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

Article	Citations
Acknowledgments to Reviewers 2021	481
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	355
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	219
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	177
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	108
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	105
RNase P: Beyond Precursor tRNA Processing	102
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	85
Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes	72
Benefits of Better Cardiovascular Health for Calcific Aortic Valve Stenosis Stratified by Polygenic Risk Score	69
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	63
OBIA: An Open Biomedical Imaging Archive	63
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	61
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	59
Whole-genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	57
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	55
Identify Non-mutational p53 Functional Deficiency in Human Cancers	54
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	54
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	48
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	46
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	43
Computational Methods for Single-Cell DNA Methylome Analysis	41
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	41
DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes	40
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	38

GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	37
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	36
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens	35
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	34
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nucleus RNA Sequencing Data	34
A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development	33
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	33
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	33
Application of Microbiome in Forensics	32
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	31
Computational Approaches and Challenges in Spatial Transcriptomics	30
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	29
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	29
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	26
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	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
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	24
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	23
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	22
SimplifyEnrichment : A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	22
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	22
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs	21
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	20
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	20
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	20
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	20
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	20
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	20
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	19
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	19
Artificial Intelligence in Omics	19
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	18
The Regulation of Gonadal Somatic Cell Differentiation in Humans	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
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	17
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	16
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	16
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	16
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	16
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	16
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	16
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	16
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	15
DyNDG: Identifying Leukemia-related Genes Based on Time-series Dynamic Network by Integrating Differential Genes	15
Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes	15
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	15
Benchmark and Evaluation for Somatic Structural Variants Detection with Long-read Sequencing Data	14
Nphos: Database and Predictor of Protein N -phosphorylation	14

Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	14
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	14
Macrophages in Hematopoiesis and Related Blood Diseases	14
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Mass Spectrometry-based Solutions for Single-cell Proteomics	13
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	13
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	13
RNA Modifications and Epitranscriptomics	13
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream	13
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	13
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	12
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	12
iRUNNER: A Baseline Mutation Burden Regression for Identifying Gene Interaction Between Rare Variants for Diseases	12
Deep Transfer Learning Links Benign Glands to Prostate Cancer Progression via Transcriptomics	12
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	12
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	12
RNA Methylome Reveals the m 6 A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	11
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	11
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	11
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11