OOIR: Observatory of International Research

Papers

(The H4-Index of BMC Bioinformatics is 38. 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 2020-11-01 to 2024-11-01.)

Article	Citations
CellProfiler 4: improvements in speed, utility and usability	914
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads	558
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants	294
So you think you can PLS-DA?	199
Statistical power for cluster analysis	164
TSEBRA: transcript selector for BRAKER	130
Prediction of liquid–liquid phase separating proteins using machine learning	103
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes	100
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction	94
Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm	90
Evaluation of a decided sample size in machine learning applications	87
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data	86
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models	82
COPLA, a taxonomic classifier of plasmids	78
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules	72
PyClone-VI: scalable inference of clonal population structures using whole genome data	69
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	68
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes	67
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images	62
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography	62
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations	57
Correlation AnalyzeR: functional predictions from gene co-expression correlations	55
MiBiOmics: an interactive web application for multi-omics data exploration and integration	54
Selecting single cell clustering parameter values using subsampling-based robustness metrics	54
Application of network link prediction in drug discovery	51

Hypergraph models of biological networks to identify genes critical to pathogenic viral response	51
SAveRUNNER: an R-based tool for drug repurposing	46
SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost	46
Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides	45
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets	45
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses	45
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks	44
IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier	43
Consensus clustering applied to multi-omics disease subtyping	43
Deep learning detection of informative features in tau PET for Alzheimer’s disease classification	42
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data	42
A novel essential protein identification method based on PPI networks and gene expression data	40
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions	40
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing	38
Optimal dimensionality selection for independent component analysis of transcriptomic data	38
Convolutional neural network for automated mass segmentation in mammography	38
TMbed: transmembrane proteins predicted through language model embeddings	38
High expression of cuproptosis-related SLC31A1 gene in relation to unfavorable outcome and deregulated immune cell infiltration in breast cancer: an analysis based on public databases	38