OOIR: Observatory of International Research

Papers

(The median citation count of Briefings in Functional Genomics is 2. 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
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	34
Environmental community transcriptomics: strategies and struggles	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
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	26
Emerging trends in functional genomics in Spiralia	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
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
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
A systematic view of computational methods for identifying driver genes based on somatic mutation data	7
Multi-omics approaches to therapeutic target identification	7
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
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
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	4
Long-read RNA sequencing can probe organelle genome pervasive transcription	4
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	4
A review: simulation tools for genome-wide interaction studies	4
Integrated multi-cohorts for characterizing the immunogenomic landscape and predicting drug response in triple-negative breast cancer	4
DeepCMI: a graph-based model for accurate prediction of circRNA–miRNA interactions with multiple information	4
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	4
Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish	4
GAM-MDR: probing miRNA–drug resistance using a graph autoencoder based on random path masking	4
Digital PCR and its applications in noninvasive prenatal testing	4
Diversity and novel mutations in membrane transporters ofMycobacterium tuberculosis	4
Comprehensive omics studies of p53 mutants in human cancer	4
Review of unsupervised pretraining strategies for molecules representation	4
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	4
Comparison of scRNA-seq data analysis method combinations	4
Briefings in functional genomics special section editorial: analysis of integrated multiple omics data	4
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	3
Functional characteristics of DNA N6-methyladenine modification based on long-read sequencing in pancreatic cancer	3
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	3
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	3

Evaluation of tools for taxonomic classification of viruses	3
Single-cell sequencing: expansion, integration and translation	3
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	3
Transcriptional advantage influence odorant receptor gene choice	3
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	2
Multi-omics integration analysis reveals the role of N6-methyladenosine in lncRNA translation during glioma stem cell differentiation	2
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	2
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	2
Integrating multi-omics data to identify dysregulated modules in endometrial cancer	2
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	2
Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective	2
Stratification of ovarian cancer patients from the prospect of drug target-related transcription factor protein activity: the prognostic and genomic landscape analyses	2
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	2
Current status and future prospects of drug–target interaction prediction	2
Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework	2
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	2
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	2
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	2
Spiralian genomics and the evolution of animal genome architecture	2
Multiomics technologies: role in disease biomarker discoveries and therapeutics	2
Integration of hybrid and self-correction method improves the quality of long-read sequencing data	2
Exploring the impact of N4-acetylcytidine modification in RNA on non-neoplastic disease: unveiling its role in pathogenesis and therapeutic opportunities	2
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	2
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	2
AMLdb: a comprehensive multi-omics platform to identify biomarkers and drug targets for acute myeloid leukemia	2
BioDKG–DDI: predicting drug–drug interactions based on drug knowledge graph fusing biochemical information	2
Editorial for BFG special issue: Computational genomics for precision medicine and personalized healthcare	2
Functional genomics of ageing: implications of chromatin landscape and beyond	2
Correction to: Emerging challenge: dynamic solution structures of nucleic acids	2