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 2021-09-01 to 2025-09-01.)

Article	Citations
Acknowledgments to Reviewers 2021	391
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	290
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	180
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	138
PSIA: A Comprehensive Knowledgebase of Plant Self-incompatibility	134
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	92
OBIA: An Open Biomedical Imaging Archive	90
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues	88
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	85
RNase P: Beyond Precursor tRNA Processing	83
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals	68
Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development	59
Identify Non-mutational p53 Functional Deficiency in Human Cancers	59
Opportunities and Challenges in Advancing Plant Research with Single-cell Omics	58
New Metabolic Alterations and a Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma	57
Whole Genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese	57
Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response	55
DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility	53
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques	49
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant	49
GDBIG: A Pioneering Birth Cohort Genomic Platform Facilitating Intergenerational Genetic Research	47
Multi-Omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces	45
Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes	44
Computational Methods for Single-Cell DNA Methylome Analysis	42
Computational Approaches and Challenges in Spatial Transcriptomics	42

Application of Microbiome in Forensics	36
SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing	34
The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility	33
Precision and Accuracy in Quantitative Measurement of Gene Expression from Single-cell/nuclei RNA Sequencing Data	33
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins	33
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment	32
ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis	31
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-Ever-Omics to Holovivology	30
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective	30
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data	29
BLUPmrMLM: A Fast mrMLM Algorithm in Genome-wide Association Studies	29
RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells	29
Dynamic DNA 5-Hydroxylmethylcytosine and RNA 5-Methycytosine Reprogramming During Early Human Development	28
Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency	26
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data	26
Harnessing Type II Cytokines to Reinvigorate Exhausted T Cells for Durable Cancer Immunotherapy	25
SimplifyEnrichment: A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results	25
Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data	24
Artificial Intelligence in Omics	23
Reprogramming of RNA m6A Modification Is Required for Acute Myeloid Leukemia Development	23
rMATS-cloud: Large-scale Alternative Splicing Analysis in the Cloud	23
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions	23
Comprehensive Characterization and Global Transcriptome Analysis of Human Fetal Liver Terminal Erythropoiesis	22
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences	21
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	19
Systematic Cross-Biospecimen Evaluation of DNA Extraction Kits for Long- and Short-Read Multi-Metagenomic Sequencing Studies	19
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
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	17
Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	17
GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes	17
The Regulation of Gonadal Somatic Cell Differentiation in Humans	17
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	16
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	16
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	16
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	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: ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics	15
PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights	15
Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing	15
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	15
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution	15
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice	14
RNA Modifications and Epitranscriptomics	14
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	14
Nphos: Database and Predictor of Protein N-phosphorylation	13
Mass Spectrometry-based Solutions for Single-cell Proteomics	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

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	12
Integrative Multi-Omics Landscape of Non-Structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses	12
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses	12
Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs	12
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
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms	12
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content	12
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution	12
ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration	11
Mapping Multi-Factor-Mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-Related Genes	11
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers	11
Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes	11
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes	11
TransDFL: Identification of Disordered Flexible Linkers in Proteins by Transfer Learning	11
Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia	11
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering	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