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 2020-04-01 to 2024-04-01.)

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	34
Critical evaluation of web-based DNA N6-methyladenine site prediction tools	28
Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective	27
Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies	21
The functional impact of nuclear reorganization in cellular senescence	21
Review of unsupervised pretraining strategies for molecules representation	20
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	18
Review of multi-omics data resources and integrative analysis for human brain disorders	18
The impact of epitranscriptomic marks on post-transcriptional regulation in plants	16
Pretraining model for biological sequence data	16
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	15
Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design	15
Functional genomics of inflamm-aging and immunosenescence	15
Current status and future prospects of drug–target interaction prediction	13
A systematic review of computational methods for predicting long noncoding RNAs	13
Network-based methods for gene function prediction	13
‘Green revolution’ dwarf genesd1of rice has gigantic impact	12
Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data	11
The non-coding epitranscriptome in cancer	11
An update: mechanisms of microRNA in primary open-angle glaucoma	11
Non-CpG methylation—a key epigenetic modification in cancer	10
Machine learning approaches for predicting biomolecule–disease associations	10
A survey on protein–DNA-binding sites in computational biology	10

Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledge	10
Application of omics research in seaweeds with a focus on red seaweeds	9
Single-cell transcriptomics allows novel insights into aging and circadian processes	9
Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	9
Noncoding RNAs: modulators and modulatable players during infection-induced stress response	9
Seven autophagy-related lncRNAs are associated with the tumor immune microenvironment in predicting survival risk of nonsmall cell lung cancer	8
Single-cell RNA sequencing analyses: interference by the genes that encode the B-cell and T-cell receptors	8
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	8
Multifactorial feature extraction and site prognosis model for protein methylation data	8
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research	8
Genome-wide screens in yeast models towards understanding chronological lifespan regulation	7
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
Computational resources for identification of cancer biomarkers from omics data	7
Single-cell sequencing: expansion, integration and translation	7
Multiomics technologies: role in disease biomarker discoveries and therapeutics	6
Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging	6
Flipping the script: viral capitalization of RNA modifications	6
Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present	6
The role of the X chromosome in infectious diseases	6
PGRNIG: novel parallel gene regulatory network identification algorithm based on GPU	6
Emerging roles of RNA modifications in genome integrity	6