OOIR: Observatory of International Research

Papers

(The TQCC of Briefings in Functional Genomics is 7. 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 2021-11-01 to 2025-11-01.)

Article	Citations
Environmental community transcriptomics: strategies and struggles	50
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	49
Single-cell transcriptomics refuels the exploration of spiralian biology	43
Role of gut-microbiota in disease severity and clinical outcomes	40
Single-cell RNA-seq data clustering by deep information fusion	28
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	27
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	24
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	24
Comprehensive omics studies of p53 mutants in human cancer	22
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	22
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	21
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	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	17
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	15
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	14
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	13
Functional genomics of ageing: implications of chromatin landscape and beyond	13
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	13
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	12
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	12
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	12
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	12
Predicting drug synergy using a network propagation inspired machine learning framework	11
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	11

STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	11
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	11
Expanding interactome analyses beyond model eukaryotes	10
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	10
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	9
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	9
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis	9
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	9
Multi-omics studies in interpreting the evolving standard model for immune functions	8
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	8
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	8
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	8
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	8
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	7
MiRNA–gene network embedding for predicting cancer driver genes	7
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	7
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	7
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	7
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
Single-cell sequencing: expansion, integration and translation	7
Spiralian genomics and the evolution of animal genome architecture	7
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	7
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	7
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	7