OOIR: Observatory of International Research

Papers

(The TQCC of Briefings in Functional Genomics is 6. 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 2021-08-01 to 2025-08-01.)

Article	Citations
Single-cell transcriptomics refuels the exploration of spiralian biology	44
Role of gut-microbiota in disease severity and clinical outcomes	41
Environmental community transcriptomics: strategies and struggles	38
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	37
Comprehensive omics studies of p53 mutants in human cancer	33
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing	29
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	26
Single-cell RNA-seq data clustering by deep information fusion	23
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	21
Revisiting hematopoiesis: applications of the bulk and single-cell transcriptomics dissecting transcriptional heterogeneity in hematopoietic stem cells	20
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	20
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	20
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	19
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	17
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	16
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	14
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	13
Functional genomics of ageing: implications of chromatin landscape and beyond	12
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	12
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	11
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	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
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	10

Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	9
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	9
Expanding interactome analyses beyond model eukaryotes	9
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	9
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	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
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	8
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	8
Multi-omics studies in interpreting the evolving standard model for immune functions	8
NTpred: a robust and precise machine learning framework forin silicoidentification of Tyrosine nitration sites in protein sequences	8
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	7
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	7
Single-cell sequencing: expansion, integration and translation	7
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	7
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	7
A systematic evaluation of the computational tools for ligand-receptor-based cell–cell interaction inference	7
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	7
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	7
Spiralian genomics and the evolution of animal genome architecture	7
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	7
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	6
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	6
A survey on protein–DNA-binding sites in computational biology	6
MiRNA–gene network embedding for predicting cancer driver genes	6
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	6
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	6
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	6
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis	6