OOIR: Observatory of International Research

Papers

(The median citation count of Briefings in Functional Genomics is 4. 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 2022-08-01 to 2026-08-01.)

Article	Citations
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	113
Role of gut-microbiota in disease severity and clinical outcomes	62
Environmental community transcriptomics: strategies and struggles	47
Single-cell transcriptomics refuels the exploration of spiralian biology	43
Single-cell RNA-seq data clustering by deep information fusion	34
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	33
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	31
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	30
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	28
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	27
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	25
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	25
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	23
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	22
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	19
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	19
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	19
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	18
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	18
Predicting drug synergy using a network propagation inspired machine learning framework	17
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	17
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	16
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	16
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	14
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	14

amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data	13
Genetically supported mediators linking peripheral metabolism to cerebral ischemia: a multi-omics characterization of HMGCR, TLR4, and MMP9 in angina pectoris and stroke	13
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	13
Multi-omics studies in interpreting the evolving standard model for immune functions	13
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	12
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	12
Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives	11
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	11
NTpred: a robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences	11
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	11
RETRACTED: Integration of single cell multiomics data by deep transfer hypergraph neural network	10
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	10
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	10
Spiralian genomics and the evolution of animal genome architecture	10
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	10
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	10
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	10
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	9
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	9
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	8
High-level RNA editing diversifies the coleoid cephalopod brain proteome	8
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	8
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	8
RETRACTED AND REPLACED: An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Mora	8
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	8
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	8
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	8
MiRNA–gene network embedding for predicting cancer driver genes	8
From bench to bedside: potential of translational research in COVID-19 and beyond	8
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	8
Retraction and replacement of: An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of	7
Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19	7
Targeting novel sites in DNA gyrase for development of anti-microbials	7
Emerging trends in functional genomics in Spiralia	7
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	7
Retraction of: Integration of single cell multiomics data by deep transfer hypergraph neural network	7
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	7
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	7
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	6
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	6
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	6
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	6
pyRforest : a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	6
Molecular insights on the origin and development of waxy genotypes in major crop plants	6
Comparison of scRNA-seq data analysis method combinations	6
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	6
A survey of biclustering and clustering methods in clustering different types of single-cell RNA sequencing data	6
Digital PCR and its applications in noninvasive prenatal testing	6
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	5
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	5

Widespread transcriptomic alterations of transient receptor potential channel genes in cancer	5
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research	5
Unraveling risk factors and transcriptomic signatures in liver cancer progression and mortality through machine learning and bioinformatics	5
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	5
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward	5
Single-cell multi-omics sequencing and its application in tumor heterogeneity	5
Molecular language models: RNNs or transformer?	5
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic	5
Multifactorial feature extraction and site prognosis model for protein methylation data	5
Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods	5
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	5
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers	5
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition	5
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	5
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	5
Gene regulatory network inference based on novel ensemble method	4
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	4
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	4
Genomics in Clinical trials for Breast Cancer	4
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease	4
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	4
Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa?	4