Genomics Proteomics & Bioinformatics

Article	Citations
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	250
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	210
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	157
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	131
Benefits of Better Cardiovascular Health for Calcific Aortic Valve Stenosis Stratified by Polygenic Risk Score	124
OBIA: An Open Biomedical Imaging Archive	95
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	81
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	80
RNase P: Beyond Precursor tRNA Processing	75
Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes	72
Benchmarking Generative AI Protein Models Reveals Differences Between Structural and Sequence-based Approaches	72
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	63
Identify Non-mutational p53 Functional Deficiency in Human Cancers	61
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	58
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	54
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	50
A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development	49
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	49
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	48
DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes	41
Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome	40
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	39
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	39
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data	38
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens	37

Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	33
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	32
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	31
Computational Methods for Single-Cell DNA Methylome Analysis	30
Computational Approaches and Challenges in Spatial Transcriptomics	28
Application of Microbiome in Forensics	27
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	27
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	27
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	26
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	26
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	25
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	24
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	24
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	23
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	23
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	23
Why Did Treg and Immune Tolerance Win Nobel Prize This Year?	23
SimplifyEnrichment : A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	22
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	22
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	22
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	22
Generalizable Single-cell Multimodal Data Integration with Self-supervised Learning	21
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	21
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	21
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	20
Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants	20
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	20
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	20
Artificial Intelligence in Omics	19
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	18
K6 Atypical Ubiquitin Chain Regulates Intracellular Serine Homeostasis Through Tor1-Npr1-Par32-Gnp1 Signaling Axis	18
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	18
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	17
Granulin+ Macrophages Promote Lineage Plasticity in Prostate Cancer Through Paracrine Signaling Loops	17
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	17
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	17
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	17
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	17
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
Benchmark and Evaluation for Somatic Structural Variants Detection with Long-read Sequencing Data	16
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	16
Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	15
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	15
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	15
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	15
RNA Modifications and Epitranscriptomics	14
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	14
Macrophages in Hematopoiesis and Related Blood Diseases	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	14

LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	14
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	13
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
Mass Spectrometry-based Solutions for Single-cell Proteomics	13
iRUNNER: A Baseline Mutation Burden Regression for Identifying Gene Interaction Between Rare Variants for Diseases	13
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	13
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
Deep Transfer Learning Links Benign Glands to Prostate Cancer Progression via Transcriptomics	12
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	12
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	12
Nphos: Database and Predictor of Protein N -phosphorylation	12
FAST: Scalable Factor Analysis for Spatial Dimension Reduction of Multi-section Spatial Transcriptomics	12
Spatial Single-cell Transcriptome Atlas of Mouse Thymus Reveals the T Lymphocyte Dynamics During Development	11
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	11
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	11
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	11
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	11
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	11
RNA Methylome Reveals the m 6 A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	11
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	11
Association of Multiple-trait Polygenic Risk Score with Obesity and Cardiometabolic Diseases in Korean Population	10
Macrophage Response to Avirulent and Virulent Mycobacterium tuberculosis and Anti-TB Effects of Exosome Treatment	10
HemaCisDB: An Interactive Database for Analyzing Cis -regulatory Elements Across Hematopoietic Malignancies	10
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	10
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	10
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	10
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	10
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	10
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	10
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	10
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	10
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	10
Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-cell Acute Lymphoblastic Leukemia	10
Harnessing Large Cohorts and AI to Bridge Genomic Discovery and Clinical Practice	10
OBC: Optimized Batch Correction with Dual-level Quality Control for Scalable Proteomics and Metabolomics	10
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	9
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	9
The Indicine X-linked CYBB L237M Mutation Can Suppress Intracellular Infection with Tubercle Bacilli	9
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	9
Implication of the Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	9
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	9
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	9
GenBase: A Nucleotide Sequence Database	9
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	9
Layering Methylome and Transcriptome in the Same Tissue Slice	9
DisConST: Distribution-aware Contrastive Learning for Spatial Domain Identification	8
Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP	8
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	8
SRPS: Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery	8
Single-cell Spatial Multiomics: Technologies, Methods, and Biological Applications	8
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	8
Noise2read: Accurately Rectify Millions of Erroneous Short Reads Through Graph Learning on Edit Distances	8
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	8
From BIG Data Center to China National Center for Bioinformation	7
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	7
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	7
Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator	7
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	7
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	7
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	7
Biological Data Resources and Machine Learning Frameworks for Hematology Research	7
On the Completeness of Existing RNA Fragment Structures	7
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	7
Distinct Co-methylation Patterns in African and European Populations and Their Genetic Associations	7
Genome-wide Association Studies of over 30,000 Samples with Bone Mineral Density at Multiple Skeletal Sites and Its Clinical Relevance	7
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	7
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	7
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	7
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	7
NSUN2-Mediated mRNA m 5 C Modification Regulates the Progression of Hepatocellular Carcinoma	6
Laws of Genome Nucleotide Composition	6
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	6
Machine Learning for AI Breeding in Plants	6
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes	6
ProtRAP-LM: Efficient Protein Relative Accessibility Prediction and Proteome-wide Membrane Protein Screening	6
Regulation of Alternative Polyadenylation Events by PABPC1 Affects Erythroid Progenitor Cell Expansion	6
Acknowledgments to Reviewers 2022	6
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	6

Single-cell RNA Sequencing Discovered Subtypes Associated with Angiogenesis and Propranolol Treatment in Infantile Hemangioma	6
Toward a New Paradigm of Genomics Research—Celebration of the 20th Anniversary of Beijing Institute of Genomics	6
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins	6
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	6
Multiomics Analysis Reveals How Intratumoral Bacteria Shape the Immune Microenvironment in Gastric Cancer	5
YanHuang Paternal Genomic Resource Suggested A Weakly-Differentiated Multi-Source Admixture Model for the Formation of Han’s Founding Ancestral Lineages	5
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	5
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	5
Urinary Proteomics: Biological Foundations, Analytical Frameworks, and Clinical Translation Across Human Diseases	5
PROBind: A Web Server for Prediction, Analysis, and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues	5
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	5
Two Isatis Genomes Reveal the Biosynthesis and Evolutionary Origin of Indigo in Plants	5
The Gap-free Petunia Genome Assemblies Reveal the Evolutionary Dynamics of the S -locus Supergene	5
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	5
Unraveling Cell of Origin in Breast Cancer via Joint Profiling of Whole Genome and Transcriptome in Individual Cells	5
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	5
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	4
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss	4
cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers	4
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data	4
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing	4
Bioinformatics Portal for Predicting Binding Regions and Modes in Protein–Nucleic Acid Interactions	4
Database Commons: A Catalog of Worldwide Biological Databases	4
BSAlign: A Library for Nucleotide Sequence Alignment	4
Morphine Re-Arranges Chromatin Spatial Architecture of Primate Cortical Neurons	4
METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC	4
Unraveling the Phylogenetic Signal of Gene Expression from Single-cell RNA-seq Data	4
A Single-cell and Spatially Resolved Cell Atlas of Human Esophageal Squamous Cell Carcinoma	4
Long-read Sequencing Reveals Repeat Expansions and Large Structural Variants in Oral Squamous Cell Carcinoma	4
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	4
An Integrative Polygenic and Epigenetic Risk Score for Overweight-related Hypertension in Chinese Population	4
Long and Accurate: How HiFi Sequencing is Transforming Genomics	4
The Bioinformatic Applications of Hi-C and Linked Reads	4
Histo-LCM-Hi-C Reveals 3D Chromatin Conformations of Spatially Localized Rare Cells in Tissues at High Resolution	4
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	3
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	3
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	3
The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research	3
Machine Learning Modeling of Protein-Intrinsic Features Predicts Tractability of Targeted Protein Degradation	3
High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras	3
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	3
Deep WGS-based STROMICS reference panel enhances genotype imputation in Chinese population	3
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	3
Evaluating AlphaFold Tools and Related Scoring Functions for Protein–peptide Complex Prediction	3
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	3
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	3
PhaSeDis: A Manually Curated Database of Phase Separation–disease Associations and Corresponding Small Molecules	3
Unveiling Neonatal Pneumonia Microbiome by High-throughput Sequencing and Droplet Culturomics	3
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics	3
MPCutter: Predicting Protease-specific Substrate Cleavage Sites Using a Protein Language Model	3
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	3
Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives	3
A Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	3