Genomics Proteomics & Bioinformatics

Article	Citations
Acknowledgments to Reviewers 2021	391
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	290
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	180
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	138
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	134
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	92
OBIA: An Open Biomedical Imaging Archive	90
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	88
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	85
RNase P: Beyond Precursor tRNA Processing	83
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	68
Identify Non-mutational p53 Functional Deficiency in Human Cancers	59
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	59
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	58
Whole Genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	57
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	57
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	55
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	53
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	49
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	49
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	47
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	45
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	44
Computational Methods for Single-Cell DNA Methylome Analysis	42
Computational Approaches and Challenges in Spatial Transcriptomics	42

Application of Microbiome in Forensics	36
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	34
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	33
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nuclei RNA Sequencing Data	33
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	33
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	32
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	31
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	30
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	30
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	29
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	29
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	29
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	28
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	26
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	26
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	25
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	25
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	24
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	23
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	23
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	23
Artificial Intelligence in Omics	23
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	22
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	21
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	19
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	19
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	17
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	17
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	17
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
The Regulation of Gonadal Somatic Cell Differentiation in Humans	17
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	16
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	16
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	16
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	15
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	15
Identifying Leukemia-related Genes based on Time-series Dynamical Network by Integrating Differential Genes	15
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	15
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	15
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	15
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	15
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	15
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	14
RNA Modifications and Epitranscriptomics	14
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	14
Mass Spectrometry-based Solutions for Single-cell Proteomics	13
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	13

Nphos: Database and Predictor of Protein N-phosphorylation	13
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	12
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	12
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	12
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	12
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	12
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	12
Integrative Multi-Omics Landscape of Non-Structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	12
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	12
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	11
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	11
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	11
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	11
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	11
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	11
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	10
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	10
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	10
Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-lineage Acute Lymphoblastic Leukemia	10
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	10
HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies	10
Macrophage Response to Avirulent and Virulent Mycobacterium tuberculosis and Anti-TB Effects of Exosome Treatment	10
SRPS: Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery	9
The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	9
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	9
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
GenBase: A Nucleotide Sequence Database	9
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	9
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	9
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	9
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	8
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	8
Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator	8
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	8
From BIG Data Center to China National Center for Bioinformation	8
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	8
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	8
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	8
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	8
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	8
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	8
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	7
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	7
Acknowledgments to Reviewers 2022	7
Machine Learning for AI Breeding in Plants	7
Biological Data Resources and Machine Learning Frameworks for Hematology Research	7
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	7
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	7
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	7
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	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
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes	7
Laws of Genome Nucleotide Composition	6
Profiling the Bisecting N-Acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry	6
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	6
NSUN2-Mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma	6
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	6
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events	6
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	6
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins	6
Toward a New Paradigm of Genomics Research—Celebration of the 20th Anniversary of Beijing Institute of Genomics	6
An Integrative Polygenic and Epigenetic Risk Score for Overweight-related Hypertension in Chinese Population	6
METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC	5
Database Commons: A Catalog of Worldwide Biological Databases	5
Long and Accurate: How HiFi Sequencing is Transforming Genomics	5
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	5
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	5
ASER: Animal Sex Reversal Database	5
Defining Proximity Proteome of Histone Modifications by Antibody-Mediated Protein A-APEX2 Labeling	5
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	5
BSAlign: A Library for Nucleotide Sequence Alignment	5
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	5
YanHuang Paternal Genomic Resource Suggested A Weakly-Differentiated Multi-Source Admixture Model for the Formation of Han’s Founding Ancestral Lineages	5

Morphine Re-Arranges Chromatin Spatial Architecture of Primate Cortical Neurons	5
High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads	5
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data	5
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	5
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	5
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	5
The Bioinformatic Applications of Hi-C and Linked Reads	4
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	4
PhaSeDis: A Manually Curated Database of Phase Separation–disease Associations and Corresponding Small Molecules	4
A Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	4
High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras	4
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	4
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing	4
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	4
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	4
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	4
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	4
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	4
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	4
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics	4
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women	4