Genomics Proteomics & Bioinformatics

Article	Citations
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types	471
Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients	403
rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study	367
GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction	318
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets	187
Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2	154
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets	142
Genome Warehouse: A Public Repository Housing Genome-scale Data	101
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	99
mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies	86
The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR	81
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads	73
simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	69
Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine	68
Single-cell Immune Landscape of Human Recurrent Miscarriage	60
Gut Microbiome Alterations in COVID-19	58
Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data	57
DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery	50
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites	47
Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis	47
Computational Tools and Resources for CRISPR/Cas Genome Editing	45
BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures	44
m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes	44
Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters	39
Quantitative Proteomics Using Isobaric Labeling: A Practical Guide	36

Computational Screening of Phase-separating Proteins	36
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	35
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	32
The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms	30
iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features	29
Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock	28
A Single-cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis	28
HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction	26
Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	26
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	26
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	25
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits	24
Computational Approaches and Challenges in Spatial Transcriptomics	24
CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes	23
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time	23
Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson’s Disease — The RESISTA-PD Trial	21
Computational Methods for Single-cell Multi-omics Integration and Alignment	21
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets	21
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement	21
Tissue-specific Gene Expression Changes Are Associated with Aging in Mice	20
Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae	19
scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data	19
CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA–Disease Associations and Its Application	19
Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis	19
SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice	18
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks	18
The mRNA–miRNA–lncRNA Regulatory Network and Factors Associated with Prognosis Prediction of Hepatocellular Carcinoma	18
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis	18
c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network	18
Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma	18
Microbial Dark Matter: from Discovery to Applications	18
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes	18
Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles	18
Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae	17
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data	17
SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites	17
GTB-PPI: Predict Protein–protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting	17
Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea	17
The Role of DNA Methylation Reprogramming During Sex Determination and Transition in Zebrafish	16
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis	16
Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes	16
A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert	16
Profiling Chromatin Accessibility at Single-cell Resolution	15
Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using A Captive Monkey Model	15
LDHA Desuccinylase Sirtuin 5 as A Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer	15
Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation	15
Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review	15
Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	15
Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity	15
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource	14

Increased Expression of Colonic Mucosal Melatonin in Patients with Irritable Bowel Syndrome Correlated with Gut Dysbiosis	14
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	14
Genomic Epidemiology of Carbapenemase-producing Klebsiella pneumoniae in China	14
Paleo-polyploidization in Lycophytes	14
scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy	14
Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation	14
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women	14
m6A-TSHub: Unveiling the Context-Specific m6A Methylation and m6A-Affecting Mutations in 23 Human Tissues	14
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers	13
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning	13
Database Commons: A Catalog of Worldwide Biological Databases	13
MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot	13
Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines	13
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci	13
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases	13
Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae	13
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	13
Long Non-coding RNA Derived from lncRNA–mRNA Co-expression Networks Modulates the Locust Phase Change	12
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs	12
inGAP-Family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities	12
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models	12
CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants	12
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	11
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	11
The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium	11
Screening of Potential Biomarkers for Gastric Cancer with Diagnostic Value Using Label-free Global Proteome Analysis	11
MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals	10
Different Gene Networks Are Disturbed by Zika Virus Infection in A Mouse Microcephaly Model	10
Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics	9
Application of Microbiome in Forensics	9
deCS: A Tool for Systematic Cell Type Annotations of Single-Cell RNA Sequencing Data Among Human Tissues	9
Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Experimental Ulcerative Colitis Mice	9
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites	9
Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis	9
OGP: A Repository of Experimentally Characterized O-glycoproteins to Facilitate Studies on O-glycosylation	9
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	9
Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis	9
Multi-omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis galbana	9
Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803	8
Global Profiling of the Lysine Crotonylome in Different Pluripotent States	8
New Metabolic Alterations and A Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	8
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics	8
PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion	8
Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	8
A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq	8
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves	8
Genome-wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer	8
Genomic Epidemiology of SARS-CoV-2 in Pakistan	8
BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images	8
Oleic Acid and Eicosapentaenoic Acid Reverse Palmitic Acid-induced Insulin Resistance in Human HepG2 Cells via the Reactive Oxygen Species/JUN Pathway	8
Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree	8
An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication	7
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	7
Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies	7
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	7
Screening Linear and Circular RNA Transcripts from Stress Granules	7
COVID-ONE-hi: The One-stop Database for COVID-19-specific Humoral Immunity and Clinical Parameters	7
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining	7
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	7
Recent Advances in Assembly of Complex Plant Genomes	7
Mapping Human Pluripotent Stem Cell-derived Erythroid Differentiation by Single-cell Transcriptome Analysis	7
Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades	7
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation	7
Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes	7
Global Profiling of 2-hydroxyisobutyrylome in Common Wheat	7
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective	7
Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis	7
Dissecting Human Gonadal Cell Lineage Specification and Sex Determination Using A Single-cell RNA-seq Approach	7
SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms	6
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	6
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	6
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	6
Defining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling	6
Reprogramming Mycobacterium tuberculosis CRISPR System for Gene Editing and Genome-wide RNA Interference Screening	6
T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese	6
Quantitative Secretome Analysis Reveals Clinical Values of Carbonic Anhydrase II in Hepatocellular Carcinoma	6
Whole-Genome Duplication Reshaped Adaptive Evolution in a Relict Plant Species, Cyclocarya Paliurus	6
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	6
NORMA: The Network Makeup Artist — A Web Tool for Network Annotation Visualization	6
DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data	5

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction	5
Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity	5
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	5
Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803	5
Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response	5
Identification of Age-associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	5
Interactive Web-Based Annotation of Plant MicroRNAs with iwa-miRNA	5
The Jasmine (Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates	5
ASER: Animal Sex Reversal Database	5
N 6 -Methyladenosine and Its Implications in Viruses	5
The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells	5
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	5
Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait	5
Characterizing RNA Pseudouridylation by Convolutional Neural Networks	5
High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells	5
Comparative Secretome Analysis of Magnaporthe oryzae Identified Proteins Involved in Virulence and Cell Wall Integrity	5
Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	5
Phosphoproteomics Reveals the AMPK Substrate Network in Response to DNA Damage and Histone Acetylation	5
Single-cell Analysis Technologies for Immuno-oncology Research: from Mechanistic Delineation to Biomarker Discovery	5
iGMDR: Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research	5
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	5
The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation	5
Immunoprofiling of Drosophila Hemocytes by Single-cell Mass Cytometry	5
Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants	5
DTFLOW: Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation	5
Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica	5
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes	5
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	5
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	5