OOIR: Observatory of International Research

Papers

(The H4-Index of BMC Bioinformatics is 42. 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 2020-03-01 to 2024-03-01.)

Article	Citations
CellProfiler 4: improvements in speed, utility and usability	561
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads	253
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants	244
PACVr: plastome assembly coverage visualization in R	217
So you think you can PLS-DA?	164
Statistical power for cluster analysis	100
TSEBRA: transcript selector for BRAKER	88
DPDDI: a deep predictor for drug-drug interactions	88
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data	86
Prediction of heart disease and classifiers’ sensitivity analysis	84
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction	78
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes	74
Prediction of liquid–liquid phase separating proteins using machine learning	73
Graph-based prediction of Protein-protein interactions with attributed signed graph embedding	72
Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm	67
COPLA, a taxonomic classifier of plasmids	64
MethylNet: an automated and modular deep learning approach for DNA methylation analysis	64
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data	63
Conditional permutation importance revisited	60
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules	59
PyClone-VI: scalable inference of clonal population structures using whole genome data	57
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models	56
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads	54
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes	54
Broad-coverage biomedical relation extraction with SemRep	51

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets	51
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography	51
Amino acid encoding for deep learning applications	50
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis	49
A random forest based computational model for predicting novel lncRNA-disease associations	48
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	47
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network	47
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data	46
Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies	46
NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis	45
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations	45
VADR: validation and annotation of virus sequence submissions to GenBank	45
MiBiOmics: an interactive web application for multi-omics data exploration and integration	44
DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	44
Correlation AnalyzeR: functional predictions from gene co-expression correlations	44
Keras R-CNN: library for cell detection in biological images using deep neural networks	44
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images	43
SAveRUNNER: an R-based tool for drug repurposing	42
Selecting single cell clustering parameter values using subsampling-based robustness metrics	42