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 2022-08-01 to 2026-08-01.)

Article	Citations
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	264
The MAGIC Cohort Study: Genetic Associations of Anisometropia in Chinese Population	228
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	147
Decoding RNA N 6-Methyladenosine Methylome of Wheat Using Machine Learning and Nanopore Direct RNA Sequencing	100
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	90
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	88
OBIA: An Open Biomedical Imaging Archive	84
Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes	79
Benchmarking Generative AI Protein Models Reveals Differences Between Structural and Sequence-based Approaches	69
RNase P: Beyond Precursor tRNA Processing	69
Benefits of Better Cardiovascular Health for Calcific Aortic Valve Stenosis Stratified by Polygenic Risk Score	66
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	60
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	55
Identify Non-mutational p53 Functional Deficiency in Human Cancers	55
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	54
NanoRAPID: A Deep Learning-based Framework for Single-molecule RNA Structure Analysis Using Nanopore Direct RNA Sequencing	53
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	48
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	46
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	43
DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes	41
Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome	39
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
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	34

GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	34
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	33
A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development	31
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	31
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data	29
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	29
Application of Microbiome in Forensics	28
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	28
Computational Approaches and Challenges in Spatial Transcriptomics	28
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	27
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	27
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	26
Why Did Treg and Immune Tolerance Win Nobel Prize This Year?	25
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	25
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	25
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	25
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	25
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	23
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	23
Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants	23
Generalizable Single-cell Multimodal Data Integration with Self-supervised Learning	23
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	23
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	21
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	21
K6 Atypical Ubiquitin Chain Regulates Intracellular Serine Homeostasis Through Tor1-Npr1-Par32-Gnp1 Signaling Axis	21
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	20
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	20
Artificial Intelligence in Omics	19
A Cattle BodyMap of Transcriptome across 52 Tissues and 3 Developmental Stages Reveals New Genetic Insights into Beef Production Traits	19
Granulin+ Macrophages Promote Lineage Plasticity in Prostate Cancer Through Paracrine Signaling Loops	18
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	18
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
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	17
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	17
Comprehensive Benchmarking with Guidelines for Analyzing Transposable Element-derived RNA Expression	17
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	16
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	16
Bispecific Antibodies in Cancer Immunotherapy: Mechanisms, Challenges, and Emerging Therapeutic Strategies	16
Benchmark and Evaluation for Somatic Structural Variants Detection with Long-read Sequencing Data	14
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	14
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	14
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	14
Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	13
WebCVTree4: Phylogenetic and Taxonomic Study Platform for Prokaryotes base on Whole Genomes	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	13

DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	13
iRUNNER: A Baseline Mutation Burden Regression for Identifying Gene Interaction Between Rare Variants for Diseases	13
Macrophages in Hematopoiesis and Related Blood Diseases	13
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	13
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	13
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	12
Nphos: Database and Predictor of Protein N -phosphorylation	12
RNA Modifications and Epitranscriptomics	12
Single-cell RNA Sequencing Reveals A Tumor-Promoting Role of EGR1+CD4+ T Cells in Papillary Thyroid Cancer	11
Mass Spectrometry-based Solutions for Single-cell Proteomics	11
Deep Transfer Learning Links Benign Glands to Prostate Cancer Progression via Transcriptomics	11
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	11
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	11
Pangenome Graph Reveals the Structural Variation Landscape in 2929 Cattle Samples and Its Impact on Gene Regulation	11
Shared Genetic Factors Between Stress-related Disorders and Cardiovascular Disease	11
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	11
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	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
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	11
Spatial Single-cell Transcriptome Atlas of Mouse Thymus Reveals the T Lymphocyte Dynamics During Development	11
FAST: Scalable Factor Analysis for Spatial Dimension Reduction of Multi-section Spatial Transcriptomics	11
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	10
Association of Multiple-trait Polygenic Risk Score with Obesity and Cardiometabolic Diseases in Korean Population	10
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	10
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	10
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	10
HemaCisDB: An Interactive Database for Analyzing Cis -regulatory Elements Across Hematopoietic Malignancies	10
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	10
RNA Methylome Reveals the m 6 A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	10
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	10