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 2021-12-01 to 2025-12-01.)

Article	Citations
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	56
Single-cell transcriptomics refuels the exploration of spiralian biology	54
Role of gut-microbiota in disease severity and clinical outcomes	47
Environmental community transcriptomics: strategies and struggles	43
Single-cell RNA-seq data clustering by deep information fusion	32
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	28
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	25
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	22
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	22
Comprehensive omics studies of p53 mutants in human cancer	21
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	21
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	21
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	19
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	17
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	15
Functional genomics of ageing: implications of chromatin landscape and beyond	15
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	15
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	13
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	13
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	13
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	13
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	12
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	12
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	12

Predicting drug synergy using a network propagation inspired machine learning framework	12
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	11
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	11
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	10
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	10
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	10
Expanding interactome analyses beyond model eukaryotes	10
amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data	9
Multi-omics studies in interpreting the evolving standard model for immune functions	9
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	8
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	8
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	8
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	8
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	7
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	7
Single-cell sequencing: expansion, integration and translation	7
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	7
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	7
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	7
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	7
Spiralian genomics and the evolution of animal genome architecture	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
Integration of single cell multiomics data by deep transfer hypergraph neural network	7
MiRNA–gene network embedding for predicting cancer driver genes	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
NTpred: a robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences	7
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	7