OOIR: Observatory of International Research

Papers

(The TQCC of Briefings in Functional Genomics is 5. 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
Pretraining model for biological sequence data	40
Environmental community transcriptomics: strategies and struggles	34
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	34
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease	33
Targeting novel sites in DNA gyrase for development of anti-microbials	27
Emerging trends in functional genomics in Spiralia	26
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	26
Computational drug repurposing for viral infectious diseases: a case study on monkeypox	22
ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing	21
Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19	20
Single-cell transcriptomics refuels the exploration of spiralian biology	17
Role of gut-microbiota in disease severity and clinical outcomes	17
Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians	16
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	14
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	14
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	14
Functional genomics in Spiralia	12
Sesame Genomic Web Resource (SesameGWR): a well-annotated data resource for transcriptomic signatures of abiotic and biotic stress responses in sesame (Sesamum indicum L.)	12
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	12
Prognostic signature analysis and survival prediction of esophageal cancer based on N6-methyladenosine associated lncRNAs	11
Gene regulatory network inference based on novel ensemble method	11
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	11
The regulatory role of non-coding RNAs and their interactions with phytochemicals in neurodegenerative diseases: a systematic review	11
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	11
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	10

Review of multi-omics data resources and integrative analysis for human brain disorders	10
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	9
Tau–FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer’s disease	9
Identifying preeclampsia-associated genes using a control theory method	9
From bench to bedside: potential of translational research in COVID-19 and beyond	9
The role of the X chromosome in infectious diseases	9
A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction	8
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	8
Respiratory tract infection: an unfamiliar risk factor in high-altitude pulmonary edema	8
Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas	8
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	7
Single-cell RNA-seq data clustering by deep information fusion	7
Microscale marvels: unveiling the macroscopic significance of micropeptides in human health	7
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research	7
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	7
Genomics in Clinical trials for Breast Cancer	7
A systematic view of computational methods for identifying driver genes based on somatic mutation data	7
Multi-omics approaches to therapeutic target identification	7
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations	6
Recent insights into crosstalk between genetic parasites and their host genome	6
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	6
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	5
DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms	5
Molecular insights on the origin and development of waxy genotypes in major crop plants	5
Multi-omics studies in interpreting the evolving standard model for immune functions	5
Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging	5
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	5
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	5
DockingGA: enhancing targeted molecule generation using transformer neural network and genetic algorithm with docking simulation	5
Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and betterde novoassemblies	5