OOIR: Observatory of International Research

Papers

(The TQCC of Briefings in Functional Genomics is 8. 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 2022-08-01 to 2026-08-01.)

Article	Citations
Experimental and computational methods for studying the dynamics of RNA–RNA interactions in SARS-COV2 genomes	113
Role of gut-microbiota in disease severity and clinical outcomes	62
Environmental community transcriptomics: strategies and struggles	47
Single-cell transcriptomics refuels the exploration of spiralian biology	43
Single-cell RNA-seq data clustering by deep information fusion	34
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome	33
Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases	31
Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning	30
Genome-wide Mendelian randomization and single-cell RNA sequencing analyses identify the causal effects of COVID-19 on 41 cytokines	28
Network-medicine approach for the identification of genetic association of parathyroid adenoma with cardiovascular disease and type-2 diabetes	27
Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research	25
A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules	25
Prediction of strand-specific and cell-type-specific G-quadruplexes based on high-resolution CUT&Tag data	23
Beyond the hype: using AI, big data, wearable devices, and the internet of things for high-throughput livestock phenotyping	22
Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies	19
Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method	19
Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes	19
Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer	18
Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens	18
Predicting drug synergy using a network propagation inspired machine learning framework	17
STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing Klf4 mRNA	17
DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features	16
Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies	16
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data	14
DeepPRMS: advanced deep learning model to predict protein arginine methylation sites	14

amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data	13
Genetically supported mediators linking peripheral metabolism to cerebral ischemia: a multi-omics characterization of HMGCR, TLR4, and MMP9 in angina pectoris and stroke	13
A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data	13
Multi-omics studies in interpreting the evolving standard model for immune functions	13
Correction to: Machine learning applications on intratumoral heterogeneity in glioblastoma using single-cell RNA sequencing data	12
Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning	12
A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs	11
NTpred: a robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences	11
ncRNALocate-EL: a multi-label ncRNA subcellular locality prediction model based on ensemble learning	11
Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives	11
RETRACTED: Integration of single cell multiomics data by deep transfer hypergraph neural network	10
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors	10
A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology	10
Spiralian genomics and the evolution of animal genome architecture	10
m6A RNA modification pathway: orchestrating fibrotic mechanisms across multiple organs	10
Genomic insights into bacteriophages: a new frontier in AMR detection and phage therapy	10
Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization	10
The frontier of precision medicine: application of single-cell multi-omics in preimplantation genetic diagnosis	9
Less is more: relative rank is more informative than absolute abundance for compositional NGS data	9
Correction to: Omics-based deep learning approaches for lung cancer decision-making and therapeutics development	8
High-level RNA editing diversifies the coleoid cephalopod brain proteome	8
Identifying magnetosome-associated genes in the extended CtrA regulon inMagnetospirillum magneticumAMB-1 using a combinational approach	8
Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting	8
RETRACTED AND REPLACED: An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Mora	8
Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification	8
DeepWalk-aware graph attention networks with CNN for circRNA–drug sensitivity association identification	8
Pregnancy-specific glycoproteins as potential drug targets for female lung adenocarcinoma patients	8
MiRNA–gene network embedding for predicting cancer driver genes	8
From bench to bedside: potential of translational research in COVID-19 and beyond	8
Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability	8