OOIR: Observatory of International Research

Papers

(The median citation count of Briefings in Functional Genomics is 3. 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 2021-11-01 to 2025-11-01.)

Article	Citations
Environmental community transcriptomics: strategies and struggles	50
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	49
Single-cell transcriptomics refuels the exploration of spiralian biology	43
Role of gut-microbiota in disease severity and clinical outcomes	40
Single-cell RNA-seq data clustering by deep information fusion	28
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	27
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	24
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	24
Comprehensive omics studies of p53 mutants in human cancer	22
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	22
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	21
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	21
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	21
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	17
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	15
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	14
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	13
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	13
Functional genomics of ageing: implications of chromatin landscape and beyond	13
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	12
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	12
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	12
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	12
Predicting drug synergy using a network propagation inspired machine learning framework	11
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	11

STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	11
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	11
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	10
Expanding interactome analyses beyond model eukaryotes	10
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	9
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	9
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	9
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	9
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	8
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	8
Multi-omics studies in interpreting the evolving standard model for immune functions	8
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	8
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	8
Spiralian genomics and the evolution of animal genome architecture	7
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	7
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	7
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	7
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	7
MiRNA–gene network embedding for predicting cancer driver genes	7
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	7
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	7
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	7
Integration of single cell multiomics data by deep transfer hypergraph neural network	7
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	7
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	7
Single-cell sequencing: expansion, integration and translation	7
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	6
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	6
A survey on protein–DNA-binding sites in computational biology	6
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	6
High-level RNA editing diversifies the coleoid cephalopod brain proteome	6
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	6
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	5
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	5
Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19	5
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	5
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	5
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	5
Emerging trends in functional genomics in Spiralia	5
From bench to bedside: potential of translational research in COVID-19 and beyond	5
Targeting novel sites in DNA gyrase for development of anti-microbials	5
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	4
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	4
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	4
Multiomics technologies: role in disease biomarker discoveries and therapeutics	4
Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods	4
A survey of biclustering and clustering methods in clustering different types of single-cell RNA sequencing data	4
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	4

Comparison of scRNA-seq data analysis method combinations	4
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	4
Molecular insights on the origin and development of waxy genotypes in major crop plants	4
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	4
Digital PCR and its applications in noninvasive prenatal testing	4
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	4
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	3
Widespread transcriptomic alterations of transient receptor potential channel genes in cancer	3
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition	3
Multifactorial feature extraction and site prognosis model for protein methylation data	3
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	3
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers	3
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic	3
Molecular language models: RNNs or transformer?	3
Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa?	3
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era	3
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	3
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward	3
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	3
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research	3
Single-cell multi-omics sequencing and its application in tumor heterogeneity	3
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	3