OOIR: Observatory of International Research

Papers

(The TQCC of Briefings in Functional Genomics is 6. 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
The non-coding epitranscriptome in cancer	12
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
Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors	11

A survey on protein–DNA-binding sites in computational biology	11
Application of omics research in seaweeds with a focus on red seaweeds	10
Computational resources for identification of cancer biomarkers from omics data	9
Single-cell sequencing: expansion, integration and translation	9
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
Tau–FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer’s disease	8
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
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
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
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