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 2021-05-01 to 2025-05-01.)

Article	Citations
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	981
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	644
Acknowledgments to Reviewers 2021	317
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	231
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	155
OBIA: An Open Biomedical Imaging Archive	153
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	116
Precision Methylome and in Vivo Methylation Kinetics Characterization of Klebsiella Pneumoniae	97
RNase P: Beyond Precursor tRNA Processing	88
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	79
scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data	75
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	75
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	71
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	51
Identify Non-mutational p53 Functional Deficiency in Human Cancers	51
SLM2 Is a Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy	51
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	49
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	49
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	46
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	45
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	44
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	42
Computational Approaches and Challenges in Spatial Transcriptomics	40
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	40
Computational Methods for Single-Cell DNA Methylome Analysis	39

Application of Microbiome in Forensics	39
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	38
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	37
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	35
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	35
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	32
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	30
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	30
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	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
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	28
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	28
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	26
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	25
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	25
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	25
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	25
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	24
Artificial Intelligence in Omics	24
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	24
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling	24
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	23
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	22
Identification of Small Open Reading Frame Encoded Proteins from the Human Genome	22
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	22
The Regulation of Gonadal Somatic Cell Differentiation in Humans	22
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	21
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	21
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	21
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	21
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	20
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	20
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	20
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	20
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	19
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-Right Shell Asymmetry in Bivalves	19
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	19
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	18
Identifying Leukemia-related Genes based on Time-series Dynamical Network by Integrating Differential Genes	18
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	16
Nphos: Database and Predictor of Protein N-phosphorylation	16
RNA Modifications and Epitranscriptomics	15
MS-based Solutions for Single Cell Proteomics	15
CVTree: A Parallel Alignment-Free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes	14
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing	14
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	14
Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer	14
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	14
Global Invasion History and Genomic Signatures of Adaptation of the Highly Invasive Sycamore Lace Bug	14

Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-Cell RNA-Seq Data	13
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level	13
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	12
The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans	12
Integrative Multi-Omics Landscape of Non-Structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	12
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	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
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	12
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis	12
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11
HemaCisDB: An Interactive Database for Analyzing Cis-Regulatory Elements Across Hematopoietic Malignancies	11
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	11
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads	11
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation	11
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	11