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 2022-08-01 to 2026-08-01.)

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1670
SALON ontology for the formal description of sequence alignments	378
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	177
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	161
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	147
REDalign: accurate RNA structural alignment using residual encoder-decoder network	136
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	134
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	133
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	129
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	128
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	122
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	119
A two-phase clustering procedure based on allele specific expression	117
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	113
A gene based combination test using GWAS summary data	96
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	92
Abstraction-based segmental simulation of reaction networks using adaptive memoization	80
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	79
A comparative analysis of topological domain callers over RNA-associated interactome	77
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	77
Multilayer network alignment based on topological assessment via embeddings	76
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	75
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	73
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	72
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	72

Deep learning and multi-omics approach to predict drug responses in cancer	70
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	70
Machine learning for multi-omics data integration in crop improvement: a systematic review	67
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	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
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	65
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	64
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation	64
Mabs, a suite of tools for gene-informed genome assembly	61
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	59
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	59
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	58
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	57
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	57
SVhound: detection of regions that harbor yet undetected structural variation	57
INFLECT: an R-package for cytometry cluster evaluation using marker modality	56
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	56
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis	53
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	53
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	52
False discovery rate estimation using candidate peptides for each spectrum	50
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	50
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	50
BADASS: BActeriocin-Diversity ASsessment Software	48