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 2020-11-01 to 2024-11-01.)

Article	Citations
Prediction of bio-sequence modifications and the associations with diseases	66
Sequence representation approaches for sequence-based protein prediction tasks that use deep learning	42
Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective	31
Critical evaluation of web-based DNA N6-methyladenine site prediction tools	30
Review of unsupervised pretraining strategies for molecules representation	28
BioDKG–DDI: predicting drug–drug interactions based on drug knowledge graph fusing biochemical information	25
Review of multi-omics data resources and integrative analysis for human brain disorders	25
The functional impact of nuclear reorganization in cellular senescence	23
Functional genomics of inflamm-aging and immunosenescence	22
Pretraining model for biological sequence data	22
Multiomics technologies: role in disease biomarker discoveries and therapeutics	21
The impact of epitranscriptomic marks on post-transcriptional regulation in plants	20
A comprehensive review for gut microbes: technologies, interventions, metabolites and diseases	19
Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design	19
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	18
Non-CpG methylation—a key epigenetic modification in cancer	16
A systematic review of computational methods for predicting long noncoding RNAs	15
Current status and future prospects of drug–target interaction prediction	14
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	14
Network-based methods for gene function prediction	13
Machine learning approaches for predicting biomolecule–disease associations	12
Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	12
An update: mechanisms of microRNA in primary open-angle glaucoma	12
The non-coding epitranscriptome in cancer	12
A survey on protein–DNA-binding sites in computational biology	11

Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors	11
Application of omics research in seaweeds with a focus on red seaweeds	10
Seven autophagy-related lncRNAs are associated with the tumor immune microenvironment in predicting survival risk of nonsmall cell lung cancer	9
Noncoding RNAs: modulators and modulatable players during infection-induced stress response	9
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research	9
Multifactorial feature extraction and site prognosis model for protein methylation data	9
Emerging roles of RNA modifications in genome integrity	9
Computational resources for identification of cancer biomarkers from omics data	9
Single-cell sequencing: expansion, integration and translation	9
PGRNIG: novel parallel gene regulatory network identification algorithm based on GPU	8
Digital PCR and its applications in noninvasive prenatal testing	8
Functional long non-coding and circular RNAs in zebrafish	8
Adaptive deep propagation graph neural network for predicting miRNA–disease associations	8
Targeting novel sites in DNA gyrase for development of anti-microbials	8
Molecular language models: RNNs or transformer?	8
Genome-wide screens in yeast models towards understanding chronological lifespan regulation	8
Tau–FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer’s disease	8
Deep learning tools are top performers in long non-coding RNA prediction	7
Spiralian genomics and the evolution of animal genome architecture	7
The role of the X chromosome in infectious diseases	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
DeepCMI: a graph-based model for accurate prediction of circRNA–miRNA interactions with multiple information	7
Flipping the script: viral capitalization of RNA modifications	7
GAM-MDR: probing miRNA–drug resistance using a graph autoencoder based on random path masking	7
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	7
Quantifying transcriptome diversity: a review	6
Identifying preeclampsia-associated genes using a control theory method	6
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	6
Deciphering RNA modifications at base resolution: from chemistry to biology	6
Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging	6
THGNCDA: circRNA–disease association prediction based on triple heterogeneous graph network	5
Distinct evolutionary pathways for the synthesis and function of tRNA modifications	5
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	5
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review	5
Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas	5
From mutation to mechanism: deciphering the molecular function of genetic variants linked to human ageing	5
Integrative analyses of transcriptome data reveal the mechanisms of post-transcriptional regulation	5
MiRNA–gene network embedding for predicting cancer driver genes	4
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era	4
Perspectives of using Cloud computing in integrative analysis of multi-omics data	4
Comprehensive omics studies of p53 mutants in human cancer	4
The regulatory role of non-coding RNAs and their interactions with phytochemicals in neurodegenerative diseases: a systematic review	4
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	4
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	4
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	4
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations	4
Integrative genomics important to understand host–pathogen interactions	4
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in 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
A systematic view of computational methods for identifying driver genes based on somatic mutation data	4

ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	3
Investigating the molecular guts of endoderm formation using zebrafish	3
Single-cell multi-omics sequencing and its application in tumor heterogeneity	3
Accurate prediction and key protein sequence feature identification of cyclins	3
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	3
DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development	3
Predicting the role of the human gut microbiome in type 1 diabetes using machine-learning methods	3
An improved hierarchical variational autoencoder for cell–cell communication estimation using single-cell RNA-seq data	3
Biophysical and modeling-based approach for the identification of inhibitors against DOHH fromLeishmania donovani	3
Predicting gastric cancer tumor mutational burden from histopathological images using multimodal deep learning	3
Evaluation of tools for taxonomic classification of viruses	3
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	3
Expanding interactome analyses beyond model eukaryotes	3
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	3
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	3
Single-cell RNA-seq data clustering by deep information fusion	2
Functional genomics in Spiralia	2
Computational drug repurposing for viral infectious diseases: a case study on monkeypox	2
Integrating functional scoring and regulatory data to predict the effect of non-coding SNPs in a complex neurological disease	2
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	2
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	2
Transcriptional advantage influence odorant receptor gene choice	2
DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms	2
Biological functions of RNA modifications	2
Single-cell transcriptomics refuels the exploration of spiralian biology	2
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	2
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	2
Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	2
Identification of long noncoding RNAs with machine learning methods: a review	2
Briefings in functional genomics special section editorial: analysis of integrated multiple omics data	2
Molecular insights on the origin and development of waxy genotypes in major crop plants	2
Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians	2
Role of gut-microbiota in disease severity and clinical outcomes	2
Comparative studies on the high-performance compression of SARS-CoV-2 genome collections	2
Infection outcome needs two to tango: human host and the pathogen	2
Stratification of ovarian cancer patients from the prospect of drug target-related transcription factor protein activity: the prognostic and genomic landscape analyses	2
Functional characteristics of DNA N6-methyladenine modification based on long-read sequencing in pancreatic cancer	2
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	2