coagulation-inflammation profiles for prognosis and stratification
Motif-based models accurately predict cell type-specific distal regulatory elements
Multi-ancestry investigation of the genomics of erectile dysfunction
Long-read sequencing of primate testis and human sperm allows identification of recombination events in individuals
Deriving consensus sepsis clusters via goal-directed subgroup identification in multi-omics study
Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers
Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum
Addressing the specific roles of histone modifications in transcriptional repression
Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation
Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase
Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus
Cross-dataset pan-cancer detection by correlating cell-free DNA fragment coverage with open chromatin sites across cell types
Domestication shaped the chromatin landscape of grain amaranth
Benchmarking informatics workflows for data-independent acquisition single-cell proteomics
Genome architecture evolution in an invasive copepod species complex
Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues
Inferring differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data with MultiVeloVAE
Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry
Cell line-matched reference enables high-precision functional genomics
G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data
Multi-centric origins and gene flow shape the diversity of β-thalassemia mutations in Southern East Asia
C > U mutations generate immunogenic peptides in SARS-CoV-2
Omnireg-gpt: a high-efficiency foundation model for comprehensive genomic sequence understanding
Deriving three one dimensional NMR spectra from a single experiment through machine learning
DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks
ERNIE-RNA: an RNA language model with structure-enhanced representations
A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes
Differential conformational expansion of NUP98-HOXA9 oncoprotein from nanosized assemblies to macrophases
CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis
Conservation and variability of long-range interactions in structurally diverse maize genomes
Approaching single-molecule assembly-free readout from medium-length encoded DNA
Bacterial chromosome conformation and cell-free gene expression in synthetic 2D compartments
scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples
Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean
Developmentally regulated genes drive phylogenomic splits in ovule evolution
Variation in surface protein expression leads to heterogeneous Trypanosoma cruzi populations during host cell infection
Augmenting microbial phylogenomic signal with tailored marker gene sets
Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen
Genetic underpinnings and causal effects of brain structure and function on chronic pain intensity
ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics
Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks
Widespread reveals hidden diversity and reshapes understanding of human whipworm infections
Click-linking: a cell-compatible protein crosslinking method based on click chemistry
Protein-level batch-effect correction enhances robustness in MS-based proteomics
Gain of Alternative Allele Expression of at rs149707223 in Schizophrenia and Bipolar Disorder: Inducing Synaptic Transmission and Behavioral Deficits in Mice
Powerful one-dimensional scan to detect heterotic quantitative trait loci
Genomic and epigenomic maps of mouse centromeres and pericentromeres
AI-powered spatial cell phenomics enhances risk stratification in non-small cell lung cancer
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells
Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction
Gene expression signatures from whole blood predict amyotrophic lateral sclerosis case status and survival
Data navigation on the ENCODE portal
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing
Condensation-dependent interactome of a chromatin remodeler underlies tumor suppressor activities
Discovery of obesity genes through cross-ancestry analysis
A highly accurate risk factor-based XGBoost multiethnic model for identifying patients with skin cancer
Paused RNA polymerase primes promoters via RNA-mediated stabilisation of transcription factor ERα
Endothelial RNF20 suppresses endothelial-to-mesenchymal transition and safeguards physiological angiocrine signaling to prevent congenital heart disease
Mechanism of trinucleotide repeat expansion by MutSβ-MutLγ and contraction by FAN1
PLM-interact: extending protein language models to predict protein-protein interactions
UNICORN: Towards universal cellular expression prediction with a multi-task learning framework
Deciphering splicing heterogeneity at single-cell resolution by SCSES
MultiGATE: integrative analysis and regulatory inference in spatial multi-omics data via graph representation learning
Computational design and evaluation of optimal bait sets for scalable proximity proteomics
Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP
Artificial intelligence coupled to pharmacometrics modelling to tailor malaria and tuberculosis treatment in Africa
HSP90 as an evolutionary capacitor drives adaptive eye size reduction via atonal
Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors
Explicit error coding can mediate gain recalibration in continuous bump attractor networks
Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures
Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing
Genetic determinants and genomic consequences of non-leukemogenic somatic point mutations
Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions
scTFBridge: a disentangled deep generative model informed by TF-motif binding for gene regulation inference in single-cell multi-omics
Analysis of cfDNA fragmentomics metrics and commercial targeted sequencing panels
Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
A comprehensive benchmark of single-cell Hi-C embedding tools
HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs
The effect of type 2 diabetes genetic predisposition on non-cardiovascular comorbidities
Dissecting regulatory non-coding GWAS loci reveals fibroblast causal genes with pathophysiological relevance to heart failure
IceQream: Quantitative chromosome accessibility analysis using physical TF models
Characterization of prevalent genetic variants in the Estonian Biobank body-mass index GWAS
Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus
HALO: hierarchical causal modeling for single cell multi-omics data
A histomorphological atlas of resected mesothelioma discovered by self-supervised learning from 3446 whole-slide images
Improved allele frequencies in gnomAD through local ancestry inference
Conformational plasticity of disordered regions enables sequence-diverse DNA recognition by transcription factor AflR
Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA
The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity
A deep single cell mass cytometry approach to capture canonical and noncanonical cell cycle states
Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set
Benchmarking scRNA-seq copy number variation callers
Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus
Polygenic risk score for type 2 diabetes shows context-dependent effects across populations
Disentangling associations between complex traits and cell types with seismic
Contribution of leukocyte telomere length to cardiovascular disease onset from genome-wide cross-trait analysis
TP63 mediates the generation of tumour-specific chromatin loops that underlie MYC activation in radiation-induced tumorigenesis
Forward and reverse genomic screens enhance the understanding of phenotypic variation in a large Chinese rhesus macaque cohort
Concordance between male- and female-specific GWAS results helps define underlying genetic architecture of complex traits
A basic framework to explain splice-site choice in eukaryotes
mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis
Genetic determinants of monocyte splicing are enriched for disease susceptibility loci
TP53 variant clusters stratify phenotypic diversity in germline carriers and reveal an osteosarcoma-prone subgroup
The pericardium forms as a distinct structure during heart formation
RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets
Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples
AI cancer driver mutation predictions are valid in real-world data
Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes
TEtrimmer: a tool to automate the manual curation of transposable elements
Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis
Graph neural networks learn emergent tissue properties from spatial molecular profiles
: a web-based application for in-depth exploration of multi-omics data with brightfield histology
Super-silencers are crucial for development and carcinogenesis in B cells
The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression
Mechanically activated snai1b coordinates the initiation of myocardial delamination for trabeculation
Shared genetic architecture contributes to risk of major cardiovascular diseases
Genetic architecture of plasma metabolome in 254,825 individuals
Learning the cellular origins across cancers using single-cell chromatin landscapes
A mesothelial differentiation gateway drives fibrosis
The reference genome of the human diploid cell line RPE-1
Prediction of cellular morphology changes under perturbations with a transcriptome-guided diffusion model
Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma
CLADES: a hybrid NeuralODE-Gillespie approach for unveiling clonal cell fate and differentiation dynamics
A quadratic paradigm describes the relationship between phenotype severity and variation
Coordinated active repression operates via transcription factor cooperativity and multiple inactive promoter states in a developing organism
Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics
A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
Unveiling causal regulatory mechanisms through cell-state parallax
A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints
DECIPHER for learning disentangled cellular embeddings in large-scale heterogeneous spatial omics data
Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases
Reprogramming the tumor microenvironment with c-MYC-based gene circuit platform to enhance specific cancer immunotherapy
Interaction of genetic variants activates latent metabolic pathways in yeast
Peripheral blood DNA methylation predicts the early onset of primary tumor in mutation carriers
Crotonylation of IDH1 alleviates MASLD progression by enhancing the TCA cycle
Revealing the biophysics of lamina-associated domain formation by integrating theoretical modeling and high-resolution imaging
Modeling integration site data for safety assessment with MELISSA
SpaIM: single-cell spatial transcriptomics imputation via style transfer
Large-scale GWAS of strabismus identifies risk loci and provides support for a link with maternal smoking
Multivariate protein landscape of host response in hospitalised patients with suspected infection in the emergency department
Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples
Finding spatially variable ligand-receptor interactions with functional support from downstream genes
The chronODE framework for modelling multi-omic time series with ordinary differential equations and machine learning
TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues
A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells
MR-EILLS: an invariance-based Mendelian randomization method integrating multiple heterogeneous GWAS summary datasets
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice
: AI generation of multiplex immunofluorescence staining from histopathology images
Biobank-scale genetic characterization of Alzheimer’s disease and related dementias across diverse ancestries
Multimodal spatial transcriptomic characterization of mouse kidney injury and repair
Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs
Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions
Microtubule mechanotransduction refines cytomegalovirus interactions with and remodeling of host chromatin
Modeling the genomic architecture of adiposity and anthropometrics across the lifespan
Epigenetic control of topoisomerase 1 activity presents a cancer vulnerability
DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins
Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis
Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family
Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome
Computationally unmasking each fatty acyl C=C position in complex lipids by routine LC-MS/MS lipidomics
European and African ancestry-specific plasma protein-QTL and metabolite-QTL analyses identify ancestry-specific T2D effector proteins and metabolites
Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese
Uncovering hidden enhancers through unbiased in vivo testing
super-pangenome provides insights into lettuce genome evolution and domestication
Local genetic sex differences in quantitative traits
IRX3 controls a SUMOylation-dependent differentiation switch in adipocyte precursor cells
Sequencing a DNA analog composed of artificial bases
Substrate accessibility regulation of human TopIIa decatenation by cohesin
Thor: a platform for cell-level investigation of spatial transcriptomics and histology
PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context
Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions
Replisomes restrict SMC translocation in vivo
Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling
Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states
High performance data integration for large-scale analyses of incomplete profiles using Batch-Effect Reduction Trees (BERT)
Whole-exome sequencing analysis identifies risk genes for schizophrenia
PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility
A framework for complex signal processing via synthetic biological operational amplifiers
vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics
Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia
Single-nuclei multiomics analysis identifies abnormal cardiomyocytes in a murine model of cardiac development
Causal mediation analysis for time-varying heritable risk factors with Mendelian randomization
DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution
SMCHD1 maintains heterochromatin, genome compartments and epigenome landscape in human myoblasts
Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling
Identification of multiple genomic alterations and prediction of neoantigens from circulating tumor cells at the single-cell level
Predicting the direction of phenotypic difference
PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model
Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains
Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning
A draft UAE-based Arab pangenome reference
Machine-learning driven strategies for adapting immunotherapy in metastatic NSCLC
Causal disentanglement for single-cell representations and controllable counterfactual generation
Machine learning in Alzheimer’s disease genetics
Mechanism of Rad51 filament formation by Rad52 and Rad55-Rad57 in homologous recombination
Single nucleosome imaging reveals principles of transient multiscale chromatin reorganization triggered by histone ADP-ribosylation at DNA lesions
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing
Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
Natural variation of an E3 ubiquitin ligase encoding gene regulates grain chalkiness in rice
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases
Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling
Comprehensive interaction modeling with machine learning improves prediction of disease risk in the UK Biobank
Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos
Personalized risk stratification in colorectal cancer via PIANOS system
Genome-level selection in tumors as a universal marker of resistance to therapy
Combined genome-wide association study of facial traits in Europeans increases explained variance and improves prediction
High-resolution mapping of single cells in spatial context
Quantitative phase imaging with temporal kinetics predicts hematopoietic stem cell diversity
The mutational landscape of SARS-CoV-2 provides new insight into viral evolution and fitness
Quantification of transcript isoforms at the single-cell level using SCALPEL
Forced expression of MSR repeat transcripts above a threshold limit breaks heterochromatin organisation
The mitotic chromosome periphery modulates chromosome mechanics
Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets
Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion
Nucleosome spacing can fine-tune higher-order chromatin assembly
Resolving out of Africa event for Papua New Guinean population using neural network
Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells
The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms
In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest
Unveiling aging heterogeneities in human dermal fibroblasts via nanosensor chemical cytometry
Early detection of emerging SARS-CoV-2 Variants from wastewater through genome sequencing and machine learning
High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics
Nuclear morphometrics coupled with machine learning identifies dynamic states of senescence across age
Automated cell annotation and classification on histopathology for spatial biomarker discovery
Cell Marker Accordion: interpretable single-cell and spatial omics annotation in health and disease
Precision-edited histone tails disrupt polycistronic gene expression controls in trypanosomes
DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads
MR-link-2: pleiotropy robust Mendelian randomization validated in three independent reference datasets of causality
Phylogenetically informed predictions outperform predictive equations in real and simulated data
Serum metabolic profiling enables diagnosis, prognosis, and monitoring for brainstem gliomas
Uncovering causal gene-tissue pairs and variants through a multivariate TWAS controlling for infinitesimal effects
Pan-cancer copy number analysis identifies optimized size thresholds and co-occurrence models for individualized risk stratification
Scaling laws of bacterial and archaeal plasmids
scICE: enhancing clustering reliability and efficiency of scRNA-seq data with multi-cluster label consistency evaluation
Distribution of copy number alterations and impact of chromosome arm call thresholds for meningioma
Prioritizing perturbation-responsive gene patterns using interpretable deep learning
Trioxane-based MS-cleavable cross-linking mass spectrometry for profiling multimeric interactions of cellular networks
Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily ()
Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy
An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data
Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures
-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity
Whole-genome sequencing of 1,060 isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids
LassoPred: a tool to predict the 3D structure of lasso peptides
Mapping the regulatory genetic landscape of complex traits using a chicken advanced intercross line
Transcripts with high distal heritability mediate genetic effects on complex metabolic traits
Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell
GPerturb: Gaussian process modelling of single-cell perturbation data
A large C-terminal Rad52 segment acts as a chaperone to Form and Stabilize Rad51 Filaments
Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer
MORC2 is a phosphorylation-dependent DNA compaction machine
Analysis of the geneome identifies RcCYP72H7 as an epoxidase in iridoid glycoside biosynthesis
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer
Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data
MassCube improves accuracy for metabolomics data processing from raw files to phenotype classifiers
DrFARM: identification of pleiotropic genetic variants in genome-wide association studies
Charting γ-secretase substrates by explainable AI
Shared genetic architecture of posttraumatic stress disorder with cardiovascular imaging, risk, and diagnoses
ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets
Prevalent chromosome fusion in Vibrio cholerae O1
Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy
cTAGE5 is essential for adipogenesis and adipose tissue development
Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
Bridging cell morphological behaviors and molecular dynamics in multi-modal spatial omics with MorphLink
Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values
Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods
High-resolution detection of copy number alterations in single cells with HiScanner
BIGFAM - variance components analysis from relatives without genotype
GAUDI: interpretable multi-omics integration with UMAP embeddings and density-based clustering
Deep generalizable prediction of RNA secondary structure via base pair motif energy
RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks
Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome
A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins
Cold-induced nucleosome dynamics linked to silencing of Arabidopsis
ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution
Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding
Divergence in a eukaryotic transcription factor’s co-TF dependence involves multiple intrinsically disordered regions
Switch-like gene expression modulates disease risk
stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs
Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas
Maximizing meiotic crossover rates reveals the map of Crossover Potential
Faster adaptation but slower divergence of X chromosomes under paternal genome elimination
Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions
A versatile information retrieval framework for evaluating profile strength and similarity
H3.3 deposition counteracts the replication-dependent enrichment of H3.1 at chromocenters in embryonic stem cells
Performance of deep-learning-based approaches to improve polygenic scores
Single-molecule direct RNA sequencing reveals the shaping of epitranscriptome across multiple species
Divergent combinations of enhancers encode spatial gene expression
Sequential structure probing of cotranscriptional RNA folding intermediates
A naturally occurring SNP modulates thermotolerance divergence among grapevines
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Exome-wide association study of blood lipids in 1,158,017 individuals from diverse populations
Non-Mendelian inheritance of DNA methylation patterns in mice
Accurate, scalable and cross-platform cell identification for high-resolution spatial transcriptomics
Genome-wide associations of structural variants with human traits through imputation from long-read assemblies
Patterns and drivers of 43,617 mosaic chromosomal alterations in blood
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs
Empirically determined baseline masking strategies and other considerations for gene-level burden tests
Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon
Genetic association and machine learning improve the prediction of type 1 diabetes risk
Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources
Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states
Pangenomic analyses of rose uncover widespread structure variation and empower genomics-directed breeding
De novo formation of -regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion
Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion
Histone acetylation-dependent clustering of BRD2 instructs transcription dynamics
Genome-wide fine-mapping improves identification of causal variants
Genomic, phenomic and geographic associations of leukocyte telomere length in the United States
Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity
Single-cell spatial transcriptomic analysis of human skin anatomy
A pangenome reference and population studies link structural variants with breeding traits in
A meta-analysis of single-nucleus expression quantitative trait loci linking genetic risk to brain disorders
Breeding ideotype maize with enhanced yield through genomics-guided pyramiding of favorable alleles
Population-level structural variant characterization using pangenome graphs
Genome-wide association analyses of autoimmune hypothyroidism reveal autoimmune and thyroid-specific contributions and an inverse relationship with cancer risk
Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila
GGC repeat expansions within new open reading frames are translated into toxic polyglycine proteins in oculopharyngodistal myopathy
Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation
Pan-cancer inference and validation of hypermorphic, hypomorphic and neomorphic mutations
Graph-based pangenome reveals structural variation dynamics during cucumber breeding
A microenvironment-determined risk continuum refines subtyping in meningioma and reveals determinants of machine learning-based tumor classification
Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding
Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model
Multi-trait and multi-ancestry genetic analysis of comorbid lung diseases and traits improves genetic discovery and polygenic risk prediction
Impact and correction of segmentation errors in spatial transcriptomics
Compressive pangenomics using mutation-annotated networks
Linking the plasma proteome to genetics in individuals from continental Africa provides insights into type 2 diabetes pathogenesis
Protein–protein interactions shape -regulatory impact of genetic variation on protein expression and complex traits
MultiSuSiE improves multi-ancestry fine-mapping in All of Us whole-genome sequencing data
Graph pan-genome illuminates evolutionary trajectories and agronomic trait architecture in allotetraploid cotton
Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion
Multitrait analyses identify genetic variants associated with aortic valve function and aortic stenosis risk
Genomic and transcriptomic analyses of aortic stenosis enhance therapeutic target discovery and disease prediction
JMJD2 regulates enhancer–promoter interactions via biomolecular condensate formation
Natural variation in OsTPS8 confers differential regulation of chalkiness and seed vigor in indica and japonica rice
Telomere-to-telomere genome assembly of a male pig provides insight into population structure and selection for body stature
Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models
A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic interaction effects
A genome-wide association study of mass spectrometry proteomics using a nanoparticle enrichment platform
Spatially resolved multi-omics of human metabolic dysfunction-associated steatotic liver disease
Scalable and accurate rare variant meta-analysis with Meta-SAIGE
Disentangling the architectural and non-architectural functions of CTCF and cohesin in gene regulation
Uniform dynamics of cohesin-mediated loop extrusion in living human cells
Computationally efficient meta-analysis of gene-based tests using summary statistics in large-scale genetic studies
Liability threshold model-based disease risk prediction based on electronic health record phenotypes
An African ancestry-specific nonsense variant in CD36 is associated with a higher risk of dilated cardiomyopathy
Spatiotemporal gene expression and cellular dynamics of the developing human heart
Genetic diversity and evolution of rice centromeres
Complete genome assemblies of two mouse subspecies reveal structural diversity of telomeres and centromeres
Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes
Locityper enables targeted genotyping of complex polymorphic genes
Meta-analysis reveals differences in somatic alterations by genetic ancestry across common cancers
Characterization of induced cohesin loop extrusion trajectories in living cells
Nucleotide dependency analysis of genomic language models detects functional elements
Population-scale gene-based analysis of whole-genome sequencing provides insights into metabolic health
A genetic map of human metabolism across the allele frequency spectrum
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq
Limited overlap between genetic effects on disease susceptibility and disease survival
Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks
Genome-wide association meta-analysis of childhood ADHD symptoms and diagnosis identifies new loci and potential effector genes
Accelerated Bayesian inference of population size history from recombining sequence data
DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution
Multiancestry brain pQTL fine-mapping and integration with genome-wide association studies of 21 neurologic and psychiatric conditions
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
A multi-tissue single-cell expression atlas in cattle
Genetic variants affecting RNA stability influence complex traits and disease risk
DNA methylation influences human centromere positioning and function
Cross-biobank generalizability and accuracy of electronic health record-based predictors compared to polygenic scores
Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity
A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism
LDAK-KVIK performs fast and powerful mixed-model association analysis of quantitative and binary phenotypes
Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize
Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas
Noncoding rare variant associations with blood traits in 166,740 UK Biobank genomes
Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes
Pangenome analysis provides insights into legume evolution and breeding
Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution
Genome assembly of two allotetraploid cotton germplasms reveals mechanisms of somatic embryogenesis and enables precise genome editing
G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing
A contextual genomic perspective on physical activity and its relationship to health, well being and illness
Improved multiancestry fine-mapping identifies -regulatory variants underlying molecular traits and disease risk
Germline genetic variation impacts clonal hematopoiesis landscape and progression to malignancy
Detecting and quantifying clonal selection in somatic stem cells
Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs
Disruption of TAD hierarchy promotes LTR co-option in cancer
Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis
Predicting resistance to chemotherapy using chromosomal instability signatures
Transferability of European-derived Alzheimer’s disease polygenic risk scores across multiancestry populations
Incorporating genetic data improves target trial emulations and informs the use of polygenic scores in randomized controlled trial design
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
A map of blood regulatory variation in South Africans enables GWAS interpretation
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
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Ancient DNA evidence for the history of the Albanians
Genetics of monozygotic twins reveals the impact of environmental sensitivity on psychiatric and neurodevelopmental phenotypes
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Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis
Analysis of the three-dimensional genome of exhausted CD8+ T cells reveals a critical role of IRF8 in their differentiation and functions in cancer
A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice
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Proteomic risk score for early prediction of kidney disease progression in individuals with high-risk genotypes
Real-world clinical utility of tumor whole-genome sequencing in solid cancers
An atlas of exposome–phenome associations in health and disease risk
Genetic regulation across germline and somatic variation on the Y chromosome contributes to type 2 diabetes
Clinical genetic variation across Hispanic populations in the Mexican Biobank
Circulating metabolites, genetics and lifestyle factors in relation to future risk of type 2 diabetes
Real-world clinical utility of comprehensive genomic profiling in advanced solid tumors
AI-enabled virtual spatial proteomics from histopathology for interpretable biomarker discovery in lung cancer
A consensus immune dysregulation framework for sepsis and critical illnesses
Genetic subtyping of obesity reveals biological insights into the uncoupling of adiposity from its cardiometabolic comorbidities
Genetic and molecular landscape of comorbidities in people living with HIV
The proteogenomic landscape of the human kidney and implications for cardio-kidney-metabolic health
Polygenic prediction of body mass index and obesity through the life course and across ancestries
Clinical utility of targeted RNA sequencing in cancer molecular diagnostics
Deep phenotyping of health–disease continuum in the Human Phenotype Project
Real-world deployment of a fine-tuned pathology foundation model for lung cancer biomarker detection
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Decoding sequence determinants of gene expression in diverse cellular and disease states
StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts
Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics
Systematically decoding pathological morphologies and molecular profiles with unified multimodal embedding
Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell
Orthrus: toward evolutionary and functional RNA foundation models
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
Differentiation of sphingomyelin and cholesterol by hyperspectral mid-infrared detection of single-bond vibrational modes in the fingerprint region
Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage
CellVoyager: AI CompBio agent generates new insights by autonomously analyzing biological data
Highly accurate ab initio gene annotation with ANNEVO
stVCR: spatiotemporal dynamics of single cells
Scaffolds with optimized quaternary symmetry for de novo cryoEM structure determination of small RNAs
DECODE: deep learning-based common deconvolution framework for various omics data
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Rate variation and recurrent sequence errors in pandemic-scale phylogenetics
Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus
Pertpy: an end-to-end framework for perturbation analysis
cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions
High-parameter spatial multi-omics through histology-anchored integration
Inferring cancer type-specific patterns of metastatic spread using Metient
Novae: a graph-based foundation model for spatial transcriptomics data
Inferring cell differentiation maps from lineage tracing data
C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels
Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes
Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
Squidiff: predicting cellular development and responses to perturbations using a diffusion model
Nicheformer: a foundation model for single-cell and spatial omics
Annotating the genome at single-nucleotide resolution with DNA foundation models
Improved reconstruction of single-cell developmental potential with CytoTRACE 2
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
gReLU: a comprehensive framework for DNA sequence modeling and design
Deep generative modeling of sample-level heterogeneity in single-cell genomics
All-at-once RNA folding with 3D motif prediction framed by evolutionary information
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem
Uncovering hidden protein modifications with native top-down mass spectrometry
EpiAgent: foundation model for single-cell epigenomics
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE
Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data
MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries
Spatial gene expression at single-cell resolution from histology using deep learning with GHIST
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions
Unified mass imaging maps the lipidome of vertebrate development
Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing
DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations
High-throughput profiling of chemical-induced gene expression across 93,644 perturbations
Morphological map of under- and overexpression of genes in human cells
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines
The Platinum Pedigree: a long-read benchmark for genetic variants
GeneAgent: self-verification language agent for gene-set analysis using domain databases
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics
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Spatial proteomic analysis in human Alzheimer’s disease brains enables identification of microenvironment-dependent microglial cell states
Optics-free spatial genomics for mapping mammalian brain aging by IRISeq
Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo
Spatial and single-cell characterization of human glioblastoma tumor microenvironment reveals malignant cellular communities
CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease
Trans-ancestry genome-wide analyses of bipolar disorder in East Asian and European populations improve genetic discovery
A genome-wide analysis of the shared genetic risk architecture of complex neurological and psychiatric disorders
Alzheimer’s disease transcriptional landscape in ex vivo human microglia
Fine-mapping genomic loci refines bipolar disorder risk genes
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Spontaneous switching in a protein signalling array reveals near-critical cooperativity
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Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types
Structural insight into how RAD51 paralog exchange regulates RAD51 filament formation
Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs
Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription
Evolution of promoter-proximal pausing enabled a new layer of transcription control
Kinetic control of mammalian transcription elongation
Dynamics of microcompartment formation at the mitosis-to-G1 transition
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus
Interactions between the genome and the nuclear lamina are multivalent and cooperative
DNA bendability regulates transcription factor binding to nucleosomes
The mitotic STAG3–cohesin complex shapes male germline nucleome
Structural insights into higher-order natural RNA-only multimers
GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion
Structural insights into transcriptional regulation by the helicase RECQL5
Single-cell long-read Hi-C, scNanoHi-C2, details 3D genome reorganization in embryonic-stage germ cells
Multiplex and multimodal mapping of variant effects in secreted proteins via MultiSTEP
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Enhancer dynamics and cellular architecture in the human spinal cord
SCOPE-C reveals long-range enhancer networks emerging as key regulators during human cortical neurogenesis
Human brain vascular multi-omics elucidates disease-risk associations
Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis
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Decoding Gene–Lifestyle Synergy in Diabetic Retinopathy Development: A Transethnic Prospective Cohort Study
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Cell type-agnostic transcriptomic signatures enable uniform comparisons of neural maturation
Neural signaling contributes to heart formation and growth in the invertebrate chordate, Ciona robusta
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Comparative gene annotation and orthology assignments across 301 species of Drosophilidae
DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction
A cost-effective and scalable barcoded library construction method for deep mutational scanning studies
Pangenome graph analysis reveals evolution of resistance breaking in spinach downy mildew
MMSpa is a deep learning-based tool that enhances the identification of spatial domains in spatial transcriptomics studies
USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Cell2Spatial is a computational framework that maps single cells to spatial transcriptomic spots to reconstruct tissue architecture
Dual transcriptional activities of PAX3 and PAX7 spatially encode spinal cell fates through distinct gene networks
Simple scaling laws control the genetic architectures of human complex traits
The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella
Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia.
Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom
A toolkit for mapping cell identities in relation to neighbors reveals conserved patterning of neuromesodermal progenitor populations
Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli
A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.
MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways.
Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis
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mFABIO: An integrative multi-tissue TWAS fine-mapping approach to prioritize potentially causal genes and tissues underlying binary traits
MR2G: A novel framework for causal network inference using GWAS summary data
Simulated sample splitting approach to address biases due to instrument selection and participant overlap in two-sample Mendelian Randomization studies
Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation
Tissue-specific transfer learning improves functional variant and therapeutic target discoveries in breast and prostate cancer
Potential Rad54 separation of function mutation highlights unique roles during homologous recombination
Epigenetic gene regulation is controlled by distinct regulatory complexes utilizing specialized paralogs of TELOMERE REPEAT BINDING FACTORS
Examining the association between fetal HLA-C, maternal KIR haplotypes and birth weight
Translation control by altered start codon usage as a means of modulating the general stress response and virulence in Listeria monocytogenes
ADNP regulates chromatin architecture and lineage fidelity during neural differentiation
The geometry of G × E: How scaling and endogenous treatment effects shape interaction direction
Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans
An evaluation of age-varying genetic effects underlying body-mass index and blood pressure in the UK Biobank
Functional interrogation of candidate cis-regulatory elements at the LDLR locus
Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts
Simplifying causal gene identification in GWAS loci
Estimating the distribution of fitness effects of loss of heterozygosity (LOH) events using an engineered library of Saccharomyces cerevisiae
Topological stratification of continuous genetic variation in large biobanks
Unraveling the genetic links between stature and disease in East Asians: A multi-biobank genetic correlation and risk prediction study
Nucleosome positioning shapes cryptic antisense transcription
The effect of long-range linkage disequilibrium on allele-frequency dynamics under stabilizing selection
Polygenic risk scores and Parkinson’s disease in South Africa advancing ancestry informed disease prediction
Genetic correlation-guided mega-analysis of DO mice provides mechanistic insight and candidate genes for age-related pathologies
Genetic underpinnings of chills from art and music
High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification
Chromatin state architecture governs transcription factor accessibility across plant genomes
Genetic variation shapes the chromatin accessibility landscape and transcriptional responses in mouse adipose tissue
A maize mutant in the glutamate receptor-like dwarf13 is modified by cis-acting natural variation and a Cornichon homolog
Decoding the germline genetic architecture of prostate cancer at a single cell resolution
Establishment and maintenance of NRT2.1 inter-individual variability in plants
Aberrant cohesin function in Saccharomyces cerevisiae activates Mcd1 degradation to promote cell lethality
Genomic evidence for a-α heterothallic and α-α unisexual mating and recombination in an environmental Cryptococcus deneoformans population
Genome-wide selection inference at short tandem repeats
Effector innovation in genome-reduced phytoplasmas and other host-dependent mollicutes
Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies
Towards a transcriptomic biomarker for the classification of melanocytic neoplasms
A survey of human cancer-germline genes: Linking X chromosome localization, DNA methylation and sex-biased expression in early embryos.
Meta-evolutionary exome analysis identifies novel type 2 diabetes mellitus genes in the UK Biobank and all of us
Genome-wide association study provides novel insight into the genetic architecture of severe obesity
Alzheimer disease is (sometimes) highly heritable: Drivers of variation in heritability estimates for binary traits, a systematic review
On the analysis of genetic association with long-read sequencing data
Identification of gene-sex hormone interactions associated with type 2 diabetes among men and women
Polycomb repressive complexes 1 and 2 independently and dynamically regulate euchromatin during cerebellar neurodevelopment
From individuals to ancestries: Towards attributing trait variation to haplotypes.
Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion
Beyond recombination: Exploring the impact of meiotic frequency on genome-wide genetic diversity
Recombination plasticity in response to temperature variation in reptiles.
The highly dynamic pangenome of basal chordates is enriched in defence and immunity genes and is inherited following the Mendelian law.
Detecting latent interaction effects when analyzing binary traits
Gene dosage and protein valency impact phase separation and fungal cell fate.
Pathway polygenic risk scores (pPRS) for the analysis of gene-environment interaction.
Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans.
Enhanced genetic fine mapping accuracy with Bayesian Linear Regression models in diverse genetic architectures.
Bayesian network imputation methods applied to multi-omics data identify putative causal relationships in a type 2 diabetes dataset containing incomplete data: An IMI DIRECT Study.
The length and strength of compartmental interactions are modulated by condensin II activity.
A mathematical framework for the quantitative analysis of genetic buffering.
Flipping the switch on some of the slowest mutating genomes: Direct measurements of plant mitochondrial and plastid mutation rates in msh1 mutants
Titin-Truncating variants predispose to dilated cardiomyopathy in populations genetically similar to african and european reference populations.
Strain background interacts with chromosome 7 aneuploidy to determine commensal and virulence phenotypes in Candida albicans
Sodium azide mutagenesis induces a unique pattern of mutations
Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation
Structural basis for higher-order DNA binding by a bacterial transcriptional regulator
1
Identification of lipid quantitative trait loci linked with cardiometabolic disease in Asian Indians and Europeans: A genome-wide association study and Mendelian randomization
6
Out-of-Equilibrium Selection Pressure Enhances Inference from Protein Sequence Data
Dynamic Self-Loops in Networks of Passive and Active Binary Elements
Invariant Measures in Time-Delay Coordinates for Unique Dynamical System Identification
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription
Manipulating Phases in Many-Body Interacting Systems with Subsystem Resetting
Dissipation Enables Robust Extensive Scaling of Multipartite Correlations
1
Active Hydrodynamic Theory of Euchromatin and Heterochromatin
33
High-Contiguity Haplotype-Resolved Genome Assembly of the Hexaploid Actinidia valvata Rootstock Sheds Light on Waterlogging Resistance Gene
A Near Telomere-to-Telomere Genome of Belamcanda chinensis Provides Insights Into Genome Evolution and the Biosynthesis of Characteristic Isoflavones
Chromosome-Level Genome Assembly of the Allotetraploid Gynostemma pentaphyllum Provides Novel Insights Into the Biosynthesis of Ginsenoside and Gypenoside LVI
DNAwhisper: An Integrated Deep Learning Pyramidal Framework for Multi-Trait Genomic Prediction and Adaptive Marker Prioritisation
Dynamics of Gene and Allelic Expression During Modern Hybrid Maize Breeding
PlantCTCIP: Chromatin Interaction Prediction Using Convolutional Neural Network and Transformer in Plants
A Super‐Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution
<atl>Haploid Mutation Mapping Identifies a Homoeologous Non‐Reciprocal Translocation Linked to Reduced Fibre and Enhanced Protein in scp iBrassica napus/i /scp</atl>
Chromosome-Scale Haplotype Genome Assemblies for the Australian Mango ‘Kensington Pride’ and a Wild Relative, Mangifera laurina, Provide Insights Into Anthracnose-Resistance and Volatile Compound Biosynthesis Genes
Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume
Auxin-Induced Nicotine Inhibition Is Mediated by NaARF5 Through the Suppression of NaERF1-Like Expression and Interaction With NaERF1-Like in Nicotiana attenuata
Subclass III SnRK2 Kinases Coordinate Starch and Storage Protein Synthesis During Maize Kernel Development
Genome and Single-Cell Transcriptome Reveal the Evolution of Holoparasitic Plants: A Case Study of Cistanche deserticola
Transposable Element-Mediated Structural Variation Drives Flower Colour Diversification in Camellia
The Rhus chinensis Genome Provides Insights Into Tannin, Flavonoid Biosynthesis, and Glandular Trichome Development
ZmMYB127 Modulates Maize Kernel Texture and Size by Integrating the Synthesis of Starch, Zein Proteins and Auxin
Dual-Layer Transcriptional-Protein Regulation by HvAP2-12 Represses HvAP2-18 Activity to Fine-Tune Barley Starch Synthesis
Systematically Revealing Quantitative Multi-Target Integrative Effects of Plants With Artificial Intelligence Method
Populus PtrbHLH011 Is a Transcriptional Co-Regulator Involved in the Activation of Cell Wall Biosynthesis by Iron Deprivation
An integrative multi-omics analysis of histone modifications and DNA methylation reveals the epigenomic landscape in apple under drought stress
A large-scale gene regulatory network for rice endosperm starch biosynthesis and its application in genetic improvement of rice quality
scpISDH/scp‐seq: a robust methodology for profiling and characterization of open chromatin
A MYB61-SWB9-KOs module regulates grain chalkiness via gibberellin biosynthesis in rice endosperm
A telomere‐to‐telomere gap‐free assembly integrating multi‐omics uncovers the genetic mechanism of fruit quality and important agronomic trait associations in pomegranate
Genome assembly and population genomic analysis reveal the genetic basis of popcorn evolution
Breaking down data silos across companies to train genome-wide predictions: A feasibility study in wheat
Rootstock of distant hybrid activates transcription factors of scion cultivar to promote growth and yield in walnut
Genetic diversity and adaptive evolutionary history of Sapindus in China: insights from whole-genome resequencing of 100 representative individuals
Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana
LGRPv2: A high-value platform for the advancement of Fabaceae genomics
An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement
Characterizing the structural variations in the genome of the mandarin variety, IrM2, induced by gamma irradiation
ZmSSRP1, transactivated by OPAQUE11, positively regulates starch biosynthesis in maize endosperm
139
Comprehensive mutagenesis defines the functional landscape of human α-tubulin
Theory of chromosome structural dynamics by processive loop extrusion
CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression
Genome-wide association mapping and targeted loss of function studies identify Shroom3 as a driver of hyperpolyploidy and ventricular dilation
ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein–protein interactions and gene essentiality across taxa
Molecular insight into the interplay among heterogeneous plasmacytes and microenvironment cells and their clinical relevance in myeloma
Position-dependent feedback drives scaling and robustness of morphogen gradients
Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors
Sperm, egg, and embryo proteins critical for genetic adaptation of herring to low salinity in the Baltic Sea
Reconstructing ancient genomes from gene counts: A robust likelihood framework with sampling bias correction
Layer-specific genetic variation unlocks secondary metabolite diversity in long-lived clonal peppermint
Functional dissection of SPOP at the amino acid level reveals a comprehensive functional landscape of variants during tumorigenesis
RETRACTED: PKNOX2 gene is significantly associated with substance dependence in European-origin women
Observational epidemiological studies can mitigate genetic confounding with a genetic relatedness matrix
Stag2-mediated chromatin dynamics regulates antibody class switch recombination
Microhomology-mediated tandem duplication is a conserved mechanism of genomic variation with implications for human disease
Quantifying direct genetic signal captured by principal component adjustment
Parallel algorithms for phylogenetic inference under a structured coalescent approximation
Cohesin acetylation and ATPase activity control cohesion and loop architecture through distinct mechanisms
Simple biological controllers drive the evolution of soft modes
Emergence of genetic sex determination in an environmentally sex-determined animal
The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians
A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion
Evidence for strong purifying selection of human 47S ribosomal RNA genes
Deep learning framework for quantifying self-organization in Myxococcus xanthus
Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia
Coalescence and translation: A language model for population genetics
Resolving competing evolutionary histories in joint ancestral state reconstruction
Chromosome-specific drift under stabilizing selection generates polygenic barriers to sex chromosome turnover
Whole-genome combinatorial gene fusions generate novel genes for advanced microbial trait development
Detecting gene–environment interactions to guide personalized intervention: Boosting distributional regression for polygenic scores
Background selection in recombining genomes and its consequences for the maintenance of variation in complex traits
Graph statistics theory of individualized quantitative genetics under haplotype-resolved genome assembly
Archaeogenetic insights into the demographic history of Late Neanderthals
A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals
Convergent evolution increases boron transport through SNPs and tandem duplications at BOR1 and BOR2 in Arabidopsis thaliana
Insights into cephalochordate genome and gene evolution from the early-diverging amphioxus Asymmetron lucayanum
Orthogonal disentanglement of single-cell multi-omics reveals private and shared drivers of tissue development and pathogenesis
A transcription regulator atlas identifies TOX3 as an Atoh1 coactivator in cerebellar development and tumorigenesis
Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes
Bridging developmental and statistical approaches to variation and evolution
The population structure in the Baltic herring reflects natural selection and local adaptation
Elucidating the design principles for engineering plant organ size
The DELAYED ABAXIAL TRICHOMES Helitron has dual functions in vegetative and pollen development in Arabidopsis thaliana
Dissecting spatial patterning and signaling with directional diffusion in spatial multi-omics
Scalable and accurate rare-variant association tests for whole genome sequencing time-to-event analysis in large biobanks
Extracellular stiffness regulates cell fate determination and drives the emergence of evolutionary novelty in the teleost heart
Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire
Stripe rust fungus subverts wheat phase separation–mediated immunity to promote infection
No evidence that haplodiploidy favors the evolution of eusociality
Mining lysine post-translational modification sites by integrating protein language model representations with structural context
Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap
Identifying genome-by-childhood trauma interactions for depression using a forest-based approach in the UK Biobank and Adolescent Brain Cognitive Development Study
Mutations and structural variants arising during double-strand break repair
Controlling for life-history traits in vertebrates reveals that effective population size does not affect mutation rate or genome size
A factor integrating transcription and repression of surface antigen genes in African trypanosomes
Pleistocene demographic histories dominate contemporary genomic diversity in a continental radiation of Himalayan–Hengduan songbirds
Fe metal–organic framework–derived heterojunction for metabolic diagnosis of thymic epithelial tumor
Functional motifs in food webs and networks
Subcellular mass spectrometry reveals proteome remodeling in an asymmetrically dividing (frog) embryonic stem cell
A data-driven chromatin model reveals spatial and dynamic features of genome organization
Incomplete lineage sorting shaped mixed traits during a colobine primate radiation
Earliest perissodactyls reveal large-scale dispersals during the PETM
Mutation rate variability in viral populations: Implications for lethal mutagenesis
Biological causes and impacts of rugged tree landscapes in phylodynamic inference
Early life-stage thermal resilience is determined by climate-linked regulatory variation
Sudan’s complex genetic admixture history drives adaptation to malaria in Sudanese Copts
Sex-allocation trade-offs and their genetic architecture revealed by experimental evolution
Deep evolutionary conservation of a sex-determining locus without sequence homology
Predicting the unseen: A diffusion-based debiasing framework for transcriptional response prediction at single-cell resolution
DNA methylation shapes transcription factor binding beyond canonical CpG contexts
Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium
Computationally efficient whole-genome quantile regression at biobank scale
MultistageOT: Multistage optimal transport infers trajectories from a snapshot of single-cell data
HLA-DQB1*03:01 strongly affects age of onset of type 1 narcolepsy independently of DQA1 and ethnicity
Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states
RAD51AP1 is a versatile RAD51 modulator
Genome of venomous caterpillar Doratifera vulnerans reveals recruitment of immune peptides and their adaptation as pain-inducing toxins
Single-molecule views of chromatin accessibility and structure during photomorphogenesis
Unmeasured prior viability selection resolves the paradox of stasis for body size in wild Soay sheep
Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series
A general framework for branch length estimation in Ancestral Recombination Graphs
Lipidomic profiling of endometrial cancer using desorption electrospray ionization mass spectrometry imaging
Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping
A chromatin-linked CPL2–PHD2/3 module sustains multiple DNA methylation pathways and Polycomb silencing
Physical models reveal indirect reader protein interactions that facilitate epigenetic crosstalk
The Kinship Formula: Inferring the numbers of all kin from any structured population projection model
A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies
Machine-learning models based on histological images from healthy donors identify imageQTLs and predict chronological age
Proximity to explosive synchronization determines network collapse and recovery trajectories in neural and economic crises
Transcriptional condensates encode a “golden mean” to optimize enhancer–promoter communication across genomic distances
Single-cell metabolome and RNA-seq multiplexing on single plant cells
Roles of transposable elements and DNA methylation in the formation of CpG islands and CpG-depleted regulatory elements
Disrupted developmental signaling induces novel transcriptional states
Joint disruption of Ret and Ednrb transcription shifts cell fate trajectories in the enteric nervous system in Hirschsprung disease
Virulence hierarchies within the Mycobacterium tuberculosis complex
Mot1 regulation of promoter binding by TBP varies with stress and gene expression levels independently of coactivator dependence
Dynamic sensor selection for biomarker discovery
Exceedingly low genetic diversity in snow leopards due to persistently small population size
Targeting the 3D genome by anthracyclines for chemotherapeutic effects
Genetic, phenotypic, and environmental drivers of local adaptation and climate change–induced maladaptation in a migratory songbird
When neighbors play a role: A systems-level analysis of protein interactions conditioning cancer driver mutation effects
Distinguishing direct interactions from global epistasis using rank statistics
A reanalysis of population dynamics in the Casas Grandes region of Northern Mexico using mitochondrial DNA
Structural basis for Rad54- and Hed1-mediated regulation of Rad51 during the transition from mitotic to meiotic recombination
Procollagen IIA mediates positive feedback control of the mouse cardiogenic transcriptional network
Patient stratification reveals the molecular basis of disease co-occurrences
De novo rates of a Trypanosoma-resistant mutation in two human populations
Factors underlying a latitudinal gradient in the S/G lignin monomer ratio in natural poplar variants
Fragmentation signatures in cancer patients resemble those of patients with vascular or autoimmune diseases
Efficiently quantifying dependence in massive scientific datasets using InterDependence Scores
Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades
Metabolomics navigates natural variation in pathogen-induced secondary metabolism across soybean cultivar populations
Inbreeding reduces fitness in spatially structured populations of a threatened rattlesnake
CRISPR–Cas9 screening reveals microproteins regulating adipocyte proliferation and lipid metabolism
NIPBL and STAG1 enable loop extrusion by providing differential DNA–cohesin affinity
Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis arenosa
How RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination without transposition
The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels
Genomic origins and evolution of neo-sex chromosomes in Pacific Island birds
A trans-species cytoplasmic polymorphism is associated with seed shape and aridity across multiple species of sunflowers
Bivalent interaction through an intrinsically disordered linker promotes transcription activation complex assembly in Notch signaling
Deletion of p63 exon 13 in mice reveals C-terminal isoform–specific functions in epithelial development
Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming
Diploidization in a wild rice allopolyploid is both episodic and gradual
Comparative performance of viral landscape phylogeography approaches
The importance of small-island populations for the long-term survival of endangered large-bodied insular mammals
Spatial metabolomics informs the use of clinical imaging for improved detection of cribriform prostate cancer
Participation bias in the estimation of heritability and genetic correlation
Reactivation of an embryonic cardiac neural crest transcriptional profile during zebrafish heart regeneration
Improving polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features
Generative prediction of causal gene sets responsible for complex traits
Evolution of gene order in prokaryotes is driven primarily by gene gain and loss
Bias-aware training and evaluation of link prediction algorithms in network biology
Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal
Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model
<atl>Jund orchestrates icis/i -regulatory element dynamics to facilitate endothelial-to-hematopoietic transition</atl>
Population sequencing for phylogenetic diversity and transmission analyses
Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts
24
A marine stem-myriapod from the Silurian Waukesha Lagerstätte, Wisconsin, USA: terrestrial traits pre-date the transition to land
Extinct Dalian horse as a genetic bridge between Late Pleistocene North American and Eurasian equids
Microfossil spiral teeth reveal mesopelagic Cyclothone (bristlemouths) fish evolved during the early Palaeogene greenhouse
Analysis of multi-trait evolution across independently evolved cavefish populations reveals shared and independent evolution of suites of traits
Testing the scale dependence of plant community assembly processes using imaging spectroscopy
Genomic diversity and selection in the racing greyhound of Great Britain
Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups
A unifying theoretical framework for tick-borne disease risk to explain conflicting results of exclosure experiments across scales
Hermaphrodites have lower metabolic rates than gonochores.
Late Ordovician calcified peyssonnelialean red algae: systematics and evolutionary significance
Diversification dynamics of the Palaeozoic actinopterygian radiation
Collagen fingerprinting and sequence analysis provides a molecular phylogeny of extinct Australian megafauna
Genome divergence between European anchovy ecotypes fuelled by structural variants originating from trans-equatorial admixture
Melting memories: decoupled effects of ice and climate during the Quaternary shaped genetic diversity in Andean Calceolaria species
Was descent in Neolithic and Bronze Age Europe patrilineal or bilateral?
Developmental lines of least resistance predict standing genetic covariation but do not constrain plasticity or rapid evolution.
Virtual endocast of the Late Miocene Hoplitomeryx matthei (Artiodactyla, Hoplitomerycidae) and brain evolution in insular ruminants.
Variation in temperature but not diet determines the stability of latitudinal clines in tolerance traits and their plasticity.
A subantarctic reigitheriid and the evolution of crushing teeth in these enigmatic Mesozoic mammals.
Variation in self-compatibility among genotypes and across ontogeny in a self-fertilizing vertebrate, Kryptolebias marmoratus.
Novel stressors and trait variation determine X-linked meiotic drive frequency.
Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss.
Historical constraints and heterospecific interference lead to maladaptive sex ratio changes in a pollinating fig wasp.
The metabolic costs of meiotic drive.
38
TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution
Rumen ciliates modulate methane emissions in ruminants
Mapping transcription factor functions in astrocytes using in vivo gain-of-function Perturb-seq
Mechanical load inhibits cancer growth in mouse and human hearts
Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load
A deep-time landscape of plant cis-regulatory sequence evolution
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Multiscale pangenome graphs empower the genomic dissection of mixed-ploidy sugarcane species
Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries
Gapless pangenome analyses reveal fast Brassica rapa subspeciation
The evolution of gene regulation in mammalian cerebellum development
Chinese Immune Multi-Omics Atlas
A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform
Chromatin buffers torsional stress during transcription
Multispecies pangenomes reveal a pervasive influence of population size on structural variation
Multiscale structure of chromatin condensates explains phase separation and material properties
High-fidelity human chromosome transfer and elimination
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Earliest oceanic tetrapod ecosystem reveals rapid complexification of Triassic marine communities
Cryo–electron microscopy visualization of RAD51 filament assembly and end-capping by XRCC3-RAD51C-RAD51D-XRCC2
The functional landscape of coding variation in the familial hypercholesterolemia gene LDLR
FIGNL1 inhibits homologous recombination in BRCA2 deficient cells by dissociating RAD51 filaments
A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness
A human pan-disease blood atlas of the circulating proteome
ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes
Dual transposon sequencing profiles the genetic interaction landscape in bacteria
Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness
Adaptations to water stress and pastoralism in the Turkana of northwest Kenya
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genomic demography predicts community dynamics in a temperate montane forest
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
<atl>Genomic diversity of the African malaria vector iAnopheles funestus/i</atl>
E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection
Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics
Stereo-cell: Spatial enhanced-resolution single-cell sequencing with high-density DNA nanoball-patterned arrays
Origins and diversity of Greenland’s Qimmit revealed with genomes of ancient and modern sled dogs
Chromosome-specific centromeric patterns define the centeny map of the human genome
73
CEMs-SELEX: DNAzyme-powered de novo biomarker discovery and noninvasive cancer diagnosis
Discovery of White Sea assemblage fossils from Laurentia
High-fidelity molecular decoding through tile-guided in situ self-assembly
Evolution of a central dopamine circuit underlies adaptation of a light-evoked sensorimotor response in the blind cavefish
The immunoproteome and multimorbidity: A Mendelian randomization study
Premature transcription termination modulates stochastic gene expression in bacteria
Aneuploidy confers environmentally robust higher evolvability than euploidy in a synthetic allotetraploid wheat
PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards
Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasma
Cross-species prediction reveals chromatin regions with increased accessibility in humans
Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation
Historical and contemporary genomes of an endangered rodent reveal shifts in environmentally associated genes
Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells
Complex peopling history and expansion events inferred from large-scale modern and ancient Y chromosome sequences
Stage-specific epigenetic priming amplifies gene activation during lineage commitment
Protein overabundance is driven by growth robustness
Accelerated discovery of cell migration regulators using label-free deep learning–based automated tracking
Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer
Structural basis of outer membrane biogenesis and cell division by Tol/Pal nanomachinery
Direct observation of Notch signaling–induced transcription hubs mediating gene-expression responses
Cis-regulatory evolution reveals sensory trade-offs as a genetic basis for temporal niche evolution in tapirs
Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila
DNA framework–based molecular transformer for logic-driven precision diagnostics
Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters
Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction
Multiple southward migrations of Neolithic Chinese farmers into Southeast Asia revealed from large-scale Y-chromosome sequences
Silencer variants are key drivers of gene up-regulation in Alzheimer’s disease
Genetic legacy and recent cross of two ancient lineages underlie the rebound of the world’s rarest primate
Cross-trait genomic modeling reveals the polygenic architecture and systemic impact of MASLD
Introgressed mitochondrial fragments from archaic hominins alter nuclear genome function in modern humans
An ancient genome duplication event drives the development and evolution of spinnerets in spiders
Ancient Yellow River ancestry and divergent admixture histories in the Qiang people
Basis for lineage-determining pioneer factors targeting distinct repressed chromatin states
Mass extinction triggered the early radiations of jawed vertebrates and their jawless relatives (gnathostomes)
Genome-wide association study reveals genetic architecture and evolution of human retinal pigmentation
Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer’s disease
Humpback whale genomes reflect the increased efficiency of commercial whaling
Evaluating the effects of archaic protein-altering variants in living human adults
CTCF-RNA interactions orchestrate cell-specific chromatin loop organization
TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction
FeaSion decodes the regulatory landscape and functional diversity of RNA polymerase II CTD phosphorylation
Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture
The bottleneck for maternal transmission of mtDNA is linked to purifying selection by autophagy
Fifteen millennia of human mitogenome evolution in Sicily
Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease
Structural and epistatic regulatory variants cause hallmark white spotting in cattle
Dynamic human admixture histories over the past ~1300 years at the northern Himalayan frontier
Pt-seq unveils the genomic binding pattern of platinum-based drugs
Circulating tumor cells as predictive biomarkers in the risk stratification of DCIS: Evidence of early dissemination
Short tandem repeats in populations of the Qinghai-Tibet Plateau and adjacent regions provide insights into high-altitude adaptation
Uncovering the regulatory landscape of early human B cell lymphopoiesis and its implications in the pathogenesis of B-ALL
Soma-derived 30-nt small RNAs are coupled with chromosome breakage and precisely target nontransposon DNA against elimination in Euplotes vannus
Pervasive sex-dependent effects in the genetic architecture of starvation resistance in Drosophila melanogaster
Plasticity of ventricle position after heart looping in heterotaxy with right isomerism
Lubiprostone in chronic kidney disease: Insights into mitochondrial function and polyamines from a randomized phase 2 clinical trial
Pathogenic variants in MAEA disrupt DNA replication fork stability and are associated with developmental abnormalities in humans
Architectural transcription factors collectively shape nuclear radial positioning of chromatin contacts
Exploring antibiotic resistance in diverse homologs of the dihydrofolate reductase protein family through broad mutational scanning
Integration of spatial protein imaging and transcriptomics in the human kidney tracks the regenerative potential of proximal tubules
Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq
A century of anthropogenic perturbations impact genomic signatures of the iconic migratory Atlantic cod
Indirect genetic effects among neighbors promote cooperation and accelerate adaptation in a small-scale human society
Static three-dimensional structures determine fast dynamics between distal loci pairs in interphase chromosomes
The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells
Learning the sequence code of protein expression in human immune cells
Image-based inference of tumor cell trajectories enables large-scale cancer progression analysis
A narrow range of transcript-error rates across the Tree of Life
Loss of the PPE71-esxX-esxY-PPE38 locus drives adaptive transcriptional responses and hypervirulence of Mycobacterium tuberculosis lineage 2
Genomic evidence for fisheries-induced evolution in Eastern Baltic cod
Feedback transcription regulation between OsNAC3 and OsDREB1A promotes postgermination growth in rice
A lipid atlas of the human kidney
Discovery of unconventional and nonintuitive self-assembling peptide materials using experiment-driven machine learning
Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population
1
DeepHeme, a high-performance, generalizable deep ensemble for bone marrow morphometry and hematologic diagnosis
13
RNA helicase DHX29 controls the translation of transcription factors involved in germinal center response and plasma cell differentiation in mice
RYBP regulates selective genomic binding of TrxG and PcG components in embryonic stem cell fate control
Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae
Mechanistic insights into coordinated var transcriptional switching in malaria parasites
A functional overlap between actively transcribed genes and chromatin insulator elements
Direct visualization and tracing of chromatin folding in the Drosophila embryo
Unique territorial and compartmental organization of chromosomes in the holocentric silkworm
Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes
Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling
Donor transcription suppresses D-loops in cis and promotes genome stability
Master transcription-factor binding sites constitute the core of early replication control elements.
Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation.
Early coordination of cell migration and cardiac fate determination during mammalian gastrulation
3
Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific
Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters
Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri
3
Characterization of genetic loci associated with allergic conjunctivitis
Machine learning-assisted diagnosis classification of primary immune dysregulation using IDDA2.1 phenotype profiling
Lifestyle-associated metabolite signatures and the risk of late-onset asthma
3
Decoding d- and l-Amino Acids: Data-Driven Recognition of Enantiomers and Post-Translational Modifications via Quantum Tunneling
Characterizing RNA Tetramer Conformational Landscape Using Explainable Machine Learning
Phase Model-Driven Deep Learning for Robust Phase Correction in High-Throughput NMR-Based Metabolomics
19
Functional insights into dispensable genes using genome-wide loss-of-function burden tests in Arabidopsis
ZmbZIP39 coordinates source-flow-sink relations to boost grain filling in maize
Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin
Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy
Structure-guided discovery of protein functions in plants
<atl>Gain and loss of gene function shaped the nickel hyperaccumulation trait in iNoccaea caerulescens/i</atl>
RING1 and BMI1 catalytic activities play distinct roles in plant PcG-mediated gene regulation
Editing of rice PSEUDO-ETIOLATION IN LIGHT microProtein genes promotes chloroplast development
<atl>Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga iAuxenochlorella/i</atl>
<atl>A comprehensive omics resource and genetic tools for genetic research and precision breeding of iCucumis melo/i ssp. iagrestis/i</atl>
InDel variation and contraction of the C-repeat binding factor family contribute to cold sensitivity in Betula fujianensis
Decoding tissue-specific enhancers in plants using massively parallel assays and deep learning
A variome–transcriptome–metabolome network links GABA biosynthesis to stress resilience in maize
PlantConnectome: A knowledge graph database encompassing amp;gt;71,000 plant articles
Reactivation of the tRNASer/tRNATyr gene cluster in Arabidopsis thaliana root tips
KIL transcription factors facilitate embryo growth in maize by promoting endosperm elimination via lytic cell death
Phosphoglycerate dehydrogenase is required for kernel development and defines a predominant serine synthesis pathway in maize
Maize ibig embryo 6/i reveals roles of plastidial and cytosolic prephenate aminotransferases in seed and plant development
The mitochondrial carrier CsTHS1 acts as a gatekeeper of theanine accumulation in late-spring new shoots of tea plants
1
Large-scale analysis of SARS-CoV-2 genomic data from sewage using eVarEPS reveals that amino acid mutations detected in sewage provide an early warning on population prevalence

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