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 2021-05-01 to 2025-05-01.)

Article	Citations
Single-cell transcriptomics refuels the exploration of spiralian biology	42
Role of gut-microbiota in disease severity and clinical outcomes	37
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	36
Environmental community transcriptomics: strategies and struggles	33
Comprehensive omics studies of p53 mutants in human cancer	30
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	27
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	27
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	26
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	22
Single-cell RNA-seq data clustering by deep information fusion	21
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	20
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	19
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	18
Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish	18
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	18
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	16
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	15
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	14
Functional genomics of ageing: implications of chromatin landscape and beyond	13
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	12
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	12
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	11
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	11
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	11
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	10

Predicting drug synergy using a network propagation inspired machine learning framework	10
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	10
Expanding interactome analyses beyond model eukaryotes	9
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	9
Review of multi-omics data resources and integrative analysis for human brain disorders	9
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	9
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
Multi-omics studies in interpreting the evolving standard model for immune functions	8
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	8
Single-cell sequencing: expansion, integration and translation	7
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	7
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	7
Spiralian genomics and the evolution of animal genome architecture	7
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	7
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	7
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	7
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	7
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	6
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	6
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review	6
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	6
Non-CpG methylation—a key epigenetic modification in cancer	6
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	5
High-level RNA editing diversifies the coleoid cephalopod brain proteome	5
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	5
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	5
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	5
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	5
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	5
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	5
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	5
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	5
Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design	5
Emerging trends in functional genomics in Spiralia	4
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	4
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens	4
Pretraining model for biological sequence data	4
MiRNA–gene network embedding for predicting cancer driver genes	4
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
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes	4
From bench to bedside: potential of translational research in COVID-19 and beyond	4
A survey on protein–DNA-binding sites in computational biology	4
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe	4
Targeting novel sites in DNA gyrase for development of anti-microbials	4
Digital PCR and its applications in noninvasive prenatal testing	3
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features	3
Current status and future prospects of drug–target interaction prediction	3
Multiomics technologies: role in disease biomarker discoveries and therapeutics	3

Molecular insights on the origin and development of waxy genotypes in major crop plants	3
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information	3
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R	3
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma	3
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model	3
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants	3
Comparison of scRNA-seq data analysis method combinations	3
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation	3
The role of the X chromosome in infectious diseases	2
Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas	2
Multifactorial feature extraction and site prognosis model for protein methylation data	2
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition	2
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine	2
Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods	2
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	2
Advancing disease genomics beyond COVID-19 and reducing health disparities: what does the future hold for Africa?	2
Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia	2
Gene regulatory network inference based on novel ensemble method	2
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases	2
Molecular language models: RNNs or transformer?	2
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data	2
Widespread transcriptomic alterations of transient receptor potential channel genes in cancer	2
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era	2
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories	2
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers	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
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features	2
Genomics in Clinical trials for Breast Cancer	2
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research	2
Single-cell multi-omics sequencing and its application in tumor heterogeneity	2
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward	2
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers	2
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic	2