Bioinformatics and Computational Biology articles for Chinese Academy of Sciences (CAS), China

Time frame: 1 June 2025 - 30 May 2026

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Count: 180

Article ‘Count’ for Bioinformatics and Computational Biology.

Journal Count Share
2 0.53
Surfactant-Modified Magnetic Nanoparticles Enable Efficient and Cost-Effective Plasma Proteomics for Enhanced Biomarker Discovery 0.07
Lung Cancer Cell–Macrophage Interaction System for Signal Pathway-Based Logic Analysis and Drug Testing 0.47
1 0.04
Genetic control of non-coding RNAs in the human brain and their implications for complex traits 0.04
29 11.23
ProteoIntegrator: A Scalable and Integrated Platform for Robust Multi-Source Proteomics Data Harmonization, Differential and Functional Analysis 0.06
A Miniaturized, Automated Proteomic Sample Preparation Platform for High-Throughput Target Deconvolution of Natural Products 0.40
Simple, Fast, and Highly Efficient One- or Two-Step Proteomic Preparation Enables Deep Profiling of Microgram-Level FF and FFPE Tissues 0.01
Development of a Fluorescence Polarization Assay for p300/CBP and Its Application Using a Direct-to-Biology Approach 0.64
A Chemically Derivatized in Silico Mass Spectral Library for Fine-Structure Annotation of Phosphoinositides 0.63
Mapping Cell Metabolic States by Image-Enabled Gating Metabolomic Cytometry 0.17
SILICO-MS: Exploring Structural Lipidomic Alterations Using an Ionization-Coupled Ozonolysis Mass Spectrometry Strategy 0.14
Automated High-Throughput Proteomics Sample Preparation Platform Using DNA Extraction Plate for Industrial Microorganisms 0.83
Multiplexed Isotope-Coded Mass Spectrometry Footprinting Enables Broad Heteroatom-Residue Mapping and Uncovers Noncanonical Ligand-Binding Sites in Amyloidosis Proteins 0.17
Dual Protease-Mediated Proteolysis Coupled with Ultrafiltration for System-Level Profiling of Drug Targets and Conformational Dynamics 0.42
Extreme Ultraviolet Photodissociation Decodes the Chain Modifications of Lipids 0.35
DLQMA: A Deep Learning Framework for Qualitative and Quantitative NMR Analysis of Complex Hydrocarbon Mixtures 0.70
VirMolAnalyte: An AI-Driven In Silico Metabolite Annotation Tool 1.00
A Streamlined Sequential Enrichment Strategy for Multi-PTM Profiling from Low Micrograms of Samples 0.01
GPMassSimulator: A Graphormer-Based Method for Glycopeptide MS/MS Spectra Prediction 0.42
Multidimensional Mass Spectral Similarity Algorithm: Discriminate Disaccharide and Flavonoid Isomers Coupled with Online Energy-Resolved Acquisition and Electron Activation Dissociation 0.71
A Detergent-Free Grinding Sample Preparation Method Dramatically Enhances PELSA for Mapping Integral Membrane Proteins–Ligand Interaction 0.75
MODAPro: Explainable Heterogeneous Networks with Variational Graph Autoencoder for Mining Disease-Specific Functional Molecules and Pathways from Omics Data 0.67
Plug-and-Play Competitive Hairpin Conversion Module Enables Enzyme-Free High-Resolution Discrimination of Single Nucleotide Polymorphisms 0.50
Transposase Acting on an RNA/DNA Hybrid in Strand-Specific Sequencing 0.14
A Meta-Learning Approach for Multicenter and Small-Data Single-Cell Image Analysis 0.10
Novel Equivalent Carbon Number Strategy for Large-Scale Lipidomics Data Analysis via Ultrahigh–Performance Liquid Chromatography–Orbitrap Astral Mass Spectrometry 0.58
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 0.08
Composite Fluorescence Encoding Technology Based on Tetrahedral DNA Framework for Logical Distinction and Multiplexed Recognition 0.32
Monitoring the Chemical Transformation and Detoxification Process of Aconitum Herbs during Processing by Maximum-Quantum Filter NMR Spectroscopy 0.17
SMART: An Approach for Accurate Formula Assignment in Spatially Resolved Metabolomics 0.11
MS2MP: A Deep Learning Framework for Metabolic Pathway Prediction from MS/MS-Based Untargeted Metabolomics 0.67
PEG Precipitation Followed by Albumin Depletion for Plasma Proteomics Analysis 0.01
Enhanced Structure-guided Molecular Networking Annotation Method for Untargeted Metabolomics Data from Orbitrap Astral Mass Spectrometer 0.48
2 1.28
High-Throughput Single-Cell-Resolved Spatial Proteomics Enabled by an Ordered Colloidal Crystal Column 0.55
One‐Step Enrichment and Quantitative Analysis of In Vivo Protein Complexes via Dimethylpiperidine Cross‐Linker DPST 0.73
1 0.01
Protein-based classification reveals an immune-hot subtype in IDH mutant astrocytoma with worse prognosis 0.01
1 0.01
Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm 0.01
8 2.62
Complete biosynthesis of nicotine 0.67
CLIM-TIME identifies metastatic microenvironment modulators for T cell therapy response 0.53
Genome sequences of extant and extinct gibbons reveal their phylogeny, demographic history, and conservation status 0.48
Single-cell nascent transcription reveals sparse genome usage and plasticity 0.17
Coalescing single-cell genomes and transcriptomes to decode breast cancer progression 0.06
A de novo-originated gene drives rose scent diversification 0.08
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution 0.03
Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium 0.61
2 0.44
A generative AI framework unifies human multi-omics to model aging, metabolic health, and intervention response 0.07
Metabolic polygenic risk scores for prediction of obesity, type 2 diabetes, and related morbidities 0.38
1 0.19
Site-specific protein lipoylation analysis via aldehyde-acetal probe labelling and reversible enrichment (DA-Lipo) 0.19
1 0.13
AI-enabled new sensing technology: colorimetric analysis of exosomes for precise diagnosis of breast cancer 0.13
1 0.38
CD4+ Tregs Regulate Heart Growth and Regeneration Through MRG15/TIP60-Mediated Epigenomic Remodeling in Proliferating Cardiomyocytes 0.38
5 1.72
Dispersal and isolation of the scaly-foot snail across abyssal insular habitats and through time 0.03
A new fossil fish sheds light on the rapid evolution of early lungfishes 0.56
An early East Asian lineage with unexpectedly low Denisovan ancestry 0.14
Linear covariation between germline and somatic mutation rates across ciliates and mammals 0.63
Independent evolutionary deterioration of the oxygen-transport system in Asian noodlefishes and Antarctic icefishes 0.37
3 1.03
A Framework Integrating Single-Cell Metallomic Data in Health Effect Analysis via Quantile Features and Machine Learning 0.55
Streamlining Quantification and Data Harmonization of Polychlorinated Alkanes Using a Platform-Independent Workflow 0.25
Structural Molecular Network for Nontargeted Screening and Prioritization of New Pollutants in Urban Wastewater 0.22
2 0.84
Stable genome structures in living fossil fishes 0.75
Deep structural clustering reveals hidden systematic biases in RNA sequencing data 0.09
2 0.20
In vivo proteomic labeling reveals diverse proteomes for therapeutic targets 0.08
High-throughput capture of actively transcribed region-interacting sequences reveals an intricate promoter-centered regulatory network 0.13
8 1.15
Chromosomal fusions trigger rediploidization of autopolyploid genomes 0.01
The 1000 Chinese Pangenome empowers medical and population genetics 0.01
Largest Silurian fish illuminates the origin of osteichthyan characters 0.38
The oldest articulated bony fish from the early Silurian period 0.34
Stress controls heterochromatin inheritance via histone H3 ubiquitylation 0.07
A conserved H3K14ub-driven H3K9me3 for chromatin compartmentalization 0.22
Establishment of chromatin architecture interplays with embryo hypertranscription 0.08
Ancient DNA reveals a two-clanned matrilineal community in Neolithic China 0.05
2 0.69
Predicting small molecule–RNA interactions without RNA tertiary structures 0.05
Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3 0.64
1 0.58
Quantitative profiling of lipid transport between organelles enabled by subcellular photocatalytic labelling 0.58
1 0.48
Hybridization mitigates climate change risk in mountainous birds 0.48
62 15.68
Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE–DD ancestry 0.07
Unveiling gene modules at Atlas scale through hierarchical clustering of single-cell data 0.13
Interpretable deep learning framework for mapping E3–substrate binding interfaces 0.15
Engineering yeast chromosomal telomeres with a bacteriophage system 0.43
Inherent MS-cleavability of diazirine photo-cross-links enables residue-level structural analysis 0.41
A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA 0.03
CAPTAIN: a multimodal foundation model pretrained on co-assayed single-cell RNA and protein 0.16
Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system 0.02
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration 0.03
Horizontal gene transfer and diploidy illuminate evolution and stress adaptation in oleaginous Scenedesmaceae (Chlorophyta) 0.06
CellNiche represents cellular microenvironments in atlas-scale spatial omics data with contrastive learning 0.10
CellLoop: Identifying single-cell 3D genome chromatin loops 0.06
An integrated germline and somatic genomic model for coronary artery disease 0.10
Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues 0.50
Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex 0.52
An H3K14ub-H3K9me3 feedback circuit governs heterochromatin spreading and inheritance in fission yeast 0.38
DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning 0.27
Molecular basis for the inhibition of de novo DNA methylation by TCL1A 0.23
Branched-chain α-keto acids impair glucose-stimulated insulin secretion in pancreatic β-cells under diabetes by reactivating the LDHA-lactate axis 0.25
Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis 0.06
Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape 0.03
Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX 0.17
Enhancing microbial metabolic capacity through high-energy electron beam-induced intense structural variations 0.18
genome analyses indicate introgression may drive local adaptation and herbicide resistance 0.05
Analysis of the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins using snFLARE-seq and mxFRIZNGRND 0.13
Genomics of rafting crustaceans reveals adaptation to climate change in tropical oceans 0.29
Genomic consequences of residual recombination in a hybrid apomictic hickory complex 0.19
An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines 0.50
A versatile platform for sequential glyco-, phospho-, and proteomics with multi-PTMs integration 0.48
Comprehensive benchmarking single and multi ancestry polygenic score methods with the PGS-hub platform 0.67
Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing 0.62
Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation 0.01
Genomic dissection of the clonal background and global dissemination of hypervirulent CG23-KL57 lineage 0.06
Pulsed evolution shaped extant angiosperm pollen disparity 0.69
Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement 0.50
The genetic architecture of brainstem structures 0.02
Near complete assembly of Drosophila melanogaster Canton S strain genome 0.35
Deciphering gene redundancy in prokaryotic genomes provides evolutionary insights for pathogenicity and its roles in clinical infections 0.05
Conservation and variability of long-range interactions in structurally diverse maize genomes 0.40
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks 0.75
Deciphering splicing heterogeneity at single-cell resolution by SCSES 0.71
scTFBridge: a disentangled deep generative model informed by TF-motif binding for gene regulation inference in single-cell multi-omics 0.07
Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA 0.17
Conformational plasticity of disordered regions enables sequence-diverse DNA recognition by transcription factor AflR 0.04
The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity 0.05
Forward and reverse genomic screens enhance the understanding of phenotypic variation in a large Chinese rhesus macaque cohort 0.79
A basic framework to explain splice-site choice in eukaryotes 0.06
Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics 0.75
Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family 0.36
Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese 0.04
A framework for complex signal processing via synthetic biological operational amplifiers 0.67
Identification of multiple genomic alterations and prediction of neoantigens from circulating tumor cells at the single-cell level 0.09
PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model 0.22
Combined genome-wide association study of facial traits in Europeans increases explained variance and improves prediction 0.11
High-resolution mapping of single cells in spatial context 0.11
An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data 0.06
Deep generalizable prediction of RNA secondary structure via base pair motif energy 0.17
cTAGE5 is essential for adipogenesis and adipose tissue development 0.35
MassCube improves accuracy for metabolomics data processing from raw files to phenotype classifiers 0.17
stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs 0.04
Divergent combinations of enhancers encode spatial gene expression 0.32
A naturally occurring SNP modulates thermotolerance divergence among grapevines 0.29
9 0.50
Genome-wide associations of structural variants with human traits through imputation from long-read assemblies 0.03
Graph-based pangenome reveals structural variation dynamics during cucumber breeding 0.03
JMJD2 regulates enhancer–promoter interactions via biomolecular condensate formation 0.02
Spatially resolved multi-omics of human metabolic dysfunction-associated steatotic liver disease 0.05
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq 0.13
A multi-tissue single-cell expression atlas in cattle 0.08
A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism 0.04
Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes 0.14
Transferability of European-derived Alzheimer’s disease polygenic risk scores across multiancestry populations 0.00
1 0.00
Polygenic prediction of body mass index and obesity through the life course and across ancestries 0.00
1 0.65
Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry 0.65
2 0.16
Spatial and single-cell characterization of human glioblastoma tumor microenvironment reveals malignant cellular communities 0.07
Trans-ancestry genome-wide analyses of bipolar disorder in East Asian and European populations improve genetic discovery 0.10
1 0.02
Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription 0.02
1 0.30
SCOPE-C reveals long-range enhancer networks emerging as key regulators during human cortical neurogenesis 0.30
1 0.13
Estimating the distribution of fitness effects of loss of heterozygosity (LOH) events using an engineered library of Saccharomyces cerevisiae 0.13
3 0.90
Auxin-Induced Nicotine Inhibition Is Mediated by NaARF5 Through the Suppression of NaERF1-Like Expression and Interaction With NaERF1-Like in Nicotiana attenuata 0.75
Genome and Single-Cell Transcriptome Reveal the Evolution of Holoparasitic Plants: A Case Study of Cistanche deserticola 0.06
LGRPv2: A high-value platform for the advancement of Fabaceae genomics 0.08
7 2.78
Comprehensive mutagenesis defines the functional landscape of human α-tubulin 0.26
Pleistocene demographic histories dominate contemporary genomic diversity in a continental radiation of Himalayan–Hengduan songbirds 0.79
Incomplete lineage sorting shaped mixed traits during a colobine primate radiation 0.13
Metabolomics navigates natural variation in pathogen-induced secondary metabolism across soybean cultivar populations 0.10
The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels 0.83
Diploidization in a wild rice allopolyploid is both episodic and gradual 0.64
<atl>Jund orchestrates icis/i -regulatory element dynamics to facilitate endothelial-to-hematopoietic transition</atl> 0.04
2 0.33
Extinct Dalian horse as a genetic bridge between Late Pleistocene North American and Eurasian equids 0.13
Late Ordovician calcified peyssonnelialean red algae: systematics and evolutionary significance 0.20
3 0.85
Rumen ciliates modulate methane emissions in ruminants 0.37
Mapping transcription factor functions in astrocytes using in vivo gain-of-function Perturb-seq 0.45
Chinese Immune Multi-Omics Atlas 0.04
6 2.24
Cross-species prediction reveals chromatin regions with increased accessibility in humans 0.42
Cis-regulatory evolution reveals sensory trade-offs as a genetic basis for temporal niche evolution in tapirs 0.04
Genetic legacy and recent cross of two ancient lineages underlie the rebound of the world’s rarest primate 0.57
Introgressed mitochondrial fragments from archaic hominins alter nuclear genome function in modern humans 0.03
An ancient genome duplication event drives the development and evolution of spinnerets in spiders 0.51
Architectural transcription factors collectively shape nuclear radial positioning of chromatin contacts 0.67
1 0.03
RYBP regulates selective genomic binding of TrxG and PcG components in embryonic stem cell fate control 0.03
1 0.50
Phase Model-Driven Deep Learning for Robust Phase Correction in High-Throughput NMR-Based Metabolomics 0.50
5 0.74
ZmbZIP39 coordinates source-flow-sink relations to boost grain filling in maize 0.15
Structure-guided discovery of protein functions in plants 0.13
Reactivation of the tRNASer/tRNATyr gene cluster in Arabidopsis thaliana root tips 0.24
Phosphoglycerate dehydrogenase is required for kernel development and defines a predominant serine synthesis pathway in maize 0.12
The mitochondrial carrier CsTHS1 acts as a gatekeeper of theanine accumulation in late-spring new shoots of tea plants 0.09
1 0.30
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 0.30

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