OOIR: Observatory of International Research

Papers

(The H4-Index of BMC Bioinformatics is 46. 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 2021-11-01 to 2025-11-01.)

Article	Citations
A novel nonparametric computational strategy for identifying differential methylation regions	1243
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	349
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	274
Abstraction-based segmental simulation of reaction networks using adaptive memoization	249
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	159
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	135
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	105
SALON ontology for the formal description of sequence alignments	98
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	96
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	95
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	95
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	93
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	91
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	82
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	81
REDalign: accurate RNA structural alignment using residual encoder-decoder network	81
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	81
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	80
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	72
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	71
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	70
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	69
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	66
Predictive modeling of gene expression regulation	64
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	62

Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	62
Examination of blood samples using deep learning and mobile microscopy	61
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	58
A gene based combination test using GWAS summary data	56
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	53
Multilayer network alignment based on topological assessment via embeddings	52
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	52
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	52
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	52
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	51
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	50
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	50
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	49
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	49
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	49
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	48
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	47
Mabs, a suite of tools for gene-informed genome assembly	47
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	47
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	46
Deep learning and multi-omics approach to predict drug responses in cancer	46