OOIR: Observatory of International Research

Papers

(The TQCC of Genomics Proteomics & Bioinformatics is 12. 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 2020-05-01 to 2024-05-01.)

Article	Citations
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types	525
Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients	435
rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study	393
GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction	367
Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2	161
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets	161
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	115
Genome Warehouse: A Public Repository Housing Genome-scale Data	105
mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies	91
The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR	84
simplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	82
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads	82
Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine	72
Single-cell Immune Landscape of Human Recurrent Miscarriage	63
Gut Microbiome Alterations in COVID-19	60
Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data	60
Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis	50
Computational Tools and Resources for CRISPR/Cas Genome Editing	49
m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes	48
Quantitative Proteomics Using Isobaric Labeling: A Practical Guide	43
Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters	39
Computational Screening of Phase-separating Proteins	37
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	36
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa	34
The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms	33

Computational Approaches and Challenges in Spatial Transcriptomics	31
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms	30
Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock	30
Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis	30
A Single-cell Transcriptome Atlas of Cashmere Goat Hair Follicle Morphogenesis	29
Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	29
iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features	29
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits	27
Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson’s Disease — The RESISTA-PD Trial	27
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	27
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time	24
CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes	23
CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA–Disease Associations and Its Application	22
Computational Methods for Single-cell Multi-omics Integration and Alignment	22
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets	21
Tissue-specific Gene Expression Changes Are Associated with Aging in Mice	21
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement	21
Microbial Dark Matter: from Discovery to Applications	20
c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network	20
Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae	20
Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea	20
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks	20
Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review	19
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes	19
GTB-PPI: Predict Protein–protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting	19
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis	19
scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data	19
The mRNA–miRNA–lncRNA Regulatory Network and Factors Associated with Prognosis Prediction of Hepatocellular Carcinoma	19
TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource	19
Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma	19
Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae	18
Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes	18
Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles	18
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis	18
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	17
A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert	17
LDHA Desuccinylase Sirtuin 5 as A Novel Cancer Metastatic Stimulator in Aggressive Prostate Cancer	16
The Role of DNA Methylation Reprogramming During Sex Determination and Transition in Zebrafish	16
Profiling Chromatin Accessibility at Single-cell Resolution	16
Genomic Epidemiology of Carbapenemase-producing Klebsiella pneumoniae in China	16
Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using A Captive Monkey Model	15
Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	15
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women	15
scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy	15
Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity	15
Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation	15
Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation	15
Paleo-polyploidization in Lycophytes	15
Increased Expression of Colonic Mucosal Melatonin in Patients with Irritable Bowel Syndrome Correlated with Gut Dysbiosis	15
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	15

MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot	14
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning	14
Database Commons: A Catalog of Worldwide Biological Databases	14
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers	14
m6A-TSHub: Unveiling the Context-Specific m6A Methylation and m6A-Affecting Mutations in 23 Human Tissues	14
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	14
Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines	14
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci	14
inGAP-Family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities	13
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs	13
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	13
Recent Advances in Assembly of Complex Plant Genomes	13
Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae	13
Screening of Potential Biomarkers for Gastric Cancer with Diagnostic Value Using Label-free Global Proteome Analysis	12
CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants	12
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models	12
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites	12
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	12
Long Non-coding RNA Derived from lncRNA–mRNA Co-expression Networks Modulates the Locust Phase Change	12