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 2021-08-01 to 2025-08-01.)

Article	Citations
Single-cell transcriptomics refuels the exploration of spiralian biology	44
Role of gut-microbiota in disease severity and clinical outcomes	41
Environmental community transcriptomics: strategies and struggles	38
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	37
Comprehensive omics studies of p53 mutants in human cancer	33
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	29
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	26
Single-cell RNA-seq data clustering by deep information fusion	23
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	21
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	20
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	20
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	20
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	19
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	17
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	16
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	14
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	13
Functional genomics of ageing: implications of chromatin landscape and beyond	12
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	12
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	11
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	11
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	11
Predicting drug synergy using a network propagation inspired machine learning framework	10
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	10
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	10

Expanding interactome analyses beyond model eukaryotes	9
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	9
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	9
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	9
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	9
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	8
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	8
Multi-omics studies in interpreting the evolving standard model for immune functions	8
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	8
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	8
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	8
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	7
Single-cell sequencing: expansion, integration and translation	7
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	7
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	7
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	7
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
Spiralian genomics and the evolution of animal genome architecture	7
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	7
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	7
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	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
MiRNA–gene network embedding for predicting cancer driver genes	6
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	6
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	6
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	6
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	6
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	5
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	5
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	5
Emerging trends in functional genomics in Spiralia	5
High-level RNA editing diversifies the coleoid cephalopod brain proteome	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	4
Targeting novel sites in DNA gyrase for development of anti-microbials	4
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	4
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	4
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	4
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	4
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	4
Digital PCR and its applications in noninvasive prenatal testing	4
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	4
From bench to bedside: potential of translational research in COVID-19 and beyond	4
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	4
Molecular insights on the origin and development of waxy genotypes in major crop plants	4
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	4
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward	3
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	3
Widespread transcriptomic alterations of transient receptor potential channel genes in cancer	3

Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa?	3
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research	3
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition	3
Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods	3
Comparison of scRNA-seq data analysis method combinations	3
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	3
Single-cell multi-omics sequencing and its application in tumor heterogeneity	3
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era	3
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers	3
Multiomics technologies: role in disease biomarker discoveries and therapeutics	3
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	3
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	3
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	3
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic	3
Multifactorial feature extraction and site prognosis model for protein methylation data	3
Molecular language models: RNNs or transformer?	3
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	3
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	3
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations	2
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease	2
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	2
Genomics in Clinical trials for Breast Cancer	2
Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework	2
Prediction of drug–protein interaction based on dual channel neural networks with attention mechanism	2
Enhancer RNA in cancer: identification, expression, resources, relationship with immunity, drugs, and prognosis	2
Exploring the impact of N4-acetylcytidine modification in RNA on non-neoplastic disease: unveiling its role in pathogenesis and therapeutic opportunities	2
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	2
The role of the X chromosome in infectious diseases	2
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	2
DeepCMI: a graph-based model for accurate prediction of circRNA–miRNA interactions with multiple information	2
Microscale marvels: unveiling the macroscopic significance of micropeptides in human health	2
EnsembleSE: identification of super-enhancers based on ensemble learning	2
Integrated multi-cohorts for characterizing the immunogenomic landscape and predicting drug response in triple-negative breast cancer	2
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	2
Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas	2
Long-read RNA sequencing can probe organelle genome pervasive transcription	2
Gene regulatory network inference based on novel ensemble method	2
Genome structural dynamics: insights from Gaussian network analysis of Hi-C data	2
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	2
Multi-omics integration analysis reveals the role of N6-methyladenosine in lncRNA translation during glioma stem cell differentiation	2