OOIR: Observatory of International Research

Papers

(The H4-Index of Bioinformatics is 67. 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 2020-06-01 to 2024-06-01.)

Article	Citations
clinker & clustermap.js: automatic generation of gene cluster comparison figures	599
YaHS: yet another Hi-C scaffolding tool	535
GraphDTA: predicting drug–target binding affinity with graph neural networks	383
Analysing high-throughput sequencing data in Python with HTSeq 2.0	381
New strategies to improve minimap2 alignment accuracy	365
Liftoff: accurate mapping of gene annotations	356
GTDB-Tk v2: memory friendly classification with the genome taxonomy database	343
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome	317
LDpred2: better, faster, stronger	277
CoV-AbDab: the coronavirus antibody database	270
STREME: accurate and versatile sequence motif discovery	258
pyGenomeTracks: reproducible plots for multivariate genomic datasets	253
CAFE 5 models variation in evolutionary rates among gene families	246
ProteinBERT: a universal deep-learning model of protein sequence and function	236
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants	200
MolTrans: Molecular Interaction Transformer for drug–target interaction prediction	187
DeepPurpose: a deep learning library for drug–target interaction prediction	175
fastsimcoal2: demographic inference under complex evolutionary scenarios	169
LocusZoom.js: interactive and embeddable visualization of genetic association study results	155
Dream: powerful differential expression analysis for repeated measures designs	149
Nebulosa recovers single-cell gene expression signals by kernel density estimation	136
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data	131
UCSC Cell Browser: visualize your single-cell data	119
Fast and sensitive taxonomic assignment to metagenomic contigs	117
Weighted minimizer sampling improves long read mapping	117

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization	112
Colour deconvolution: stain unmixing in histological imaging	109
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response	105
COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19	104
Unsupervised topological alignment for single-cell multi-omics integration	98
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning	97
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects	97
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python	97
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit	96
ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2	96
ShinyCell: simple and sharable visualization of single-cell gene expression data	95
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation	94
MUFFIN: multi-scale feature fusion for drug–drug interaction prediction	90
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides	90
MGIDI: toward an effective multivariate selection in biological experiments	90
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data	89
TITAN: T-cell receptor specificity prediction with bimodal attention networks	87
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores	87
plotsr: visualizing structural similarities and rearrangements between multiple genomes	86
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees	86
LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM	85
Predicting human microbe–drug associations via graph convolutional network with conditional random field	84
DNA Features Viewer: a sequence annotation formatting and plotting library for Python	84
Accurate, scalable cohort variant calls using DeepVariant and GLnexus	83
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data	82
Fast gap-affine pairwise alignment using the wavefront algorithm	82
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation	81
HiSCF: leveraging higher-order structures for clustering analysis in biological networks	81
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control	80
methylclock: a Bioconductor package to estimate DNA methylation age	80
propeller: testing for differences in cell type proportions in single cell data	78
SoluProt: prediction of soluble protein expression in Escherichia coli	75
Structure-aware protein–protein interaction site prediction using deep graph convolutional network	74
Make Interactive Complex Heatmaps in R	73
Protein interaction interface region prediction by geometric deep learning	71
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser	70
DELPHI: accurate deep ensemble model for protein interaction sites prediction	70
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules	70
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization	69
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function	69
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference	68
PyMod 3: a complete suite for structural bioinformatics in PyMOL	68
Impact of protein conformational diversity on AlphaFold predictions	67
GraphQA: protein model quality assessment using graph convolutional networks	67
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis	67
HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism	67