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 2021-08-01 to 2025-08-01.)

Article	Citations
Acknowledgments to Reviewers 2021	1125
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	725
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	380
PSIA: A Comprehensive Knowledgebase of Plant Self-Incompatibility	275
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	175
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	133
OBIA: An Open Biomedical Imaging Archive	128
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	90
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	90
RNase P: Beyond Precursor tRNA Processing	84
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	83
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	83
Whole Genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	64
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	60
Identify Non-mutational p53 Functional Deficiency in Human Cancers	59
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	56
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	56
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	55
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	54
Application of Microbiome in Forensics	53
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	53
Computational Methods for Single-Cell DNA Methylome Analysis	47
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	44
Computational Approaches and Challenges in Spatial Transcriptomics	44
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	42

SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	39
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	37
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	36
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	34
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	33
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	33
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	32
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	31
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	31
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	31
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	30
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	29
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	28
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	28
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	28
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	26
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	25
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	25
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	24
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	23
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	23
Artificial Intelligence in Omics	23
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	23
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	22
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	21
The Regulation of Gonadal Somatic Cell Differentiation in Humans	21
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	21
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	19
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	19
Identification of Small Open Reading Frame-encoded Proteins in the Human Genome	18
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	16
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	15
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	15
Identifying Leukemia-related Genes based on Time-series Dynamical Network by Integrating Differential Genes	15
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	15
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	15
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	15
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	15
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	15
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	15
Correction to: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	14
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	14
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	14
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	14
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
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	13
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	13
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	13
Mass Spectrometry-based Solutions for Single-cell Proteomics	13

Nphos: Database and Predictor of Protein N-phosphorylation	13
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	12
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	12
RNA Modifications and Epitranscriptomics	12
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	12
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	12
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	12