Genomics Proteomics & Bioinformatics

Article	Citations
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types	677
Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients	496
rMVP: A Memory-Efficient, Visualization-Enhanced, and Parallel-Accelerated Tool for Genome-Wide Association Study	487
GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction	459
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets	208
Direct Comparative Analyses of 10X Genomics Chromium and Smart-Seq2	183
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	148
Genome Warehouse: A Public Repository Housing Genome-Scale Data	128
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	99
High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads	92
The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR	87
Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota are Attributable to Its Key Ingredient Berberine	77
Single-Cell Immune Landscape of Human Recurrent Miscarriage	75
Evaluation of Cell Type Annotation R Packages on Single-Cell RNA-Seq Data	72
Gut Microbiome Alterations in COVID-19	68
Computational Tools and Resources for CRISPR/Cas Genome Editing	58
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	55
Quantitative Proteomics Using Isobaric Labeling: A Practical Guide	54
Computational Approaches and Challenges in Spatial Transcriptomics	47
Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis	45
Computational Screening of Phase-Separating Proteins	39
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	39
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	38
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	35
CVTree: A Parallel Alignment-Free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes	33

Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson’s Disease — The RESISTA-PD Trial	33
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	32
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits	32
Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock	32
A Single-Cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis	31
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource	29
Computational Methods for Single-Cell Multi-Omics Integration and Alignment	27
CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA–Disease Associations and Its Application	26
Application of Deep Learning on Single-Cell RNA Sequencing Data Analysis: A Review	25
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	25
Transcriptomic Profiling of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium over Time	25
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis	24
c-CSN: Single-Cell RNA Sequencing Data Analysis by Conditional Cell-Specific Network	24
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	24
A Chromosome-Level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert	24
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes	24
Microbial Dark Matter: From Discovery to Applications	23
scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data	23
Profiling Chromatin Accessibility at Single-Cell Resolution	22
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-Cell Datasets	22
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement	21
Recent Advances in Assembly of Complex Plant Genomes	21
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-Seq Data Analysis	20
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	20
The Role of DNA Methylation Reprogramming During Sex Determination and Transition in Zebrafish	20
The mRNA–miRNA–lncRNA Regulatory Network and Factors Associated with Prognosis Prediction of Hepatocellular Carcinoma	20
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks	20
Genomic Epidemiology of Carbapenemase-Producing Klebsiella Pneumoniae in China	19
Life History Recorded in the Vagino-Cervical Microbiome Along with Multi-Omes	19
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	19
Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using a Captive Monkey Model	19
Increased Expression of Colonic Mucosal Melatonin in Patients with Irritable Bowel Syndrome Correlated with Gut Dysbiosis	19
Single-Cell Long Non-Coding RNA Landscape of T Cells in Human Cancer Immunity	18
scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-Cell Graph Entropy	18
Single-Cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	18
Database Commons: A Catalog of Worldwide Biological Databases	18
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	18
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-Specific Phosphorylation Sites	17
m6A-TSHub: Unveiling the Context-Specific m6A Methylation and m6A-Affecting Mutations in 23 Human Tissues	17
Glycoproteogenomics: Setting the Course for Next-Generation Cancer Neoantigen Discovery for Cancer Vaccines	17
Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Experimental Ulcerative Colitis Mice	17
LDHA Desuccinylase Sirtuin 5 as a Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer	17
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning	16
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers	16
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women	16
Precision Methylome and in Vivo Methylation Kinetics Characterization of Klebsiella Pneumoniae	16
Screening of Potential Biomarkers for Gastric Cancer with Diagnostic Value Using Label-Free Global Proteome Analysis	15
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci	15
Dissecting Human Gonadal Cell Lineage Specification and Sex Determination Using a Single-Cell RNA-Seq Approach	15
Machine Learning Modeling of Protein-Intrinsic Features Predicts Tractability of Targeted Protein Degradation	15

inGAP-Family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities	14
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models	14
Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in a Three-Generation Pedigree	14
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	14
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs	14
NSUN2-Mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma	13
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	13
Application of Microbiome in Forensics	12
Oleic Acid and Eicosapentaenoic Acid Reverse Palmitic Acid-Induced Insulin Resistance in Human HepG2 Cells via the Reactive Oxygen Species/JUN Pathway	12
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	11
A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-Seq, and Single-Cell RNA-Seq	11
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	11
Integration of Computational Analysis and Spatial Transcriptomics in Single-Cell Studies	11
Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis	11
Different Gene Networks are Disturbed by Zika Virus Infection in a Mouse Microcephaly Model	11
Global Profiling of 2-Hydroxyisobutyrylome in Common Wheat	10
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	10
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	10
Genome-Wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer	10
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-Coding Variants	10
The Jasmine (Jasminum Sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates	10
The First High-Quality Reference Genome of Sika Deer Provides Insights into High-Tannin Adaptation	10
Artificial Intelligence in Omics	10
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	10
OGP: A Repository of Experimentally Characterized O-Glycoproteins to Facilitate Studies on O-Glycosylation	10
Sequence-Based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes	9
DTFLOW: Inference and Visualization of Single-Cell Pseudotime Trajectory Using Diffusion Propagation	9
Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait	9
Integrative Multi-Omics Landscape of Non-Structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	9
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics	9
Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response	9
Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803	9
deCS: A Tool for Systematic Cell Type Annotations of Single-Cell RNA Sequencing Data Among Human Tissues	9
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	9
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction	9
Global Profiling of the Lysine Crotonylome in Different Pluripotent States	9
N 6 -Methyladenosine and Its Implications in Viruses	9
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	8
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	8
Mapping Human Pluripotent Stem Cell-Derived Erythroid Differentiation by Single-Cell Transcriptome Analysis	8
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	8
Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma Gondii	8
Screening Linear and Circular RNA Transcripts from Stress Granules	8
BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images	8
SLM2 Is a Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy	8
Immunoprofiling of Drosophila Hemocytes by Single-Cell Mass Cytometry	8
Phosphoproteomics Reveals the AMPK Substrate Network in Response to DNA Damage and Histone Acetylation	8
Genomic Epidemiology of SARS-CoV-2 in Pakistan	8
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	8
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	8
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	7
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-Free Mice	7
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining	7
Defining Proximity Proteome of Histone Modifications by Antibody-Mediated Protein A-APEX2 Labeling	7
Profiling the Bisecting N-Acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry	7
Advanced Single-Cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis	7
Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades	7
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	7
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	7
An Integrated Systems Biology Approach Identifies the Proteasome as a Critical Host Machinery for ZIKV and DENV Replication	7
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	7
Reprogramming Mycobacterium Tuberculosis CRISPR System for Gene Editing and Genome-Wide RNA Interference Screening	7
Computational Methods for Single-Cell DNA Methylome Analysis	7
COVID-ONE-hi: The One-Stop Database for COVID-19-Specific Humoral Immunity and Clinical Parameters	7
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	7
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	7
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-Cell Epitopes	7
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	7
High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells	7
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	7
Interactive Web-Based Annotation of Plant MicroRNAs with iwa-miRNA	6
Mako: A Graph-Based Pattern Growth Approach to Detect Complex Structural Variants	6
Robust Benchmark Structural Variant Calls of an Asian Using State-of-the-Art Long-Read Sequencing Technologies	6
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	6
Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei (Rubus Corchorifolius)	6
Comparative Secretome Analysis of Magnaporthe oryzae Identified Proteins Involved in Virulence and Cell Wall Integrity	6
Characterizing RNA Pseudouridylation by Convolutional Neural Networks	6
FertilityOnline: A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery	6
Single-Cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-Genesis in Pigs	6
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	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
CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes	6
Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples	6
Single-Cell Analysis Technologies for Immuno-Oncology Research: From Mechanistic Delineation to Biomarker Discovery	6
DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-Omics Genomic Data	6
Single-Cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction	5
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	5
Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches	5
DNA Methylation Reshapes Sex Development in Zebrafish	5
DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning	5
Single-Cell RNA Sequencing Deciphers Immune Landscape of Human Recurrent Miscarriage	5
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	5
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	5
scEMAIL: Universal and Source-Free Annotation Method for scRNA-Seq Data with Novel Cell-Type Perception	5
Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-Order Genomic Interactions	5
MicroRNA–Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice	5
Characteristics of N 6-Methyladenosine Modification During Sexual Reproduction of Chlamydomonas Reinhardtii	5
Computational Assessment of Protein–Protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes	5
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	5
Elucidation of the MicroRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity	5
NORMA: The Network Makeup Artist — A Web Tool for Network Annotation Visualization	5
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	5
Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start	5
PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community	5
Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories	5
eTumorMetastasis: A Network-Based Algorithm Predicts Clinical Outcomes Using Whole-Exome Sequencing Data of Cancer Patients	5
DEBKS: A Tool to Detect Differentially Expressed Circular RNAs	5
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	5
PlantCADB: A Comprehensive Plant Chromatin Accessibility Database	4
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	4
MACMIC Reveals a Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes	4
GranatumX: A Community-Engaging, Modularized, and Flexible Webtool for Single-Cell Data Analysis	4
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction	4
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	4
RePhine: An Integrative Method for Identification of Drug Response-Related Transcriptional Regulators	4
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	4
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	4
inMTSCCA: An Integrated Multi-Task Sparse Canonical Correlation Analysis for Multi-Omic Brain Imaging Genetics	4
From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-Seq Data	4
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	4
SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers	4
A Chromosome-Level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation	4
ASER: Animal Sex Reversal Database	4
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities	4
rePROBE: Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays	4
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses	4
OBIA: An Open Biomedical Imaging Archive	4
Npac Is a Co-Factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells	4