OOIR: Observatory of International Research

Papers

(The H4-Index of BMC Bioinformatics is 48. 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 2022-05-01 to 2026-05-01.)

Article	Citations
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	1532
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	446
SALON ontology for the formal description of sequence alignments	331
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	162
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	137
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	130
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	119
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	118
A two-phase clustering procedure based on allele specific expression	117
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	116
Machine learning for multi-omics data integration in crop improvement: a systematic review	111
Mabs, a suite of tools for gene-informed genome assembly	102
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	101
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	99
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	95
REDalign: accurate RNA structural alignment using residual encoder-decoder network	92
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	88
Deep learning and multi-omics approach to predict drug responses in cancer	72
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	71
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	71
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	70
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	70
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	67
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	67
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	67

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	65
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	65
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	64
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	63
Multilayer network alignment based on topological assessment via embeddings	62
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	62
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	61
A comparative analysis of topological domain callers over RNA-associated interactome	61
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation	60
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	60
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	59
A gene based combination test using GWAS summary data	56
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	54
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	54
Abstraction-based segmental simulation of reaction networks using adaptive memoization	53
SVhound: detection of regions that harbor yet undetected structural variation	52
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	52
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	52
DiseaseNet: a transfer learning approach to noncommunicable disease classification	51
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	51
Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples	51
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	48
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	48
BADASS: BActeriocin-Diversity ASsessment Software	48