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 2020-05-01 to 2024-05-01.)

Article	Citations
Prediction of bio-sequence modifications and the associations with diseases	64
Sequence representation approaches for sequence-based protein prediction tasks that use deep learning	37
Critical evaluation of web-based DNA N6-methyladenine site prediction tools	28
Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective	27
Review of unsupervised pretraining strategies for molecules representation	22
The functional impact of nuclear reorganization in cellular senescence	21
Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies	21
A comprehensive review for gut microbes: technologies, interventions, metabolites and diseases	19
BioDKG–DDI: predicting drug–drug interactions based on drug knowledge graph fusing biochemical information	19
Review of multi-omics data resources and integrative analysis for human brain disorders	18
Functional genomics of inflamm-aging and immunosenescence	17
Pretraining model for biological sequence data	17
Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design	16
The impact of epitranscriptomic marks on post-transcriptional regulation in plants	16
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	15
A systematic review of computational methods for predicting long noncoding RNAs	13
Network-based methods for gene function prediction	13
Current status and future prospects of drug–target interaction prediction	13
‘Green revolution’ dwarf genesd1of rice has gigantic impact	12
The non-coding epitranscriptome in cancer	11
Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	11
An update: mechanisms of microRNA in primary open-angle glaucoma	11
Non-CpG methylation—a key epigenetic modification in cancer	11
Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data	11
A survey on protein–DNA-binding sites in computational biology	10

Machine learning approaches for predicting biomolecule–disease associations	10
Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors	10
Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledge	10
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	10
Noncoding RNAs: modulators and modulatable players during infection-induced stress response	9
Single-cell transcriptomics allows novel insights into aging and circadian processes	9
Application of omics research in seaweeds with a focus on red seaweeds	9
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research	9
Seven autophagy-related lncRNAs are associated with the tumor immune microenvironment in predicting survival risk of nonsmall cell lung cancer	8
Computational resources for identification of cancer biomarkers from omics data	8
Multifactorial feature extraction and site prognosis model for protein methylation data	8
Digital PCR and its applications in noninvasive prenatal testing	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
Single-cell sequencing: expansion, integration and translation	7
Genome-wide screens in yeast models towards understanding chronological lifespan regulation	7
Flipping the script: viral capitalization of RNA modifications	6
Emerging roles of RNA modifications in genome integrity	6
The role of the X chromosome in infectious diseases	6
PGRNIG: novel parallel gene regulatory network identification algorithm based on GPU	6
Multiomics technologies: role in disease biomarker discoveries and therapeutics	6
Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present	6
Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging	6
Adaptive deep propagation graph neural network for predicting miRNA–disease associations	5
Targeting novel sites in DNA gyrase for development of anti-microbials	5
Deep learning tools are top performers in long non-coding RNA prediction	5
Integrative analyses of transcriptome data reveal the mechanisms of post-transcriptional regulation	5
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	5
Functional long non-coding and circular RNAs in zebrafish	5
Distinct evolutionary pathways for the synthesis and function of tRNA modifications	5
Tau–FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer’s disease	5
Deciphering RNA modifications at base resolution: from chemistry to biology	5