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 2022-05-01 to 2026-05-01.)

Article	Citations
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	93
Environmental community transcriptomics: strategies and struggles	71
Role of gut-microbiota in disease severity and clinical outcomes	60
Single-cell transcriptomics refuels the exploration of spiralian biology	39
Single-cell RNA-seq data clustering by deep information fusion	38
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	28
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	27
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	26
Comprehensive omics studies of p53 mutants in human cancer	26
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	25
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	24
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	24
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	23
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	22
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	21
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	18
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	18
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	17
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	16
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	16
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	16
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	15
Predicting drug synergy using a network propagation inspired machine learning framework	15
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	15
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	14

Expanding interactome analyses beyond model eukaryotes	14
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	14
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	13
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	12
amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data	12
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	12
Multi-omics studies in interpreting the evolving standard model for immune functions	12
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	11
Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives	11
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	10
NTpred: a robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences	10
Spiralian genomics and the evolution of animal genome architecture	10
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	10
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	10
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	10
Single-cell sequencing: expansion, integration and translation	10
RETRACTED: Integration of single cell multiomics data by deep transfer hypergraph neural network	9
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	9
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	8
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	8
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	8
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	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
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	8
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	8
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	8
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	7
A survey on protein–DNA-binding sites in computational biology	7
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	7
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	7
High-level RNA editing diversifies the coleoid cephalopod brain proteome	7
MiRNA–gene network embedding for predicting cancer driver genes	7
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	7
Retraction of: Integration of single cell multiomics data by deep transfer hypergraph neural network	6
Emerging trends in functional genomics in Spiralia	6
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	6
From bench to bedside: potential of translational research in COVID-19 and beyond	6
Retraction and replacement of: An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of	6
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	6
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	6
Targeting novel sites in DNA gyrase for development of anti-microbials	6
Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19	6
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	6
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	6
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	5
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	5
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	5
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	5
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	5
Molecular insights on the origin and development of waxy genotypes in major crop plants	5

Comparison of scRNA-seq data analysis method combinations	5
pyRforest : a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	5
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	5
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	5
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	5
A survey of biclustering and clustering methods in clustering different types of single-cell RNA sequencing data	5
Digital PCR and its applications in noninvasive prenatal testing	5
Multiomics technologies: role in disease biomarker discoveries and therapeutics	5
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward	5
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	5
Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods	5
Single-cell multi-omics sequencing and its application in tumor heterogeneity	4
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers	4
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data	4
Unraveling risk factors and transcriptomic signatures in liver cancer progression and mortality through machine learning and bioinformatics	4
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	4
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic	4
Widespread transcriptomic alterations of transient receptor potential channel genes in cancer	4
Molecular language models: RNNs or transformer?	4
Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa?	4
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease	4
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition	4
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research	4
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	4
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	4
Multifactorial feature extraction and site prognosis model for protein methylation data	4