OOIR: Observatory of International Research

Papers

(The TQCC of Genomics Proteomics & Bioinformatics is 10. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-11-01 to 2024-11-01.)

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
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	39
Computational Screening of Phase-Separating Proteins	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
Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock	32
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
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
Transcriptomic Profiling of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium over Time	25
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
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
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
scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data	23
Microbial Dark Matter: From Discovery to Applications	23
Profiling Chromatin Accessibility at Single-Cell Resolution	22
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-Cell Datasets	22
Recent Advances in Assembly of Complex Plant Genomes	21
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement	21
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks	20
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
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
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
Database Commons: A Catalog of Worldwide Biological Databases	18
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	18
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
LDHA Desuccinylase Sirtuin 5 as a Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer	17
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
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
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning	16
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
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

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
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
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	13
NSUN2-Mediated mRNA m5C Modification Regulates the Progression of Hepatocellular Carcinoma	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
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
Integration of Computational Analysis and Spatial Transcriptomics in Single-Cell Studies	11
A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-Seq, and Single-Cell RNA-Seq	11
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	11
Multi-Omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis Galbana	11
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
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