Genomics Proteomics & Bioinformatics

Article	Citations
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	1022
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	671
Acknowledgments to Reviewers 2021	333
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	245
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	159
PSIA: A Comprehensive Knowledgebase of Plant Self-Incompatibility	157
OBIA: An Open Biomedical Imaging Archive	118
Precision Methylome and in Vivo Methylation Kinetics Characterization of Klebsiella Pneumoniae	110
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	88
RNase P: Beyond Precursor tRNA Processing	80
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	79
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	77
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	75
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	53
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	53
Identify Non-mutational p53 Functional Deficiency in Human Cancers	53
SLM2 Is a Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy	53
scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data	51
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	50
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	50
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	46
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	45
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	43
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	41
Computational Methods for Single-Cell DNA Methylome Analysis	40

Computational Approaches and Challenges in Spatial Transcriptomics	40
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	39
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	38
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	37
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	35
Application of Microbiome in Forensics	34
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	32
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	30
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	29
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	29
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	29
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	28
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	28
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	28
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	28
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	28
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	27
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	27
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	26
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	26
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	26
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	25
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	24
Artificial Intelligence in Omics	24
The Regulation of Gonadal Somatic Cell Differentiation in Humans	23
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	23
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	23
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	23
Identification of Small Open Reading Frame Encoded Proteins from the Human Genome	22
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	21
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	21
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	21
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	20
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	20
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	20
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	20
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	19
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	19
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	19
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	18
Identifying Leukemia-related Genes based on Time-series Dynamical Network by Integrating Differential Genes	18
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	16
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	16
Nphos: Database and Predictor of Protein N-phosphorylation	15
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	15
MS-based Solutions for Single Cell Proteomics	15
RNA Modifications and Epitranscriptomics	15
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	14
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	14
CVTree: A Parallel Alignment-Free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes	14

Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	14
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-Cell RNA-Seq Data	13
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	13
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	13
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	12
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	12
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	12
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	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
Integrative Multi-Omics Landscape of Non-Structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	12
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis	12
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	11
HemaCisDB: An Interactive Database for Analyzing Cis-Regulatory Elements Across Hematopoietic Malignancies	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
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	11
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	11
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	11
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	10
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	10
Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-lineage Acute Lymphoblastic Leukemia	10
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	10
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	10
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	10
The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	10
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	9
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	9
REVA as A Well-Curated Database for Human Expression-Modulating Variants	9
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-Free Mice	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
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	9
From BIG Data Center to China National Center for Bioinformation	9
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	9
GenBase: A Nucleotide Sequence Database	9
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	9
scDPN for High-Throughput Single-Cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence	9
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	9
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	9
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	8
BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images	8
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	8
Biological Data Resources and Machine Learning Frameworks for Hematology Research	8
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	8
Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples	8
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	8
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	8
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	8
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	7
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes	7
Laws of Genome Nucleotide Composition	7
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	7
Single-Cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-Genesis in Pigs	7
Acknowledgments to Reviewers 2022	7
Machine Learning for AI Breeding in Plants	7
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	7
A Single-Cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis	7
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	7
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	7
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	6
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	6
NSUN2-Mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma	6
ASER: Animal Sex Reversal Database	6
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	6
Morphine Re-Arranges Chromatin Spatial Architecture of Primate Cortical Neurons	6
Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	6
Toward a New Paradigm of Genomics Research—Celebration of the 20th Anniversary of Beijing Institute of Genomics	6
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	6
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	6
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	6
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	6
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	6
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events	6
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	6
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins	6
Defining Proximity Proteome of Histone Modifications by Antibody-Mediated Protein A-APEX2 Labeling	6

Profiling the Bisecting N-Acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry	6
BSAlign: A Library for Nucleotide Sequence Alignment	6
The Bioinformatic Applications of Hi-C and Linked Reads	5
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	5
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	5
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	5
High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads	5
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	5
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing	5
PhaSeDis: A Manually Curated Database of Phase Separation–Disease Associations and Corresponding Small Molecules	5
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	5
Long and Accurate: How HiFi Sequencing is Transforming Genomics	5
Metagenomic Analysis Reveals a Possible Association Between Respiratory Infection and Periodontitis	5
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	5
Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	5
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	5
Database Commons: A Catalog of Worldwide Biological Databases	5
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	4
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women	4
Machine Learning Modeling of Protein-Intrinsic Features Predicts Tractability of Targeted Protein Degradation	4
Single-Cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	4
Characteristics of N 6-Methyladenosine Modification During Sexual Reproduction of Chlamydomonas Reinhardtii	4
Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson’s Disease — The RESISTA-PD Trial	4
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	4
Unveiling Neonatal Pneumonia Microbiome by High-Throughput Sequencing and Droplet Culturomics	4
Aberrant Somatic Hypermutation at Super-enhancer Drives B Cell Lymphoma Transformation	4
First Glimpse of Gut Microbiota of Quarantine Insects in China	4
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks	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
From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-Seq Data	4
Centromere Landscapes Resolved from Hundreds of Human Genomes	4
GranatumX: A Community-Engaging, Modularized, and Flexible Webtool for Single-Cell Data Analysis	4
RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases	4