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 2022-01-01 to 2026-01-01.)

Article	Citations
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	59
Single-cell transcriptomics refuels the exploration of spiralian biology	57
Role of gut-microbiota in disease severity and clinical outcomes	55
Environmental community transcriptomics: strategies and struggles	44
Single-cell RNA-seq data clustering by deep information fusion	34
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	30
Comprehensive omics studies of p53 mutants in human cancer	26
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	25
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	23
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	22
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	22
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	21
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	21
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	19
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	19
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	17
Functional genomics of ageing: implications of chromatin landscape and beyond	16
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	15
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	14
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	14
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	13
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	13
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	13
Predicting drug synergy using a network propagation inspired machine learning framework	12
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	12

DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	12
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	12
Expanding interactome analyses beyond model eukaryotes	12
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	11
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	11
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	11
amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data	10
Multi-omics studies in interpreting the evolving standard model for immune functions	10
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	10
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	9
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	8
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	8
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	8
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	8
Single-cell sequencing: expansion, integration and translation	8
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	8
NTpred: a robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences	8
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	8
Spiralian genomics and the evolution of animal genome architecture	8
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
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	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	7
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	7
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	7
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	7
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	7
A survey on protein–DNA-binding sites in computational biology	7
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	7
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	6
High-level RNA editing diversifies the coleoid cephalopod brain proteome	6
Emerging trends in functional genomics in Spiralia	6
MiRNA–gene network embedding for predicting cancer driver genes	6
Molecular insights on the origin and development of waxy genotypes in major crop plants	5
Comparison of scRNA-seq data analysis method combinations	5
From bench to bedside: potential of translational research in COVID-19 and beyond	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
Targeting novel sites in DNA gyrase for development of anti-microbials	5
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	5
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	5
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	5
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	5
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	5
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	5
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	5
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	5
A survey of biclustering and clustering methods in clustering different types of single-cell RNA sequencing data	5
pyRforest : a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	4

Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	4
Digital PCR and its applications in noninvasive prenatal testing	4
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	4
Molecular language models: RNNs or transformer?	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
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	4
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era	4
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward	4
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	4
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	4
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers	4
Single-cell multi-omics sequencing and its application in tumor heterogeneity	4
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	4
Gene regulatory network inference based on novel ensemble method	3
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition	3
Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas	3
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic	3
Exploring the impact of N4-acetylcytidine modification in RNA on non-neoplastic disease: unveiling its role in pathogenesis and therapeutic opportunities	3
Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework	3
Long-read RNA sequencing can probe organelle genome pervasive transcription	3
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	3
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	3
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research	3
Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa?	3
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	3
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations	3
Genomics in Clinical trials for Breast Cancer	3
INTS7 modulates cell proliferation and apoptosis via promoting cell cycle progression in lung adenocarcinoma	3
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	3
Multifactorial feature extraction and site prognosis model for protein methylation data	3
Widespread transcriptomic alterations of transient receptor potential channel genes in cancer	3
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease	3
Multi-omics integration analysis reveals the role of N6-methyladenosine in lncRNA translation during glioma stem cell differentiation	3
DeepCMI: a graph-based model for accurate prediction of circRNA–miRNA interactions with multiple information	3
Microscale marvels: unveiling the macroscopic significance of micropeptides in human health	3