Genomics Proteomics & Bioinformatics

Article	Citations
Acknowledgments to Reviewers 2021	1125
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	725
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	380
PSIA: A Comprehensive Knowledgebase of Plant Self-Incompatibility	275
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	175
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	133
OBIA: An Open Biomedical Imaging Archive	128
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	90
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	90
RNase P: Beyond Precursor tRNA Processing	84
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	83
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	83
Whole Genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	64
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	60
Identify Non-mutational p53 Functional Deficiency in Human Cancers	59
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	56
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	56
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	55
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	54
Application of Microbiome in Forensics	53
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	53
Computational Methods for Single-Cell DNA Methylome Analysis	47
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	44
Computational Approaches and Challenges in Spatial Transcriptomics	44
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	42

SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	39
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	37
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	36
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	34
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	33
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	33
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	32
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	31
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	31
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	31
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	30
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	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	28
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	28
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	26
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	25
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	25
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	24
Artificial Intelligence in Omics	23
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	23
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	23
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	23
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	22
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	21
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	21
The Regulation of Gonadal Somatic Cell Differentiation in Humans	21
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	19
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	19
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	16
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	15
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	15
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	15
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	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: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	15
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	15
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	15
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	14
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	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
Mass Spectrometry-based Solutions for Single-cell Proteomics	13
Nphos: Database and Predictor of Protein N-phosphorylation	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	13
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

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
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	12
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	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
RNA Modifications and Epitranscriptomics	12
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	12
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	11
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	11
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	11
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	11
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	11
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	11
Integrative Multi-Omics Landscape of Non-Structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	11
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	10
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	10
HemaCisDB: An Interactive Database for Analyzing Cis-Regulatory Elements Across Hematopoietic Malignancies	10
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	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
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	9
SRPS: Survival Reinforced Transfer Learning for Multicentric Proteomic Subtyping and Biomarker Discovery	9
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	9
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	9
The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	9
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	9
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	9
GenBase: A Nucleotide Sequence Database	9
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	9
From BIG Data Center to China National Center for Bioinformation	9
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	8
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	8
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	8
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	8
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	8
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	8
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	8
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	8
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	8
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	8
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	8
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	7
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	7
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	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
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	7
Machine Learning for AI Breeding in Plants	7
Acknowledgments to Reviewers 2022	7
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	7
Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator	7
Biological Data Resources and Machine Learning Frameworks for Hematology Research	7
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
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	6
YanHuang Paternal Genomic Resource Suggested A Weakly-Differentiated Multi-Source Admixture Model for the Formation of Han’s Founding Ancestral Lineages	6
BSAlign: A Library for Nucleotide Sequence Alignment	6
Laws of Genome Nucleotide Composition	6
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	6
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	6
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	6
NSUN2-Mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma	6
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events	6
An Integrative Polygenic and Epigenetic Risk Score for Overweight-related Hypertension in Chinese Population	6
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	6
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	5
Profiling the Bisecting N-Acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry	5
Defining Proximity Proteome of Histone Modifications by Antibody-Mediated Protein A-APEX2 Labeling	5
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	5
ASER: Animal Sex Reversal Database	5
Database Commons: A Catalog of Worldwide Biological Databases	5
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	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
Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics	4

Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	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
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	4
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	4
High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras	4
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	4
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	4
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	4
Machine Learning Modeling of Protein-Intrinsic Features Predicts Tractability of Targeted Protein Degradation	4
A Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	4
Unveiling Neonatal Pneumonia Microbiome by High-Throughput Sequencing and Droplet Culturomics	4
The Bioinformatic Applications of Hi-C and Linked Reads	4
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data	4
Long and Accurate: How HiFi Sequencing is Transforming Genomics	4
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	4
PhaSeDis: A Manually Curated Database of Phase Separation–disease Associations and Corresponding Small Molecules	4