Genomics Proteomics & Bioinformatics

Article	Citations
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	264
The MAGIC Cohort Study: Genetic Associations of Anisometropia in Chinese Population	228
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	147
Decoding RNA N 6-Methyladenosine Methylome of Wheat Using Machine Learning and Nanopore Direct RNA Sequencing	100
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	90
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	88
OBIA: An Open Biomedical Imaging Archive	84
Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes	79
Benchmarking Generative AI Protein Models Reveals Differences Between Structural and Sequence-based Approaches	69
RNase P: Beyond Precursor tRNA Processing	69
Benefits of Better Cardiovascular Health for Calcific Aortic Valve Stenosis Stratified by Polygenic Risk Score	66
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	60
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	59
Identify Non-mutational p53 Functional Deficiency in Human Cancers	55
Calling for Diversity: Improving Transfusion Safety Through High-Throughput Blood Group Microarray Genotyping	55
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	54
NanoRAPID: A Deep Learning-based Framework for Single-molecule RNA Structure Analysis Using Nanopore Direct RNA Sequencing	53
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	48
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	46
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	43
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	39
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	39
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens	38
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	34

GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	34
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	33
A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development	31
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	31
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data	29
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	29
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	28
Computational Approaches and Challenges in Spatial Transcriptomics	28
Application of Microbiome in Forensics	28
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	27
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	27
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	26
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	25
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	25
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	25
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	25
Why Did Treg and Immune Tolerance Win Nobel Prize This Year?	25
Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants	23
Generalizable Single-cell Multimodal Data Integration with Self-supervised Learning	23
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	23
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	23
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	23
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	21
K6 Atypical Ubiquitin Chain Regulates Intracellular Serine Homeostasis Through Tor1-Npr1-Par32-Gnp1 Signaling Axis	21
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	21
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	20
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	20
Artificial Intelligence in Omics	19
A Cattle BodyMap of Transcriptome across 52 Tissues and 3 Developmental Stages Reveals New Genetic Insights into Beef Production Traits	19
Granulin+ Macrophages Promote Lineage Plasticity in Prostate Cancer Through Paracrine Signaling Loops	18
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	18
mTM-align2: A Server for Real-time Protein Structure Database Search and Alignment	18
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	18
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	17
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	17
Comprehensive Benchmarking with Guidelines for Analyzing Transposable Element-derived RNA Expression	17
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	16
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	16
Bispecific Antibodies in Cancer Immunotherapy: Mechanisms, Challenges, and Emerging Therapeutic Strategies	16
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	14
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	14
Benchmark and Evaluation for Somatic Structural Variants Detection with Long-read Sequencing Data	14
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	14
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	13
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	13
iRUNNER: A Baseline Mutation Burden Regression for Identifying Gene Interaction Between Rare Variants for Diseases	13
Macrophages in Hematopoiesis and Related Blood Diseases	13
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	13

LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	13
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13
Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	13
WebCVTree4: Phylogenetic and Taxonomic Study Platform for Prokaryotes base on Whole Genomes	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	12
Nphos: Database and Predictor of Protein N -phosphorylation	12
RNA Modifications and Epitranscriptomics	12
Pangenome Graph Reveals the Structural Variation Landscape in 2929 Cattle Samples and Its Impact on Gene Regulation	11
Shared Genetic Factors Between Stress-related Disorders and Cardiovascular Disease	11
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	11
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	11
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	11
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	11
Spatial Single-cell Transcriptome Atlas of Mouse Thymus Reveals the T Lymphocyte Dynamics During Development	11
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	11
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	11
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	11
Single-cell RNA Sequencing Reveals A Tumor-Promoting Role of EGR1+CD4+ T Cells in Papillary Thyroid Cancer	11
Mass Spectrometry-based Solutions for Single-cell Proteomics	11
Deep Transfer Learning Links Benign Glands to Prostate Cancer Progression via Transcriptomics	11
FAST: Scalable Factor Analysis for Spatial Dimension Reduction of Multi-section Spatial Transcriptomics	11
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	11
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	10
RNA Methylome Reveals the m 6 A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	10
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	10
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	10
Association of Multiple-trait Polygenic Risk Score with Obesity and Cardiometabolic Diseases in Korean Population	10
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	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
HemaCisDB: An Interactive Database for Analyzing Cis -regulatory Elements Across Hematopoietic Malignancies	10
Harnessing Large Cohorts and AI to Bridge Genomic Discovery and Clinical Practice	9
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	9
MicroWorldOmics: All-in-one Desktop Solution for Microbiome Profiling, Virome Analysis, and Unexplored “Dark Matter” Discovery	9
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	9
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	9
Macrophage Response to Avirulent and Virulent Mycobacterium tuberculosis and Anti-TB Effects of Exosome Treatment	9
Layering Methylome and Transcriptome in the Same Tissue Slice	9
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	9
OBC: Optimized Batch Correction with Dual-level Quality Control for Scalable Proteomics and Metabolomics	9
Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-cell Acute Lymphoblastic Leukemia	9
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	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	8
Implication of the Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	8
DisConST: Distribution-aware Contrastive Learning for Spatial Domain Identification	8
SRPS: Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery	8
The Indicine X-linked CYBB L237M Mutation Can Suppress Intracellular Infection with Tubercle Bacilli	8
GenBase: A Nucleotide Sequence Database	8
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	8
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	8
Noise2read: Accurately Rectify Millions of Erroneous Short Reads Through Graph Learning on Edit Distances	7
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	7
From BIG Data Center to China National Center for Bioinformation	7
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	7
Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP	7
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	7
Genome-wide Association Studies of over 30,000 Samples with Bone Mineral Density at Multiple Skeletal Sites and Its Clinical Relevance	7
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	7
Single-cell Spatial Multiomics: Technologies, Methods, and Biological Applications	6
Biological Data Resources and Machine Learning Frameworks for Hematology Research	6
Machine Learning for AI Breeding in Plants	6
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins	6
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	6
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	6
Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator	6
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	6
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	6
Distinct Co-methylation Patterns in African and European Populations and Their Genetic Associations	6
ProtRAP-LM: Efficient Protein Relative Accessibility Prediction and Proteome-wide Membrane Protein Screening	6
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	6
π-HelixNovo2: Making Accurate Online De Novo Peptide Sequencing Available to All	6
On the Completeness of Existing RNA Fragment Structures	6
Single-cell Multiomic and Spatiotemporal Dissection of the Liver Circadian Clock	6
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	6
CTSC–RAB38 Potentiates Responsiveness to PD-1 Blockade in Esophageal Squamous Cell Carcinoma	6
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	6
Acknowledgments to Reviewers 2022	6

Single-cell RNA Sequencing Discovered Subtypes Associated with Angiogenesis and Propranolol Treatment in Infantile Hemangioma	5
Urinary Proteomics: Biological Foundations, Analytical Frameworks, and Clinical Translation Across Human Diseases	5
Two Isatis Genomes Reveal the Biosynthesis and Evolutionary Origin of Indigo in Plants	5
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes	5
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	5
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	5
PROBind: A Web Server for Prediction, Analysis, and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues	5
The Gap-free Petunia Genome Assemblies Reveal the Evolutionary Dynamics of the S -locus Supergene	5
Laws of Genome Nucleotide Composition	5
NSUN2-Mediated mRNA m 5 C Modification Regulates the Progression of Hepatocellular Carcinoma	5
Toward a New Paradigm of Genomics Research—Celebration of the 20th Anniversary of Beijing Institute of Genomics	5
Regulation of Alternative Polyadenylation Events by PABPC1 Affects Erythroid Progenitor Cell Expansion	5
Unraveling Cell of Origin in Breast Cancer via Joint Profiling of Whole Genome and Transcriptome in Individual Cells	5
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	5
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	4
cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers	4
Long and Accurate: How HiFi Sequencing is Transforming Genomics	4
High Mutation Rates in Non-human Primates Edited by Cytosine Base Editors	4
An Integrative Polygenic and Epigenetic Risk Score for Overweight-related Hypertension in Chinese Population	4
Multi-omics Analysis Reveals How Intratumoral Bacteria Shape the Immune Microenvironment in Gastric Cancer	4
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	4
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	4
Database Commons: A Catalog of Worldwide Biological Databases	4
scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution	4
Integrating Genomic Studies into Large Birth Cohorts	4
Morphine Re-Arranges Chromatin Spatial Architecture of Primate Cortical Neurons	4
Characterization of Cancer Hallmark Enhancer RNA Uncovers Novel Strategies for Precision Oncology	4
YanHuang Paternal Genomic Resource Suggests A Weakly-differentiated Multi-source Admixture in the Formation of Han Founding Ancestral Lineages	4
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	4
METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC	4
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss	4
Long-read Sequencing: from Complete Molecules to Context-resolved Biology	4
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	4
BSAlign: A Library for Nucleotide Sequence Alignment	4
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	4
A Single-cell and Spatially Resolved Cell Atlas of Human Esophageal Squamous Cell Carcinoma	3
Bioinformatics Portal for Predicting Binding Regions and Modes in Protein–Nucleic Acid Interactions	3
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing	3
Histo-LCM-Hi-C Reveals 3D Chromatin Conformations of Spatially Localized Rare Cells in Tissues at High Resolution	3
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	3
Unveiling Neonatal Pneumonia Microbiome by High-throughput Sequencing and Droplet Culturomics	3
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	3
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	3
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	3
Long-read Sequencing Reveals Repeat Expansions and Large Structural Variants in Oral Squamous Cell Carcinoma	3
The Bioinformatic Applications of Hi-C and Linked Reads	3
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	3
SAA1 Promotes Pro-inflammatory Macrophage-mediated Bone Invasion in Silent Corticotroph Adenomas	3
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics	3
A Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	3
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	3
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	3
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data	3
Unraveling the Phylogenetic Signal of Gene Expression from Single-cell RNA-seq Data	3
MPCutter: Predicting Protease-specific Substrate Cleavage Sites Using a Protein Language Model	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
High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras	3
PhaSeDis: A Manually Curated Database of Phase Separation–disease Associations and Corresponding Small Molecules	3