Genomics Proteomics & Bioinformatics

Article	Citations
Acknowledgments to Reviewers 2021	463
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	338
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	206
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	168
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	104
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	98
RNase P: Beyond Precursor tRNA Processing	97
Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes	80
Benefits of Better Cardiovascular Health for Calcific Aortic Valve Stenosis Stratified by Polygenic Risk Score	70
OBIA: An Open Biomedical Imaging Archive	66
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	62
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	61
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	60
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	56
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	54
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	53
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	52
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	52
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	45
Identify Non-mutational p53 Functional Deficiency in Human Cancers	43
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	41
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	39
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	38
Computational Methods for Single-Cell DNA Methylome Analysis	37
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	36

DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes	35
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	35
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens	34
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data	33
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	33
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	31
Application of Microbiome in Forensics	31
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	30
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	30
Computational Approaches and Challenges in Spatial Transcriptomics	30
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	29
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	29
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	28
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	27
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	26
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	25
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	25
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	24
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	23
SimplifyEnrichment : A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	22
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	21
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	21
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	20
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	19
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	19
Artificial Intelligence in Omics	19
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	19
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	19
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	19
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	18
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	18
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	18
The Regulation of Gonadal Somatic Cell Differentiation in Humans	18
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	18
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	16
Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	16
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	16
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	16
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	16
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	16
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	16
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	16
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	16
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	15
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	15
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	14
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	14
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	14

Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	14
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	14
Mass Spectrometry-based Solutions for Single-cell Proteomics	13
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
RNA Modifications and Epitranscriptomics	13
Nphos: Database and Predictor of Protein N -phosphorylation	13
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	12
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	12
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	12
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	12
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	12
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	12
Macrophages in Hematopoiesis and Related Blood Diseases	12
RNA Methylome Reveals the m 6 A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	12
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	11
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	11
Association of Multiple-trait Polygenic Risk Score with Obesity and Cardiometabolic Diseases in Korean Population	11
Deep Transfer Learning Links Benign Glands to Prostate Cancer Progression via Transcriptomics	11
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	10
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	10
Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-cell Acute Lymphoblastic Leukemia	10
HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies	10
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	10
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	10
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	10
Macrophage Response to Avirulent and Virulent Mycobacterium tuberculosis and Anti-TB Effects of Exosome Treatment	10
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	10
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	9
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	9
Harnessing Large Cohorts and AI to Bridge Genomic Discovery and Clinical Practice	9
DisConST: Distribution-aware Contrastive Learning for Spatial Domain Identification	9
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	9
SRPS: Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery	9
Implication of the Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	9
From BIG Data Center to China National Center for Bioinformation	8
GenBase: A Nucleotide Sequence Database	8
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	8
Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP	8
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	8
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	8
Genome-wide Association Studies of over 30,000 Samples with Bone Mineral Density at Multiple Skeletal Sites and Its Clinical Relevance	8
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	8
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	8
Biological Data Resources and Machine Learning Frameworks for Hematology Research	8
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	8
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	8
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	8
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	8
Noise2read: Accurately Rectify Millions of Erroneous Short Reads Through Graph Learning on Edit Distances	8
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri -Containing Lineage in Primate Guts	8
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	8
Distinct Co-methylation Patterns in African and European Populations and Their Genetic Associations	7
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	7
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	7
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	7
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	7
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	7
Machine Learning for AI Breeding in Plants	7
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	7
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins	7
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	7
Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator	7
Acknowledgments to Reviewers 2022	7
Laws of Genome Nucleotide Composition	7
Two Isatis Genomes Reveal the Biosynthesis and Evolutionary Origin of Indigo in Plants	6
NSUN2-Mediated mRNA m 5 C Modification Regulates the Progression of Hepatocellular Carcinoma	6
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes	6
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	6
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	6
Toward a New Paradigm of Genomics Research—Celebration of the 20th Anniversary of Beijing Institute of Genomics	6
Regulation of Alternative Polyadenylation Events by PABPC1 Affects Erythroid Progenitor Cell Expansion	6
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	6
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	5
YanHuang Paternal Genomic Resource Suggested A Weakly-Differentiated Multi-Source Admixture Model for the Formation of Han’s Founding Ancestral Lineages	5
BSAlign: A Library for Nucleotide Sequence Alignment	5

METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC	5
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	5
Profiling the Bisecting N-Acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry	5
An Integrative Polygenic and Epigenetic Risk Score for Overweight-related Hypertension in Chinese Population	5
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	5
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss	5
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	5
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	5
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events	5
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	5
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	5
A Single-cell and Spatially Resolved Cell Atlas of Human Esophageal Squamous Cell Carcinoma	4
Temporarily withdrawn	4
Long and Accurate: How HiFi Sequencing is Transforming Genomics	4
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	4
The Bioinformatic Applications of Hi-C and Linked Reads	4
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	4
High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras	4
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	4
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing	4
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	4
Morphine Re-Arranges Chromatin Spatial Architecture of Primate Cortical Neurons	4
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics	4
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data	4
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	4
cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers	4
Database Commons: A Catalog of Worldwide Biological Databases	4
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	4
Histo-LCM-Hi-C Reveals 3D Chromatin Conformations of Spatially Localized Rare Cells in Tissues at High Resolution	4
Unveiling Neonatal Pneumonia Microbiome by High-Throughput Sequencing and Droplet Culturomics	4
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	4