Genomics Proteomics & Bioinformatics

Article	Citations
Acknowledgments to Reviewers 2021	440
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	317
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	200
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	159
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	98
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	93
OBIA: An Open Biomedical Imaging Archive	92
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	76
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	67
RNase P: Beyond Precursor tRNA Processing	64
Identify Non-mutational p53 Functional Deficiency in Human Cancers	63
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	60
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	59
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	55
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	54
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	54
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	49
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	49
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	49
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	42
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	40
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nuclei RNA Sequencing Data	39
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	37
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	36

GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	36
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	34
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	33
Computational Methods for Single-Cell DNA Methylome Analysis	33
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	32
Application of Microbiome in Forensics	32
Computational Approaches and Challenges in Spatial Transcriptomics	32
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	30
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	30
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	29
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	28
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	28
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	27
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	27
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	26
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	25
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	25
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	25
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	24
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	22
Artificial Intelligence in Omics	22
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	19
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	19
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	19
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	18
The Regulation of Gonadal Somatic Cell Differentiation in Humans	18
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	18
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	18
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	18
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	18
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	18
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	17
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	17
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	16
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	16
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	16
Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	16
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	16
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	15
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	15
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	15
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	14
Mass Spectrometry-based Solutions for Single-cell Proteomics	14
Nphos: Database and Predictor of Protein N-phosphorylation	14
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	14
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	14
RNA Modifications and Epitranscriptomics	14
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13

GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	13
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	13
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	13
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	13
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	13
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
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	12
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	12
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	12
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	12
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	11
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	11
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11
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
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	10
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources	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	10
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	10
Draft Genome of White-Blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation	10
The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes	10
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	9
GenBase: A Nucleotide Sequence Database	9
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	9
DisConST: Distribution-aware Contrastive Learning for Spatial Domain Identification	9
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	9
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	9
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	9
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	8
From BIG Data Center to China National Center for Bioinformation	8
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	8
Biological Data Resources and Machine Learning Frameworks for Hematology Research	8
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	8
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	8
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	8
CircAge: A Comprehensive Resource for Aging-associated Circular RNAs Across Species and Tissues	8
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	8
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	8
FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis	8
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	8
Machine Learning for AI Breeding in Plants	8
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	7
NSUN2-Mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma	7
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	7
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	7
Acknowledgments to Reviewers 2022	7
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	7
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins	7
Laws of Genome Nucleotide Composition	7
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	7
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	7
Decoding Human Biology and Disease Using Single-Cell Omics Technologies	7
m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes	7
Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator	7
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	7
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants	6
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	6
ASER: Animal Sex Reversal Database	6
YanHuang Paternal Genomic Resource Suggested A Weakly-Differentiated Multi-Source Admixture Model for the Formation of Han’s Founding Ancestral Lineages	6
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events	6
Two Isatis Genomes Reveal the Biosynthesis and Evolutionary Origin of Indigo in Plants	6
BSAlign: A Library for Nucleotide Sequence Alignment	6
An Integrative Polygenic and Epigenetic Risk Score for Overweight-related Hypertension in Chinese Population	6
Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment	6
Toward a New Paradigm of Genomics Research—Celebration of the 20th Anniversary of Beijing Institute of Genomics	6
UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP	6
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation	6
Profiling the Bisecting N-Acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry	6
METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in NSCLC	5
Long and Accurate: How HiFi Sequencing is Transforming Genomics	5
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	5
The Bioinformatic Applications of Hi-C and Linked Reads	5
Histo-LCM-Hi-C Reveals 3D Chromatin Conformations of Spatially Localized Rare Cells in Tissues at High Resolution	5

Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies	5
Morphine Re-Arranges Chromatin Spatial Architecture of Primate Cortical Neurons	5
Database Commons: A Catalog of Worldwide Biological Databases	5
Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing	5
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	5
Multiome-wide Association Studies: Novel Approaches for Understanding Diseases	5
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss	5
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	5
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	5
cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers	5
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	4
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	4
PhaSeDis: A Manually Curated Database of Phase Separation–disease Associations and Corresponding Small Molecules	4
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	4
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	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
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	4
LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data	4
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	4
A Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	4
Machine Learning Modeling of Protein-Intrinsic Features Predicts Tractability of Targeted Protein Degradation	4
Unveiling Neonatal Pneumonia Microbiome by High-Throughput Sequencing and Droplet Culturomics	4