OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 66. 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
YaHS: yet another Hi-C scaffolding tool	923
clinker & clustermap.js: automatic generation of gene cluster comparison figures	740
GTDB-Tk v2: memory friendly classification with the genome taxonomy database	552
New strategies to improve minimap2 alignment accuracy	538
Analysing high-throughput sequencing data in Python with HTSeq 2.0	484
Liftoff: accurate mapping of gene annotations	451
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome	434
ProteinBERT: a universal deep-learning model of protein sequence and function	352
LDpred2: better, faster, stronger	350
CAFE 5 models variation in evolutionary rates among gene families	324
STREME: accurate and versatile sequence motif discovery	313
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants	236
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs	231
fastsimcoal2: demographic inference under complex evolutionary scenarios	217
DeepPurpose: a deep learning library for drug–target interaction prediction	198
LocusZoom.js: interactive and embeddable visualization of genetic association study results	190
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization	176
Nebulosa recovers single-cell gene expression signals by kernel density estimation	168
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data	168
ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2	160
Fast and sensitive taxonomic assignment to metagenomic contigs	153
UCSC Cell Browser: visualize your single-cell data	149
Colour deconvolution: stain unmixing in histological imaging	135
propeller:testing for differences in cell type proportions in single cell data	130
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response	129

The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects	122
ShinyCell: simple and sharable visualization of single-cell gene expression data	122
plotsr: visualizing structural similarities and rearrangements between multiple genomes	122
MGIDI: toward an effective multivariate selection in biological experiments	120
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation	116
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data	111
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit	109
Make Interactive Complex Heatmaps in R	107
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python	105
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides	104
MUFFIN: multi-scale feature fusion for drug–drug interaction prediction	104
TITAN: T-cell receptor specificity prediction with bimodal attention networks	104
Accurate, scalable cohort variant calls using DeepVariant and GLnexus	102
SoluProt: prediction of soluble protein expression inEscherichia coli	99
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules	97
Structure-aware protein–protein interaction site prediction using deep graph convolutional network	96
Impact of protein conformational diversity on AlphaFold predictions	95
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation	94
BWA-MEME: BWA-MEM emulated with a machine learning approach	92
Cellsnp-lite: an efficient tool for genotyping single cells	91
HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism	87
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning	84
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization	84
PyMod 3: a complete suite for structural bioinformatics in PyMOL	83
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data	82
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	80
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis	78
Conditional out-of-distribution generation for unpaired data using transfer VAE	76
Protein interaction interface region prediction by geometric deep learning	76
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data	75
Bacteriophage classification for assembled contigs using graph convolutional network	75
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps	74
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping	73
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry	73
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins	72
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts	71
TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding	69
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data	68
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery	68
Humanization of antibodies using a machine learning approach on large-scale repertoire data	68
Mutalyzer 2: next generation HGVS nomenclature checker	66
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction	66