OOIR: Observatory of International Research

Papers

(The median citation count of Briefings in Functional Genomics is 1. 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 2021-02-01 to 2025-02-01.)

Article	Citations
Application of CRISPR screens to investigate mammalian cell competition	32
Environmental community transcriptomics: strategies and struggles	31
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	29
Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19	25
The three-dimensional genome in zebrafish development	25
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	23
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	22
Respiratory tract infection: an unfamiliar risk factor in high-altitude pulmonary edema	22
A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction	22
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	18
Computational drug repurposing for viral infectious diseases: a case study on monkeypox	16
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	15
Role of gut-microbiota in disease severity and clinical outcomes	14
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	14
From bench to bedside: potential of translational research in COVID-19 and beyond	13
ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing	12
Genomics in Clinical trials for Breast Cancer	12
Emerging trends in functional genomics in Spiralia	12
Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians	11
The role of the X chromosome in infectious diseases	11
Single-cell transcriptomics refuels the exploration of spiralian biology	11
The regulatory role of non-coding RNAs and their interactions with phytochemicals in neurodegenerative diseases: a systematic review	11
Biological functions of RNA modifications	10
Prognostic signature analysis and survival prediction of esophageal cancer based on N6-methyladenosine associated lncRNAs	10
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	9

Tau–FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer’s disease	9
Pretraining model for biological sequence data	9
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	9
Review of multi-omics data resources and integrative analysis for human brain disorders	9
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease	9
Functional genomics in Spiralia	8
Targeting novel sites in DNA gyrase for development of anti-microbials	8
Gene regulatory network inference based on novel ensemble method	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 comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	8
Identifying preeclampsia-associated genes using a control theory method	8
DockingGA: enhancing targeted molecule generation using transformer neural network and genetic algorithm with docking simulation	7
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	7
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	7
Microscale marvels: unveiling the macroscopic significance of micropeptides in human health	7
Sesame Genomic Web Resource (SesameGWR): a well-annotated data resource for transcriptomic signatures of abiotic and biotic stress responses in sesame (Sesamum indicum L.)	7
Single-cell RNA-seq data clustering by deep information fusion	6
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research	6
Multi-omics approaches to therapeutic target identification	6
Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging	6
A systematic view of computational methods for identifying driver genes based on somatic mutation data	6
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations	5
Multi-omics studies in interpreting the evolving standard model for immune functions	5
Diversity and novel mutations in membrane transporters ofMycobacterium tuberculosis	5
Recent insights into crosstalk between genetic parasites and their host genome	5
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	5
New tools for ‘ZEBRA-FISHING’	5
DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development	4
Molecular insights on the origin and development of waxy genotypes in major crop plants	4
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	4
DeepCMI: a graph-based model for accurate prediction of circRNA–miRNA interactions with multiple information	4
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	4
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	4
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	4
DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms	4
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	4
Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and betterde novoassemblies	4
Review of unsupervised pretraining strategies for molecules representation	4
The functional impact of nuclear reorganization in cellular senescence	4
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	4
Single-cell sequencing: expansion, integration and translation	3
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	3
Comparison of scRNA-seq data analysis method combinations	3
A review: simulation tools for genome-wide interaction studies	3
Current status and future prospects of drug–target interaction prediction	3
AMLdb: a comprehensive multi-omics platform to identify biomarkers and drug targets for acute myeloid leukemia	3
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	3
Comprehensive omics studies of p53 mutants in human cancer	3
Briefings in functional genomics special section editorial: analysis of integrated multiple omics data	3
Multi-omics integration analysis reveals the role of N6-methyladenosine in lncRNA translation during glioma stem cell differentiation	3

ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	3
Long-read RNA sequencing can probe organelle genome pervasive transcription	3
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	3
Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework	3
Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective	3
Integrating multi-omics data to identify dysregulated modules in endometrial cancer	3
Investigating the molecular guts of endoderm formation using zebrafish	2
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	2
Integrative analyses of transcriptome data reveal the mechanisms of post-transcriptional regulation	2
Digital PCR and its applications in noninvasive prenatal testing	2
Integrated multi-cohorts for characterizing the immunogenomic landscape and predicting drug response in triple-negative breast cancer	2
Functional genomics of inflamm-aging and immunosenescence	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
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	2
Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish	2
Perspectives of using Cloud computing in integrative analysis of multi-omics data	2
Multiomics technologies: role in disease biomarker discoveries and therapeutics	2
Functional characteristics of DNA N6-methyladenine modification based on long-read sequencing in pancreatic cancer	2
Evaluation of tools for taxonomic classification of viruses	2
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	2
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	2
BioDKG–DDI: predicting drug–drug interactions based on drug knowledge graph fusing biochemical information	2
Transcriptional advantage influence odorant receptor gene choice	2
Machine learning approaches for predicting biomolecule–disease associations	2
The non-coding epitranscriptome in cancer	2
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	2
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	2
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	2
Editorial for BFG special issue: Computational genomics for precision medicine and personalized healthcare	2
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review	1
On the importance of evolutionary constraint for regulatory sequence identification	1
Functional genomics of ageing: implications of chromatin landscape and beyond	1
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	1
GAM-MDR: probing miRNA–drug resistance using a graph autoencoder based on random path masking	1
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	1
Identification of long noncoding RNAs with machine learning methods: a review	1
Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design	1
Single-cell genomics to study developmental cell fate decisions in zebrafish	1
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	1
Stratification of ovarian cancer patients from the prospect of drug target-related transcription factor protein activity: the prognostic and genomic landscape analyses	1
Neoepitopes prediction strategies: an integration of cancer genomics and immunoinformatics approaches	1
Predicting gastric cancer tumor mutational burden from histopathological images using multimodal deep learning	1
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	1
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	1
Genome-wide screens in yeast models towards understanding chronological lifespan regulation	1
Spiralian genomics and the evolution of animal genome architecture	1
Competing endogenous RNAs in head and neck squamous cell carcinoma: a review	1
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	1
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	1
Prediction of drug–protein interaction based on dual channel neural networks with attention mechanism	1
Accurate prediction and key protein sequence feature identification of cyclins	1
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	1
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	1
Exploring the impact of N4-acetylcytidine modification in RNA on non-neoplastic disease: unveiling its role in pathogenesis and therapeutic opportunities	1
Correction to: Emerging challenge: dynamic solution structures of nucleic acids	1
Network-based methods for gene function prediction	1
A comprehensive review of deep learning-based variant calling methods	1
Adaptive deep propagation graph neural network for predicting miRNA–disease associations	1
Integration of hybrid and self-correction method improves the quality of long-read sequencing data	1