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 2020-04-01 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
Review of multi-omics data resources and integrative analysis for human brain disorders	18
BioDKG–DDI: predicting drug–drug interactions based on drug knowledge graph fusing biochemical information	18
Pretraining model for biological sequence data	16
The impact of epitranscriptomic marks on post-transcriptional regulation in plants	16
Functional genomics of inflamm-aging and immunosenescence	15
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
Network-based methods for gene function prediction	13
Current status and future prospects of drug–target interaction prediction	13
A systematic review of computational methods for predicting long noncoding RNAs	13
‘Green revolution’ dwarf genesd1of rice has gigantic impact	12
An update: mechanisms of microRNA in primary open-angle glaucoma	11
Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data	11
The non-coding epitranscriptome in cancer	11
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
Non-CpG methylation—a key epigenetic modification in cancer	10

Machine learning approaches for predicting biomolecule–disease associations	10
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
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
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
Seven autophagy-related lncRNAs are associated with the tumor immune microenvironment in predicting survival risk of nonsmall cell lung cancer	8
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
Genome-wide screens in yeast models towards understanding chronological lifespan regulation	7
Digital PCR and its applications in noninvasive prenatal testing	7
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
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
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
Deciphering RNA modifications at base resolution: from chemistry to biology	5
Distinct evolutionary pathways for the synthesis and function of tRNA modifications	5
Targeting novel sites in DNA gyrase for development of anti-microbials	5
Adaptive deep propagation graph neural network for predicting miRNA–disease associations	5
Tau–FG-nucleoporin98 interaction and impaired nucleocytoplasmic transport in Alzheimer’s disease	5
Quantifying transcriptome diversity: a review	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
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations	4
Deep learning tools are top performers in long non-coding RNA prediction	4
From mutation to mechanism: deciphering the molecular function of genetic variants linked to human ageing	4
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review	4
Comprehensive omics studies of p53 mutants in human cancer	4
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	4
Functional long non-coding and circular RNAs in zebrafish	4
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	4
A systematic view of computational methods for identifying driver genes based on somatic mutation data	4
Integrative genomics important to understand host–pathogen interactions	3
Spiralian genomics and the evolution of animal genome architecture	3
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	3
MiRNA–gene network embedding for predicting cancer driver genes	3
An improved hierarchical variational autoencoder for cell–cell communication estimation using single-cell RNA-seq data	3
Accurate prediction and key protein sequence feature identification of cyclins	3
DNA methylation and histone modifications are essential for regulation of stem cell formation and differentiation in zebrafish development	3
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	3
Integrating functional scoring and regulatory data to predict the effect of non-coding SNPs in a complex neurological disease	3

COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	3
Identifying preeclampsia-associated genes using a control theory method	3
Expanding interactome analyses beyond model eukaryotes	3
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	2
Investigating the molecular guts of endoderm formation using zebrafish	2
Molecular insights on the origin and development of waxy genotypes in major crop plants	2
Functional genomics in Spiralia	2
Single-cell multi-omics sequencing and its application in tumor heterogeneity	2
Infection outcome needs two to tango: human host and the pathogen	2
Identification of long noncoding RNAs with machine learning methods: a review	2
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	2
Role of gut-microbiota in disease severity and clinical outcomes	2
Single-cell transcriptomics refuels the exploration of spiralian biology	2
Biophysical and modeling-based approach for the identification of inhibitors against DOHH fromLeishmania donovani	2
Stratification of ovarian cancer patients from the prospect of drug target-related transcription factor protein activity: the prognostic and genomic landscape analyses	2
THGNCDA: circRNA–disease association prediction based on triple heterogeneous graph network	2
Evaluation of tools for taxonomic classification of viruses	2
DeepCMI: a graph-based model for accurate prediction of circRNA–miRNA interactions with multiple information	2
The regulatory role of non-coding RNAs and their interactions with phytochemicals in neurodegenerative diseases: a systematic review	2
Comparative studies on the high-performance compression of SARS-CoV-2 genome collections	2
Depositing annotated sequences in GenBank: there needs to be a better way	2
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	2