Briefings in Functional Genomics

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.)
ArticleCitations
Single-cell transcriptomics refuels the exploration of spiralian biology42
Role of gut-microbiota in disease severity and clinical outcomes37
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes36
Environmental community transcriptomics: strategies and struggles33
Comprehensive omics studies of p53 mutants in human cancer30
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing27
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning27
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome26
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases22
Single-cell RNA-seq data clustering by deep information fusion21
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells20
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data19
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping18
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research18
Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish18
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines16
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes15
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules14
Functional genomics of ageing: implications of chromatin landscape and beyond13
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer12
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes12
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies11
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method11
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens11
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies10
Predicting drug synergy using a network propagation inspired machine learning framework10
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA10
Review of multi-omics data resources and integrative analysis for human brain disorders9
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features9
Expanding interactome analyses beyond model eukaryotes9
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites9
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data8
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis8
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data8
Multi-omics studies in interpreting the evolving standard model for immune functions8
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference7
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs7
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research7
Single-cell sequencing: expansion, integration and translation7
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data7
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning7
Spiralian genomics and the evolution of animal genome architecture7
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs7
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences7
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning6
Non-CpG methylation—a key epigenetic modification in cancer6
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors6
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology6
Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review6
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis5
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability5
Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design5
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development5
High-level RNA editing diversifies the coleoid cephalopod brain proteome5
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients5
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis5
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting5
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification5
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification5
Less is more: relative rank is more informative than absolute abundance for compositional NGS data5
A survey on protein–DNA-binding sites in computational biology4
Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe4
Targeting novel sites in DNA gyrase for development of anti-microbials4
Emerging trends in functional genomics in Spiralia4
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach4
A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens4
Pretraining model for biological sequence data4
MiRNA–gene network embedding for predicting cancer driver genes4
Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-194
A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes4
From bench to bedside: potential of translational research in COVID-19 and beyond4
Promoter–motif extraction from co-regulated genes and their relevance to co-expression usingE. colias a model3
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants3
Comparison of scRNA-seq data analysis method combinations3
Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation3
Digital PCR and its applications in noninvasive prenatal testing3
RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features3
Current status and future prospects of drug–target interaction prediction3
Multiomics technologies: role in disease biomarker discoveries and therapeutics3
Molecular insights on the origin and development of waxy genotypes in major crop plants3
iEnhancer-SKNN: a stacking ensemble learning-based method for enhancer identification and classification using sequence information3
pyRforest: a comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R3
miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma3
iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features2
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases2
Genomics in Clinical trials for Breast Cancer2
SCMcluster: a high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data2
Widespread transcriptomic alterations of transient receptor potential channel genes in cancer2
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era2
Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories2
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers2
Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease2
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data2
Multifactorial feature extraction and site prognosis model for protein methylation data2
An overview of key online resources for human genomics: a powerful and open toolbox for in silico research2
Single-cell multi-omics sequencing and its application in tumor heterogeneity2
Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward2
Detecting early-warning signals for influenza by dysregulated dynamic network biomarkers2
Significance of understanding the genomics of host–pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic2
The role of the X chromosome in infectious diseases2
Gene regulatory network inference based on novel ensemble method2
Integrating multi-omics data to analyze the potential pathogenic mechanism of CTSH gene involved in type 1 diabetes in the exocrine pancreas2
Molecular language models: RNNs or transformer?2
SAMP: Identifying antimicrobial peptides by an ensemble learning model based on proportionalized split amino acid composition2
Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine2
Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods2
Correction to: STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA2
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 leukemia2
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