OOIR: Observatory of International Research

Papers

(The TQCC of Genomics Proteomics & Bioinformatics is 11. 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 2022-06-01 to 2026-06-01.)

Article	Citations
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	259
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	215
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	179
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	135
The MAGIC Cohort Study: Genetic Associations of Anisometropia in Chinese Population	97
Benefits of Better Cardiovascular Health for Calcific Aortic Valve Stenosis Stratified by Polygenic Risk Score	83
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	82
RNase P: Beyond Precursor tRNA Processing	77
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	77
OBIA: An Open Biomedical Imaging Archive	73
Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes	63
Benchmarking Generative AI Protein Models Reveals Differences Between Structural and Sequence-based Approaches	63
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	59
Calling for Diversity: Improving Transfusion Safety Through High-Throughput Blood Group Microarray Genotyping	54
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	51
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	51
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	50
Identify Non-mutational p53 Functional Deficiency in Human Cancers	50
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	45
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	45
DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes	43
Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome	41
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	39
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens	38
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	35

GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	33
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	31
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	31
Computational Methods for Single-Cell DNA Methylome Analysis	31
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	29
Computational Approaches and Challenges in Spatial Transcriptomics	27
Application of Microbiome in Forensics	27
A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development	26
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data	26
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	24
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	24
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	24
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	24
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	24
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	23
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	23
SimplifyEnrichment : A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	23
Why Did Treg and Immune Tolerance Win Nobel Prize This Year?	23
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	23
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	23
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	22
Generalizable Single-cell Multimodal Data Integration with Self-supervised Learning	22
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	22
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	22
Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants	20
K6 Atypical Ubiquitin Chain Regulates Intracellular Serine Homeostasis Through Tor1-Npr1-Par32-Gnp1 Signaling Axis	20
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	20
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	20
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	19
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	19
Artificial Intelligence in Omics	19
mTM-align2: A Server for Real-time Protein Structure Database Search and Alignment	18
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	18
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	18
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	17
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	17
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
Granulin+ Macrophages Promote Lineage Plasticity in Prostate Cancer Through Paracrine Signaling Loops	17
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	16
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	16
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	15
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	15
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	15
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	15
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	14
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	14
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	14
RNA Modifications and Epitranscriptomics	14
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	14

Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	14
Benchmark and Evaluation for Somatic Structural Variants Detection with Long-read Sequencing Data	14
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
Nphos: Database and Predictor of Protein N -phosphorylation	13
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	12
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	12
Mass Spectrometry-based Solutions for Single-cell Proteomics	12
Macrophages in Hematopoiesis and Related Blood Diseases	12
iRUNNER: A Baseline Mutation Burden Regression for Identifying Gene Interaction Between Rare Variants for Diseases	12
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	12
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	11
Deep Transfer Learning Links Benign Glands to Prostate Cancer Progression via Transcriptomics	11
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	11
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	11
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	11
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	11
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	11
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	11
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	11
RNA Methylome Reveals the m 6 A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	11
FAST: Scalable Factor Analysis for Spatial Dimension Reduction of Multi-section Spatial Transcriptomics	11
Spatial Single-cell Transcriptome Atlas of Mouse Thymus Reveals the T Lymphocyte Dynamics During Development	11