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Nuclear genetic modulation of tissue-specific mitochondrial RNA processing contributes to common disease risk
|
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Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression
|
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Admixture-informed polygenic risk reporting using the ePRS framework
|
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Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
|
|
Spatial-aware detection of copy number alterations from spatial transcriptomics using SpaCNA
|
|
Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients
|
|
Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation
|
|
Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials
|
|
Proteome-wide prediction of the functional impact of missense variants with ProteoCast
|
|
Dynamic partitioning of a critical elongation factor between LEC and SEC regulates cellular snRNA and proliferation-related mRNA transcription
|
|
HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states
|
|
Early and late RNA eQTL are driven by different genetic mechanisms
|
|
szKendall: spatial-structural-zero-aware dissimilarity measures for subtype discovery using single cell Hi-C data
|
|
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
|
|
TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls
|
|
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
|
|
Horizontal gene transfer and diploidy illuminate evolution and stress adaptation in oleaginous Scenedesmaceae (Chlorophyta)
|
|
CellNiche represents cellular microenvironments in atlas-scale spatial omics data with contrastive learning
|
|
Longitudinal protein profiling of blood during childhood into early adulthood
|
|
Leveraging cell-type specificity and similarity improves single-cell eQTL fine-mapping
|
|
Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution
|
|
Multivariate genetic analysis reveals three distinct pathological dimensions in musculoskeletal disorders
|
|
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
|
|
UK BioCoin: swift trait-specific summary statistics regression for UK Biobank
|
|
Conserved and divergent gene regulatory networks for crop drought resistance
|
|
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
|
|
Histone diversity in the archaeal domain of life
|
|
Meta-encoder: a unified integration framework for multiple pathological foundation models in cancer detection
|
|
Comparison and optimization of cellular neighbor preference methods for quantitative tissue analysis
|
|
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
|
|
An information content principle explains regulatory patterns of gene expression across human tissues
|
|
Characterizing gene perturbations in single cells via network divergence analysis
|
|
RESCUE: recovery of unattributed expression patterns in spatial transcriptomics
|
|
Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication
|
|
Assembling unmapped reads reveals hidden variation in South Asian genomes
|
|
Break-induced replication is enhanced by a phospho-activated RPA-binding module in Pol32
|
|
The adaptive molecular landscape of reprogrammed telomeric sequences
|
|
Combining multiplexed assays of variant effect for enhanced BRCA2 variant classification
|
|
Genetic genealogy of the Piast dynasty and related European royal families
|
|
Improved tumor-only variant calling and mutation burden estimation with VarNet-T
|
|
RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions
|
|
Scaling up Bayesian population phylogenomics through virtual dimension reduction
|
|
African-specific genetic loci determine iron status and risk of severe malaria and bacteremia in African children
|
|
CellLoop: Identifying single-cell 3D genome chromatin loops
|
|
Genetic architecture of lumbar spinal stenosis
|
|
Experimental assessment of AI-based interactome mapping
|
|
Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function
|
|
Collective behavior and memory states in flow networks with tunable bistability
|
|
Whole-proteome phage immunoprecipitation sequencing reveals germ cell tumor–specific immunosignature
|
|
MIC-Drop-seq: scalable single-cell phenotyping of mutant vertebrate embryos
|
|
An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation
|
|
The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos
|
|
The global phylogeography of rapidly expanding multidrug resistant Ural lineage 4.2 Mycobacterium tuberculosis
|
|
Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling
|
|
Cell neighborhood topology directs rare cell population identification
|
|
Determinants of chromosome-specific telomere lengths among 2573 All of Us participants
|
|
TONSOKU prevents the formation of large tandem duplications and restrains ATR–WEE1 checkpoint activation
|
|
TONSL suppresses polymerase theta-dependent tandem duplications through chromatin-guided repair
|
|
Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish
|
|
An integrated germline and somatic genomic model for coronary artery disease
|
|
A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators
|
|
Leveraging weighted embedding and Transformer architecture to improve phenotype prediction of complex traits for crops
|
|
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
|
|
A single cluster of RNA Polymerase II molecules is stably associated with active genes
|
|
Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues
|
|
Transcriptional competence defines the heterochromatin nucleating potential of isolated MSR units
|
|
Network model for alignment, stitching and slice-to-volume 3D reconstruction of large-scale spatially resolved slices
|
|
Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling
|
|
Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics
|
|
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
|
|
A blueprint for local and distal invasion programs in glioblastoma
|
|
Mapping the heritability of disease: a nationwide study
|
|
FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis
|
|
Condensin accelerates long-range intra-chromosomal interactions
|
|
Illuminating cell states by a comprehensive and interpretable single cell foundation model
|
|
Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome
|
|
Extensive enhancer crosstalk controls activation during adipogenesis
|
|
An international multi-centre study to develop and validate federated learning-based prognostic models for anal cancer
|
|
EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles
|
|
Optimizing global genomic surveillance for early detection of emerging SARS-CoV-2 variants
|
|
DIS3 mutations enhance AID-driven translocations during B-cell activation, promoting transformation to multiple myeloma
|
|
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
|
|
scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies
|
|
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
|
|
Exon inclusion signatures enable accurate estimation of splicing factor activity
|
|
A paired sequence language model for protein-protein interaction modeling
|
|
Regionalized regulation of actomyosin organization influences cardiomyocyte cell shape changes during chamber curvature formation
|
|
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci
|
|
Long-read sequencing of families reveals increased germline and postzygotic mutation rates in repetitive DNA
|
|
Mechanisms of gene regulation by SRCAP and H2A.Z
|
|
Molecular basis for the inhibition of de novo DNA methylation by TCL1A
|
|
Linker histones consolidate heterogenous nucleosome fiber contacts by linking together multiple nucleosomes
|
|
DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning
|
|
An H3K14ub-H3K9me3 feedback circuit governs heterochromatin spreading and inheritance in fission yeast
|
|
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
|
|
The dynamic distribution of genetic tandem amplifications in a heteroresistant Escherichia coli population revealed by ultra-deep long read sequencing
|
|
Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis
|
|
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
|
|
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer
|
|
High-throughput chemical proteomics workflow for profiling protein citrullination dynamics
|
|
Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX
|
|
Spatial perturb-seq: single-cell functional genomics within intact tissue architecture
|
|
SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling
|
|
Genetic modifiers of -ε4-associated cognitive decline
|
|
Nonlinear genomic selection index accelerates multi-trait crop improvement
|
|
Enhancing microbial metabolic capacity through high-energy electron beam-induced intense structural variations
|
|
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
|
|
Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation
|
|
Combining xQTL and genome-wide association studies from diverse populations improves druggable gene discovery
|
|
eQTL in diseased colon tissue identifies potential target genes associated with IBD
|
|
PanMETAI - a high performance tabular foundation model for accurate pancreatic cancer diagnosis via NMR metabolomics
|
|
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
|
|
A catalogue of early diverged contemporary human genome variation reveals distinct Khoe-San populations
|
|
KidneyGenAfrica multi-cohort Genome-wide association study and polygenic prediction of kidney function in 110,000 Africans
|
|
XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry
|
|
A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis
|
|
MYC modulates TOP2A diffusion to promote substrate detection and activity
|
|
Partitioned polygenic scores show mechanistic heterogeneity in type 2 diabetes and hypertension comorbidity
|
|
High-throughput multi-organ proteomics workflow for drug efficacy and toxicity analysis
|
|
Electrostatic properties of disordered regions control transcription factor search and pioneer activity
|
|
Analysis of the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins using snFLARE-seq and mxFRIZNGRND
|
|
Convergent extreme reductive evolution in ancient planthopper symbioses
|
|
Radical footprinting in mammalian whole blood
|
|
Adgrg6/Gpr126 is required for compact wall integrity and establishing trabecular identity during cardiac trabeculation
|
|
Cross ionization mode chemical similarity prediction between tandem mass spectra in metabolomics
|
|
Genomics of rafting crustaceans reveals adaptation to climate change in tropical oceans
|
|
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
|
|
FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models
|
|
scLong: a billion-parameter foundation model for capturing long-range gene context in single-cell transcriptomics
|
|
Genomic consequences of residual recombination in a hybrid apomictic hickory complex
|
|
Protein-protein interactions are a major source of epistasis in genetic interaction networks
|
|
Integrative functional genomics analysis identifies pleiotropic genes for vascular diseases
|
|
An experimentally-informed polymer model reveals high resolution organization of genomic loci
|
|
Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics
|
|
Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data
|
|
An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines
|
|
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)
|
|
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
|
|
Supercharging-enhanced nDIA-MS enables global profiling of drug-induced proteome solubility shifts
|
|
Crowdsourced biodiversity monitoring fills gaps in global plant trait mapping
|
|
Dual promoter–enhancer activities reflect a unified regulatory logic
|
|
A comprehensive tandem repeat catalog of the human genome
|
|
A versatile platform for sequential glyco-, phospho-, and proteomics with multi-PTMs integration
|
|
An adaptive, continuous-learning framework for clinical decision-making from proteome-wide biofluid data
|
|
Three open questions in polygenic score portability
|
|
A proteogenomic atlas of 1032 brain metastases identifies molecular subtypes, immune landscapes, and therapeutic vulnerabilities
|
|
Comprehensive benchmarking single and multi ancestry polygenic score methods with the PGS-hub platform
|
|
BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters
|
|
Essential role of NONO-HOXA1-Wnt axis in cardiomyocyte differentiation
|
|
Automated mapping of DNA replication fork progression in human cells with ForkML
|
|
The role of low-complexity repeats in RNA–RNA interactions and a deep learning framework for duplex prediction
|
|
NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes
|
|
Epigenome-wide analysis identifies DNA methylation mediators of treatment-related cardiometabolic risk in survivors of childhood cancer
|
|
Improving polygenic score prediction for underrepresented groups through transfer learning
|
|
Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling
|
|
Cross-ancestry comparison of aptamer and antibody protein measures
|
|
Neural crest cell-derived DKK1 and NEDD4 modulate Wnt signalling in the second heart field to orchestrate outflow tract development
|
|
ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning
|
|
Preventing premature deaths through polygenic risk scores
|
|
PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells
|
|
Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics
|
|
A dual context-aware basecaller for nanopore direct RNA sequencing
|
|
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
|
|
The ratio of circulatory levels of sphingolipids to steroids predicts asthma exacerbations
|
|
TidyMass2: advancing LC-MS untargeted metabolomics through metabolite origin inference and metabolic feature-based functional module analysis
|
|
Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN
|
|
Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data
|
|
Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion
|
|
Genetic insights and mechanistic parallels in gestational diabetes mellitus and type 2 diabetes
|
|
Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility
|
|
Genetic and non-genetic factors distinctly shape the variation of the immune response in cattle
|
|
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
|
|
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
|
|
Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing
|
|
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA
|
|
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
|
|
Global solidarity in genomic surveillance improves early detection of acute respiratory virus threats
|
|
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
|
|
Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation
|
|
Functional implications of polygenic risk for schizophrenia in human neurons
|
|
Rad51 determines pathway usage in post-replication repair
|
|
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
|
|
Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations
|
|
Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications
|
|
Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies
|
|
DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
|
|
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
|
|
The Health for Life in Singapore (HELIOS) Study: delivering precision medicine research for Asian populations
|
|
CellScope: high-performance cell atlas workflow with tree-structured representation
|
|
Plasma protein profiling predicts cancer in patients with non-specific symptoms
|
|
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
|
|
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
|
|
Prostate cancer cells converge to an inflammatory-like state upon metastatic dissemination
|
|
Large-scale drug sensitivity, gene dependency, and proteogenomic analyses of telomere maintenance mechanisms in cancer cells
|
|
Mapping rare protein-coding variants on multi-organ imaging traits
|
|
Cross-platform clinical proteomics using the Charité open standard for plasma proteomics (OSPP)
|
|
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
|
|
Mapping cis- and trans-regulatory target genes of human-specific deletions
|
|
Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass
|
|
Recombination junctions from antibody isotype switching classify immune and DNA repair dysfunction
|
|
Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA
|
|
Analysis genome of Pseudotaxus chienii reveals insights into the origin and evolution of taxane biosynthesis
|
|
Circulating causal protein networks linked to future risk of myocardial infarction
|
|
Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework
|
|
Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis
|
|
Chromosome-level assembly and analysis of three hydroxy fatty acid-producing Physaria species
|
|
Accurate imputation of pathway-specific gene expression in spatial transcriptomics with PASTA
|
|
Widespread naturally variable human exons aid genetic interpretation
|
|
omprehensive discovery of m6A sites in the human transcriptome at single-molecule resolution
|
|
Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement
|
|
Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma
|
|
Genome-wide screen reveals dependence of break induced replication on several distinct checkpoints
|
|
scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase
|
|
A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry
|
|
Single-array measurements reveal non-uniform, mosaic-like chemosensory arrays in bacteria
|
|
Complex genetic effects linked to plasma protein abundance in the UK Biobank
|
|
Identification of a deep-branching lineage of algae using environmental plastid genomes
|
|
Cost-effective non-additive GWAS across 2329 diseases in 500,349 individuals
|
|
Flexible read-aware genotype imputation from sequence using biobank sized reference panels
|
|
Structural basis of double-stranded RNA recognition by the J2 monoclonal antibody
|
|
FastCCC: a permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies
|
|
Evaluating transportability of in vitro cellular models to in vivo human phenotypes using gene perturbation data
|
|
Genetic profiling of the circulating proteome in common diseases suggests causal proteins and improves risk prediction
|
|
Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions
|
|
A multimodal knowledge-enhanced whole-slide pathology foundation model
|
|
Co-condensation between transcription factor and cBAF selectively modulates chromatin remodeling and gene expression
|
|
Co-expression-wide association studies link genetically regulated interactions with complex traits
|
|
scDrugMap: benchmarking large foundation models for drug response prediction
|
|
CellMentor: cell-type aware dimensionality reduction for single-cell RNA-sequencing data
|
|
Generalizable morphological profiling of cells by interpretable unsupervised learning
|
|
Cohesin forms fountains at active enhancers in C. elegans
|
|
Biologically-informed integration of drug representations for breast cancer treatment using deep learning
|
|
CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoire
|
|
Airqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping
|
|
Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor
|
|
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
|
|
The bHLH transcription factor PIL1 orchestrates starch synthesis in key cereal crops
|
|
RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing
|
|
Transformer-based deep learning enhances discovery in migraine GWAS
|
|
Patient-derived colon epithelial organoids reveal lipid-related metabolic dysfunction in pediatric ulcerative colitis
|
|
Repurposing clinically safe drugs for DNA repair pathway choice in CRISPR genome editing and synthetic lethality
|
|
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
|
|
Benchmarking pre-trained genomic language models for RNA sequence-related predictive applications
|
|
Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits
|
|
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
|
|
MetaboLM: a metabolomic language model for multi-disease early prediction and risk stratification
|
|
Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual
|
|
Near complete assembly of Drosophila melanogaster Canton S strain genome
|
|
Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation
|
|
RAD51 D-loop structures reveal the mechanism of eukaryotic RAD51-mediated strand exchange
|
|
Deciphering gene redundancy in prokaryotic genomes provides evolutionary insights for pathogenicity and its roles in clinical infections
|
|
Acquisition of ampliconic sequences marks a selfish mouse -haplotype
|
|
Benchmarking DNA foundation models for genomic and genetic tasks
|
|
Impact of common variants on brain gene expression from RNA to protein to schizophrenia risk
|
|
Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance
|
|
Insights into natural neocentromere evolution from a cattle T2T X chromosome
|
|
Expanding the utility of variant effect predictions with phenotype-specific models
|
|
Multimodal single cell analyses reveal gene networks of planarian stem cell differentiation
|
|
Compressed sensing expands the multiplexity of imaging mass cytometry
|
|
Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology
|
|
Human plasma proteomic profile of clonal hematopoiesis
|
|
A deep learning-based multiscale integration of spatial omics with tumor morphology
|
|
Recessive variants in the intergenic locus cause monogenic kidney disease responsive to anti-proteinuric treatment
|
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Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays
|
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Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes
|
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AI-augmented intraoperative decision-making workflows in diffuse midline glioma biopsy using cryosection pathology
|
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scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization
|
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Integrating axis quantitative trait loci looks beyond cell types and offers insights into brain-related traits
|
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Transcription start sites experience a high influx of heritable variants fueled by early development
|
|
Genetics and context for precision health in Greater Boston
|
|
Integrated spatial proteomic analysis of breast cancer heterogeneity unravels cancer cell phenotypic plasticity
|
|
3D spatial organization of heterogeneous + progenitors in the zebrafish heart field pre-patterns cardiovascular development
|
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Explainable AI unravels sepsis heterogeneity via coagulation-inflammation profiles for prognosis and stratification
|
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Motif-based models accurately predict cell type-specific distal regulatory elements
|
|
Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum
|
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Deriving consensus sepsis clusters via goal-directed subgroup identification in multi-omics study
|
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Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers
|
|
Multi-ancestry investigation of the genomics of erectile dysfunction
|
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Targeted sequencing and iterative assembly of near-complete genomes
|
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Long-read sequencing of primate testis and human sperm allows identification of recombination events in individuals
|
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Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals key associations with AD pathology
|
|
Addressing the specific roles of histone modifications in transcriptional repression
|
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Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation
|
|
Domestication shaped the chromatin landscape of grain amaranth
|
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Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus
|
|
Genome architecture evolution in an invasive copepod species complex
|
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Cross-dataset pan-cancer detection by correlating cell-free DNA fragment coverage with open chromatin sites across cell types
|
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Benchmarking informatics workflows for data-independent acquisition single-cell proteomics
|
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Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase
|
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Multi-centric origins and gene flow shape the diversity of β-thalassemia mutations in Southern East Asia
|
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Cell line-matched reference enables high-precision functional genomics
|
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Inferring differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data with MultiVeloVAE
|
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Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues
|
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G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data
|
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Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry
|
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Deriving three one dimensional NMR spectra from a single experiment through machine learning
|
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Omnireg-gpt: a high-efficiency foundation model for comprehensive genomic sequence understanding
|
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C > U mutations generate immunogenic peptides in SARS-CoV-2
|
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Differential conformational expansion of NUP98-HOXA9 oncoprotein from nanosized assemblies to macrophases
|
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DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks
|
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A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes
|
|
ERNIE-RNA: an RNA language model with structure-enhanced representations
|
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Conservation and variability of long-range interactions in structurally diverse maize genomes
|
|
CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis
|
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Approaching single-molecule assembly-free readout from medium-length encoded DNA
|
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Bacterial chromosome conformation and cell-free gene expression in synthetic 2D compartments
|
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Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean
|
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scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples
|
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Developmentally regulated genes drive phylogenomic splits in ovule evolution
|
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Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae
|
|
Genetic underpinnings and causal effects of brain structure and function on chronic pain intensity
|
|
Augmenting microbial phylogenomic signal with tailored marker gene sets
|
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Variation in surface protein expression leads to heterogeneous Trypanosoma cruzi populations during host cell infection
|
|
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen
|
|
ELLA: modeling subcellular spatial variation of gene expression within cells in high-resolution spatial transcriptomics
|
|
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks
|
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Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral
|
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Widespread reveals hidden diversity and reshapes understanding of human whipworm infections
|
|
Click-linking: a cell-compatible protein crosslinking method based on click chemistry
|
|
Gain of Alternative Allele Expression of at rs149707223 in Schizophrenia and Bipolar Disorder: Inducing Synaptic Transmission and Behavioral Deficits in Mice
|
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Protein-level batch-effect correction enhances robustness in MS-based proteomics
|
|
Genomic and epigenomic maps of mouse centromeres and pericentromeres
|
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AI-powered spatial cell phenomics enhances risk stratification in non-small cell lung cancer
|
|
Powerful one-dimensional scan to detect heterotic quantitative trait loci
|
|
Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction
|
|
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells
|
|
Gene expression signatures from whole blood predict amyotrophic lateral sclerosis case status and survival
|
|
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing
|
|
Condensation-dependent interactome of a chromatin remodeler underlies tumor suppressor activities
|
|
Data navigation on the ENCODE portal
|
|
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
|
|
UNICORN: Towards universal cellular expression prediction with a multi-task learning framework
|
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PLM-interact: extending protein language models to predict protein-protein interactions
|
|
Mechanism of trinucleotide repeat expansion by MutSβ-MutLγ and contraction by FAN1
|
|
Deciphering splicing heterogeneity at single-cell resolution by SCSES
|
|
MultiGATE: integrative analysis and regulatory inference in spatial multi-omics data via graph representation learning
|
|
Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP
|
|
Computational design and evaluation of optimal bait sets for scalable proximity proteomics
|
|
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
|
|
Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions
|
|
Genetic determinants and genomic consequences of non-leukemogenic somatic point mutations
|
|
Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing
|
|
scTFBridge: a disentangled deep generative model informed by TF-motif binding for gene regulation inference in single-cell multi-omics
|
|
A comprehensive benchmark of single-cell Hi-C embedding tools
|
|
Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
|
|
Analysis of cfDNA fragmentomics metrics and commercial targeted sequencing panels
|
|
Dissecting regulatory non-coding GWAS loci reveals fibroblast causal genes with pathophysiological relevance to heart failure
|
|
The effect of type 2 diabetes genetic predisposition on non-cardiovascular comorbidities
|
|
HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs
|
|
IceQream: Quantitative chromosome accessibility analysis using physical TF models
|
|
Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus
|
|
Characterization of prevalent genetic variants in the Estonian Biobank body-mass index GWAS
|
|
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
|
|
Benchmarking scRNA-seq copy number variation callers
|
|
Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set
|
|
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
|
|
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
|
|
TP63 mediates the generation of tumour-specific chromatin loops that underlie MYC activation in radiation-induced tumorigenesis
|
|
Contribution of leukocyte telomere length to cardiovascular disease onset from genome-wide cross-trait analysis
|
|
The pericardium forms as a distinct structure during heart formation
|
|
TP53 variant clusters stratify phenotypic diversity in germline carriers and reveal an osteosarcoma-prone subgroup
|
|
Genetic determinants of monocyte splicing are enriched for disease susceptibility loci
|
|
mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis
|
|
A basic framework to explain splice-site choice in eukaryotes
|
|
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
|
|
RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets
|
|
: a web-based application for in-depth exploration of multi-omics data with brightfield histology
|
|
TEtrimmer: a tool to automate the manual curation of transposable elements
|
|
Super-silencers are crucial for development and carcinogenesis in B cells
|
|
Graph neural networks learn emergent tissue properties from spatial molecular profiles
|
|
Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes
|
|
Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis
|
|
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
|
|
Coordinated active repression operates via transcription factor cooperativity and multiple inactive promoter states in a developing organism
|
|
A quadratic paradigm describes the relationship between phenotype severity and variation
|
|
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
|
|
Reprogramming the tumor microenvironment with c-MYC-based gene circuit platform to enhance specific cancer immunotherapy
|
|
Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases
|
|
Interaction of genetic variants activates latent metabolic pathways in yeast
|
|
DECIPHER for learning disentangled cellular embeddings in large-scale heterogeneous spatial omics data
|
|
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
|
|
SpaIM: single-cell spatial transcriptomics imputation via style transfer
|
|
Modeling integration site data for safety assessment with MELISSA
|
|
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
|
|
: AI generation of multiplex immunofluorescence staining from histopathology images
|
|
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice
|
|
Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs
|
|
Multimodal spatial transcriptomic characterization of mouse kidney injury and repair
|
|
Biobank-scale genetic characterization of Alzheimer’s disease and related dementias across diverse ancestries
|
|
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
|
|
Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family
|
|
Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis
|
|
Epigenetic control of topoisomerase 1 activity presents a cancer vulnerability
|
|
DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins
|
|
European and African ancestry-specific plasma protein-QTL and metabolite-QTL analyses identify ancestry-specific T2D effector proteins and metabolites
|
|
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
|
|
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
|
|
Thor: a platform for cell-level investigation of spatial transcriptomics and histology
|
|
Substrate accessibility regulation of human TopIIa decatenation by cohesin
|
|
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
|
|
Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling
|
|
Replisomes restrict SMC translocation in vivo
|
|
High performance data integration for large-scale analyses of incomplete profiles using Batch-Effect Reduction Trees (BERT)
|
|
Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states
|
|
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
|
|
vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics
|
|
A framework for complex signal processing via synthetic biological operational amplifiers
|
|
Single-nuclei multiomics analysis identifies abnormal cardiomyocytes in a murine model of cardiac development
|
|
Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia
|
|
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
|
|
Predicting the direction of phenotypic difference
|
|
Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains
|
|
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
|
|
PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model
|
|
Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning
|
|
Machine-learning driven strategies for adapting immunotherapy in metastatic NSCLC
|
|
A draft UAE-based Arab pangenome reference
|
|
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
|
|
Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
|
|
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing
|
|
Natural variation of an E3 ubiquitin ligase encoding gene regulates grain chalkiness in rice
|
|
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
|
|
Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases
|
|
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
|
|
Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos
|
|
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
|
|
Personalized risk stratification in colorectal cancer via PIANOS system
|
|
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
|
|
Nucleosome spacing can fine-tune higher-order chromatin assembly
|
|
Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells
|
|
Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion
|
|
Resolving out of Africa event for Papua New Guinean population using neural network
|
|
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
|
|
High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics
|
|
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
|
|
Cell Marker Accordion: interpretable single-cell and spatial omics annotation in health and disease
|
|
Nuclear morphometrics coupled with machine learning identifies dynamic states of senescence across age
|
|
Automated cell annotation and classification on histopathology for spatial biomarker discovery
|
|
DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads
|
|
Precision-edited histone tails disrupt polycistronic gene expression controls in trypanosomes
|
|
Phylogenetically informed predictions outperform predictive equations in real and simulated data
|
|
Serum metabolic profiling enables diagnosis, prognosis, and monitoring for brainstem gliomas
|
|
MR-link-2: pleiotropy robust Mendelian randomization validated in three independent reference datasets of causality
|
|
Uncovering causal gene-tissue pairs and variants through a multivariate TWAS controlling for infinitesimal effects
|
|
Prioritizing perturbation-responsive gene patterns using interpretable deep learning
|
|
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
|
|
Pan-cancer copy number analysis identifies optimized size thresholds and co-occurrence models for individualized risk stratification
|
|
Scaling laws of bacterial and archaeal plasmids
|
|
Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
|
|
Charting γ-secretase substrates by explainable AI
|
|
High-resolution detection of copy number alterations in single cells with HiScanner
|
|
A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins
|
|
Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy
|
|
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
|
|
Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily ()
|
|
Cold-induced nucleosome dynamics linked to silencing of Arabidopsis
|
|
Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell
|
|
An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data
|
|
Analysis of the geneome identifies RcCYP72H7 as an epoxidase in iridoid glycoside biosynthesis
|
|
Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data
|
|
Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values
|
|
A large C-terminal Rad52 segment acts as a chaperone to Form and Stabilize Rad51 Filaments
|
|
DrFARM: identification of pleiotropic genetic variants in genome-wide association studies
|
|
-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity
|
|
Transcripts with high distal heritability mediate genetic effects on complex metabolic traits
|
|
Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods
|
|
Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution
|
|
GAUDI: interpretable multi-omics integration with UMAP embeddings and density-based clustering
|
|
Whole-genome sequencing of 1,060 isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids
|
|
MassCube improves accuracy for metabolomics data processing from raw files to phenotype classifiers
|
|
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy
|
|
LassoPred: a tool to predict the 3D structure of lasso peptides
|
|
cTAGE5 is essential for adipogenesis and adipose tissue development
|
|
Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer
|
|
Bridging cell morphological behaviors and molecular dynamics in multi-modal spatial omics with MorphLink
|
|
Mapping the regulatory genetic landscape of complex traits using a chicken advanced intercross line
|
|
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer
|
|
Deep generalizable prediction of RNA secondary structure via base pair motif energy
|
|
Trioxane-based MS-cleavable cross-linking mass spectrometry for profiling multimeric interactions of cellular networks
|
|
BIGFAM - variance components analysis from relatives without genotype
|
|
Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome
|
|
GPerturb: Gaussian process modelling of single-cell perturbation data
|
|
RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks
|
|
Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures
|
|
MORC2 is a phosphorylation-dependent DNA compaction machine
|
|
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
|
|
Switch-like gene expression modulates disease risk
|
|
Divergence in a eukaryotic transcription factor’s co-TF dependence involves multiple intrinsically disordered regions
|
|
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
|
|
Single-molecule direct RNA sequencing reveals the shaping of epitranscriptome across multiple species
|
|
Divergent combinations of enhancers encode spatial gene expression
|
|
Performance of deep-learning-based approaches to improve polygenic scores
|
|
Sequential structure probing of cotranscriptional RNA folding intermediates
|
|
A naturally occurring SNP modulates thermotolerance divergence among grapevines
|
|
Charting unknown metabolic reactions by mass spectrometry-resolved stable-isotope tracing metabolomics
|
|
A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy
|
|
Multi-tissue expression and splicing data prioritise anatomical subsite- and sex-specific colorectal cancer susceptibility genes
|
|
Single-cell and spatial transcriptome analyses reveal tumor heterogeneity and immune remodeling involved in pituitary neuroendocrine tumor progression
|
|
Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications
|
|
High resolution clonal architecture of hypomutated Wilms tumours
|
|
scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links
|
|
Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L.
|
|
Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures
|
|
Pleiotropic and sex-specific genetic mechanisms of circulating metabolic markers
|
|
Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa
|
|
BIT: Bayesian Identification of Transcriptional regulators from epigenomics-based query region sets
|
|
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis
|
|
Depletion-dependent activity-based protein profiling using SWATH/DIA-MS detects serine hydrolase lipid remodeling in lung adenocarcinoma progression
|
|
A machine learning and centrifugal microfluidics platform for bedside prediction of sepsis
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Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells
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A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections
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Whole-genome sequencing analyses suggest novel genetic factors associated with Alzheimer’s disease and a cumulative effects model for risk liability
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Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification
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The ALX4 dimer structure provides insight into how disease alleles impact function
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Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity
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Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis
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Insights from the Biorepository and Integrative Genomics pediatric resource
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Imputing single-cell protein abundance in multiplex tissue imaging
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Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors
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Reveal genomic insights into cotton domestication and improvement using gene level functional haplotype-based GWAS
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SKSR1 identified as key virulence factor in Cryptosporidium by genetic crossing
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Stochastic gene expression in auxin signaling in the floral meristem of Arabidopsis thaliana
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STP: single-cell partition for subcellular spatially-resolved transcriptomics
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Genetic surveillance of Plasmodium falciparum populations following treatment policy revisions in the Greater Mekong Subregion
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A probabilistic graphical model for estimating selection coefficients of nonsynonymous variants from human population sequence data
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Epigenome-wide DNA methylation association study of CHIP provides insight into perturbed gene regulation
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CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells
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Chromosome fusions shaped karyotype evolution and evolutionary relationships in the model family Brassicaceae
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A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics
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Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis
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CREATE: cell-type-specific cis-regulatory element identification via discrete embedding
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Nucleosome dynamics render heterochromatin accessible in living human cells
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LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics
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Tracing human genetic histories and natural selection with precise local ancestry inference
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Holocene shifts in marine mammal distributions around Northern Greenland revealed by sedimentary ancient DNA
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High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion
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Combining cross-sectional and longitudinal genomic approaches to identify determinants of cognitive and physical decline
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The impact of ancestral, genetic, and environmental influences on germline de novo mutation rates and spectra
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DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy
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FABP4 inhibition suppresses bone resorption and protects against postmenopausal osteoporosis in ovariectomized mice
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Sex differences in the genetic regulation of the human plasma proteome
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Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity
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Spatial mapping of the brain metabolome lipidome and glycome
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Twin pair analysis uncovers links between DNA methylation, mitochondrial DNA quantity and obesity
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RNA transcripts serve as a template for double-strand break repair in human cells
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Massively parallel jumping assay decodes Alu retrotransposition activity
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Chromatin state origins of uterine leiomyoma
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scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data
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Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction
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Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli
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Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold
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Genomic, transcriptomic, and immunogenomic landscape of over 1300 sarcomas of diverse histology subtypes
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Limiting the impact of protein leakage in single-cell proteomics
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Generative and predictive neural networks for the design of functional RNA molecules
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Labelizer: systematic selection of protein residues for covalent fluorophore labeling
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Genetic ancestry and population structure in the All of Us Research Program cohort
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Identification of leukemia-enriched signature through the development of a comprehensive pediatric single-cell atlas
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Restoring flowcell type and basecaller configuration from FASTQ files of nanopore sequencing data
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De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level
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