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 2021-04-01 to 2025-04-01.)

Article	Citations
Innovative Low-cost Probe Generation Empowers Targeted Long-read RNA Sequencing	931
PHISDetector: A Tool to Detect Diverse In Silico Phage–Host Interaction Signals for Virome Studies	622
Identification of Small Open Reading Frame Encoded Proteins from the Human Genome	297
Correction to: Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells	217
Acknowledgments to Reviewers 2021	148
The First High-Quality Reference Genome of Sika Deer Provides Insights into High-Tannin Adaptation	147
Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish	113
Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data	87
Metagenomic Analysis Reveals a Possible Association Between Respiratory Infection and Periodontitis	85
The Regulation of Gonadal Somatic Cell Differentiation in Humans	76
Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells	73
A Two-color Single-molecule Sequencing Platform and Its Clinical Applications	72
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products	69
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning	51
Genomic Shift in Population Dynamics of mcr-1-Positive Escherichia Coli in Human Carriage	49
Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes But Stable Dosage Compensation in Mammals	48
KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data	46
GenBase: A Nucleotide Sequence Database	45
Hidden Links Between Skin Microbiome and Skin Imaging Phenome	44
APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control	42
MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data	42
SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers	40
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes	40
Computational Assessment of the Expression-Modulating Potential for Non-Coding Variants	39
Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Experimental Ulcerative Colitis Mice	37

Transcriptome-Wide Dynamics of m6A mRNA Methylation During Porcine Spermatogenesis	37
DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps	34
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes	33
CBioProfiler: A Web and Standalone Pipeline for Cancer Biomarker and Subtype Characterization	33
WheatCENet: A Database for Comparative Co-Expression Networks Analysis of Allohexaploid Wheat and Its Progenitors	32
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data	31
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci	30
Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer	28
Sequence-Based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes	28
A Beloved Bioinformatician Buddy—In Memory of Professor Weimin Zhu	28
Gut Microbiome Variation Along a Lifestyle Gradient Reveals Threats Faced by Asian Elephants	27
Acid–Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer	25
Cancer is a Survival Process under Persistent Microenvironmental and Cellular Stresses	25
Exploration of Target Spaces in the Human Genome for Protein and Peptide Drugs	25
Comprehensive Characterization of the Integrin Family Across 32 Cancer Types	24
scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-Cell Graph Entropy	22
Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma	22
AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning	22
TSNAdb v2.0: The Updated Version of Tumor-Specific Neoantigen Database	22
mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants	22
High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion	22
NetGO 3.0: Protein Language Model Improves Large-Scale Functional Annotations	22
m6A-TSHub: Unveiling the Context-Specific m6A Methylation and m6A-Affecting Mutations in 23 Human Tissues	22
The Bioinformatic Applications of Hi-C and Linked Reads	21
LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals	20
Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri-Containing Lineage in Primate Guts	20
Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep	20
Harnessing the Foundation Model for Exploration of Single-cell Expression Atlases in Plants	20
Single-cell Atlas of Developing Mouse Palates Reveals Cellular and Molecular Transitions in Periderm Cell Fate	19
A Developmental Gene Expression Atlas Reveals Novel Biological Basis of Complex Phenotypes in Sheep	19
PhaSeDis: A Manually Curated Database of Phase Separation–Disease Associations and Corresponding Small Molecules	19
Acknowledgments to Reviewers 2023	19
Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis	18
HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells	18
High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras	18
The Genome Architecture of the Copepod Eurytemora carolleeae — the Highly Invasive Atlantic Clade of the Eurytemora affinis Species Complex	18
LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank	18
Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types	18
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-Free Mice	17
RCoV19: A One-Stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-Warning	17
AVM: A Manually Curated Database of Aerosol-transmitted Virus Mutations, Human Diseases, and Drugs	16
RNase P: Beyond Precursor tRNA Processing	14
From BIG Data Center to China National Center for Bioinformation	14
Cancer Stemness Online: A Resource for Investigating Cancer Stemness and Associations with Immune Response	14
EryDB: A Transcriptomic Profile Database for Erythropoiesis and Erythroid-related Diseases	14
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription	14
N 6 -Methyladenosine and Its Implications in Viruses	13
VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns	12
VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences	12
scDPN for High-Throughput Single-Cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence	12

The Proteome Landscape of Human Placentas for Monochorionic Twins with Selective Intrauterine Growth Restriction	12
CIEC: Cross-tissue Immune Cell Type Enrichment and Expression Map Visualization for Cancer	11
NORMA: The Network Makeup Artist — A Web Tool for Network Annotation Visualization	11
Precision Methylome and in Vivo Methylation Kinetics Characterization of Klebsiella Pneumoniae	11
REVA as A Well-Curated Database for Human Expression-Modulating Variants	11
What Has Genomics Taught an Evolutionary Biologist?	11
Single-Cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction	11
Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice	11
eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs	11
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics	11
CpG Island Definition and Methylation Mapping of the T2T-YAO Genome	11
Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq	11