Genomics Proteomics & Bioinformatics

Article	Citations
Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish	775
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	546
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	541
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	530
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining	240
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	192
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	168
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	128
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	103
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	99
GenBase: A Nucleotide Sequence Database	68
KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data	59
RePhine: An Integrative Method for Identification of Drug Response-Related Transcriptional Regulators	58
Quantitative Secretome Analysis Reveals Clinical Values of Carbonic Anhydrase II in Hepatocellular Carcinoma	58
Gut Microbiome Variation Along a Lifestyle Gradient Reveals Threats Faced by Asian Elephants	56
Metagenomic Analysis Reveals a Possible Association Between Respiratory Infection and Periodontitis	54
A Beloved Bioinformatician Buddy—In Memory of Professor Weimin Zhu	44
Acknowledgments to Reviewers 2021	39
Exploration of Target Spaces in the Human Genome for Protein and Peptide Drugs	39
Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines	35
Computational Assessment of the Expression-Modulating Potential for Non-Coding Variants	34
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	33
CBioProfiler: A Web and Standalone Pipeline for Cancer Biomarker and Subtype Characterization	33
Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer	32
High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion	32

Genomic Shift in Population Dynamics of mcr-1-Positive Escherichia Coli in Human Carriage	31
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	29
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	27
Cancer is a Survival Process under Persistent Microenvironmental and Cellular Stresses	26
c-CSN: Single-Cell RNA Sequencing Data Analysis by Conditional Cell-Specific Network	26
Npac Is a Co-Factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells	25
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	25
DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps	24
Direct Comparative Analyses of 10X Genomics Chromium and Smart-Seq2	24
Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes But Stable Dosage Compensation in Mammals	24
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	24
Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors	23
The First High-Quality Reference Genome of Sika Deer Provides Insights into High-Tannin Adaptation	22
Sequence-Based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes	22
SPA: A Quantitation Strategy for MS Data in Patient-Derived Xenograft Models	22
mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants	21
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci	21
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	20
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	20
Hidden Links Between Skin Microbiome and Skin Imaging Phenome	20
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	20
MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data	20
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	19
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	19
The Regulation of Gonadal Somatic Cell Differentiation in Humans	18
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	18
The mRNA–miRNA–lncRNA Regulatory Network and Factors Associated with Prognosis Prediction of Hepatocellular Carcinoma	18
scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-Cell Graph Entropy	18
m6A-TSHub: Unveiling the Context-Specific m6A Methylation and m6A-Affecting Mutations in 23 Human Tissues	18
Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Experimental Ulcerative Colitis Mice	18
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	18
An Integrated Systems Biology Approach Identifies the Proteasome as a Critical Host Machinery for ZIKV and DENV Replication	17
The Bioinformatic Applications of Hi-C and Linked Reads	17
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	17
SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers	17
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	16
OBIA: An Open Biomedical Imaging Archive	16
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	16
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs	16
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-Seq Data via DeeReCT-TSS	15
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	15
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	14
Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in a Three-Generation Pedigree	14
COCOA: A Framework for Fine-scale Mapping Cell-type-specific Chromatin Compartments with Epigenomic Information	14
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	14
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	13
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	13
Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis	12
Machine Learning Modeling of Protein-Intrinsic Features Predicts Tractability of Targeted Protein Degradation	12

NORMA: The Network Makeup Artist — A Web Tool for Network Annotation Visualization	11
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction	11
RCoV19: A One-Stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-Warning	11
Single-Cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction	11
The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation	11
scEMAIL: Universal and Source-Free Annotation Method for scRNA-Seq Data with Novel Cell-Type Perception	11
The Genome Architecture of the Copepod Eurytemora carolleeae — the Highly Invasive Atlantic Clade of the Eurytemora affinis Species Complex	11
Mining Unknown Porcine Protein Isoforms by Tissue-Based Map of Proteome Enhances Pig Genome Annotation	10
Preclinical-to-Clinical Anti-Cancer Drug Response Prediction and Biomarker Identification Using TINDL	10
REVA as A Well-Curated Database for Human Expression-Modulating Variants	10
redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-Cell RNA-Seq Data and Applications in Cancer	10
RNase P: Beyond Precursor tRNA Processing	10
scDPN for High-Throughput Single-Cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence	10
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics	10
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	10
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	9
Profiling Chromatin Accessibility at Single-Cell Resolution	9
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women	9
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	9
EryDB: A Transcriptomic Profile Database for Erythropoiesis and Erythroid-related Diseases	9
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-Free Mice	9
Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson’s Disease — The RESISTA-PD Trial	9
VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns	9
CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer	9
Acknowledgments to Reviewers 2023	9
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	9
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning	9
From BIG Data Center to China National Center for Bioinformation	9
OGP: A Repository of Experimentally Characterized O-Glycoproteins to Facilitate Studies on O-Glycosylation	8
What Has Genomics Taught an Evolutionary Biologist?	8
Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei (Rubus Corchorifolius)	8
TCRosetta: An Integrated Analysis and Annotation Platform for T-cell Receptor Sequences	8
N 6 -Methyladenosine and Its Implications in Viruses	8
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses	8
The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	8
Elucidation of the MicroRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity	8
RNA2Immune: A Database of Experimentally Supported Data Linking Non-Coding RNA Regulation to the Immune System	8
GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis	8
Cancer Stemness Online: A Resource for Investigating Cancer Stemness and Associations with Immune Response	8
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	8
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	7
A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-Seq, and Single-Cell RNA-Seq	7
DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-Omics Genomic Data	7
Novel Time-Dependent Multi-Omics Integration in Sepsis-Associated Liver Dysfunction	7
Oleic Acid and Eicosapentaenoic Acid Reverse Palmitic Acid-Induced Insulin Resistance in Human HepG2 Cells via the Reactive Oxygen Species/JUN Pathway	7
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	7
eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs	7
HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells	7
SLM2 Is a Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy	7
Precision Methylome and in Vivo Methylation Kinetics Characterization of Klebsiella Pneumoniae	7
RNA Modifications and Epitranscriptomics	7
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks	7
CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-Related Genes and Clinical Manifestations	7
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	7
CVTree: A Parallel Alignment-Free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes	7
Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis	7
A Global Multiregional Proteomic Map of the Human Cerebral Cortex	7
HPC-Atlas: Computationally Constructing a Comprehensive Atlas of Human Protein Complexes	7
DEBKS: A Tool to Detect Differentially Expressed Circular RNAs	7
From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-Seq Data	6
Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes	6
Non-Small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-Smokers	6
A Single-Cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis	6
deCS: A Tool for Systematic Cell Type Annotations of Single-Cell RNA Sequencing Data Among Human Tissues	6
FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks	6
A Yeast BiFC-Seq Method for Genome-Wide Interactome Mapping	6
rePROBE: Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays	6
Single-Cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	6
Genomes of Two Flying Squid Species Provide Novel Insights into Adaptations of Cephalopods to Pelagic Life	6
GranatumX: A Community-Engaging, Modularized, and Flexible Webtool for Single-Cell Data Analysis	6
First Glimpse of Gut Microbiota of Quarantine Insects in China	6
Single-Cell Analysis Technologies for Immuno-Oncology Research: From Mechanistic Delineation to Biomarker Discovery	6
COVID-ONE-hi: The One-Stop Database for COVID-19-Specific Humoral Immunity and Clinical Parameters	6
Single-Cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-Genesis in Pigs	6
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	6
NOGEA: A Network-Oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning	6
inMTSCCA: An Integrated Multi-Task Sparse Canonical Correlation Analysis for Multi-Omic Brain Imaging Genetics	5
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	5
Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer	5
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	5

Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples	5
Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories	5
Machine Learning for AI Breeding in Plants	5
Aberrant Somatic Hypermutation at Super-enhancer Drives B Cell Lymphoma Transformation	5
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	5
FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval	5
Computational Tools and Resources for CRISPR/Cas Genome Editing	5
BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images	5
Genome Warehouse: A Public Repository Housing Genome-Scale Data	5
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	5
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	5
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits	5
Chromosome-Level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants	5
Robust Benchmark Structural Variant Calls of an Asian Using State-of-the-Art Long-Read Sequencing Technologies	5
Identification of Age-Associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium	5
LDHA Desuccinylase Sirtuin 5 as a Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer	5
On the Responsible Use of Chatbots in Bioinformatics	5
Dissecting Human Gonadal Cell Lineage Specification and Sex Determination Using a Single-Cell RNA-Seq Approach	5
Nphos: Database and Predictor of Protein N-phosphorylation	5
Identify Non-mutational p53 Functional Deficiency in Human Cancers	4
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	4
RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases	4
Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-cell RNA Sequencing	4
T2T-YAO Reference Genome of Han Chinese — New Step in Advancing Precision Medicine in China	4
Centromere Landscapes Resolved from Hundreds of Human Genomes	4
Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients	4
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types	4
Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome	4
Characteristics of N 6-Methyladenosine Modification During Sexual Reproduction of Chlamydomonas Reinhardtii	4
T2T-YAO, T2T-SHUN, and More	4
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	4
The Jasmine (Jasminum Sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates	4
SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations	4
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets	4
Genome Assembly and Winged fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses	4
FertilityOnline: A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery	4
scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data	4
A Novel Targeted Long-read Sequencing Approach Boosts Transcriptomic Profiling	4
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese	4
Quantitative Proteomics Using Isobaric Labeling: A Practical Guide	4