OOIR: Observatory of International Research

Papers

(The H4-Index of BMC Bioinformatics is 45. 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 2021-09-01 to 2025-09-01.)

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1511
A novel nonparametric computational strategy for identifying differential methylation regions	1105
REDalign: accurate RNA structural alignment using residual encoder-decoder network	317
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	253
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	213
Predictive modeling of gene expression regulation	151
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	132
SALON ontology for the formal description of sequence alignments	95
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	86
Abstraction-based segmental simulation of reaction networks using adaptive memoization	86
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	85
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	85
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	83
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	77
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	73
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	72
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	70
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	69
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	67
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	63
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	62
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	60
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	59
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	59
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	58

CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	57
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	54
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	53
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	53
Multilayer network alignment based on topological assessment via embeddings	53
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	52
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	51
Mabs, a suite of tools for gene-informed genome assembly	50
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	50
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	50
A gene based combination test using GWAS summary data	47
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	46
Examination of blood samples using deep learning and mobile microscopy	46
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	46
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	46
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	46
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	45
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	45
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	45
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	45