OOIR: Observatory of International Research

Papers

(The H4-Index of BMC Bioinformatics is 42. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1333
A novel nonparametric computational strategy for identifying differential methylation regions	940
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	268
REDalign: accurate RNA structural alignment using residual encoder-decoder network	218
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	176
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	139
Predictive modeling of gene expression regulation	127
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	100
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	95
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	90
SALON ontology for the formal description of sequence alignments	79
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	77
Abstraction-based segmental simulation of reaction networks using adaptive memoization	71
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	66
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	65
airpg: automatically accessing the inverted repeats of archived plastid genomes	65
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	62
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	60
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	60
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	58
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	57
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	55
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	55
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	55
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	53

PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomics	51
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	50
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	49
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	49
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images	48
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	47
Implementation of machine learning in the clinic: challenges and lessons in prospective deployment from the System for High Intensity EvaLuation During Radiation Therapy (SHIELD-RT) randomized control	47
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	46
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	45
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	44
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	44
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	44
A gene based combination test using GWAS summary data	44
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	43
Multilayer network alignment based on topological assessment via embeddings	43
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon	43
Examination of blood samples using deep learning and mobile microscopy	43
Deep learning and multi-omics approach to predict drug responses in cancer	42
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	42