Bioinformatics

Article	Citations
clinker & clustermap.js: automatic generation of gene cluster comparison figures	551
YaHS: yet another Hi-C scaffolding tool	435
GraphDTA: predicting drug–target binding affinity with graph neural networks	350
Analysing high-throughput sequencing data in Python with HTSeq 2.0	332
Liftoff: accurate mapping of gene annotations	320
New strategies to improve minimap2 alignment accuracy	302
GTDB-Tk v2: memory friendly classification with the genome taxonomy database	278
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome	275
CoV-AbDab: the coronavirus antibody database	258
LDpred2: better, faster, stronger	247
STREME: accurate and versatile sequence motif discovery	235
pyGenomeTracks: reproducible plots for multivariate genomic datasets	228
CAFE 5 models variation in evolutionary rates among gene families	221
A multimodal deep learning framework for predicting drug–drug interaction events	196
ProteinBERT: a universal deep-learning model of protein sequence and function	194
TransformerCPI: improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments	188
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants	185
DeepPurpose: a deep learning library for drug–target interaction prediction	166
MolTrans: Molecular Interaction Transformer for drug–target interaction prediction	166
fastsimcoal2: demographic inference under complex evolutionary scenarios	148
Metaviral SPAdes: assembly of viruses from metagenomic data	146
LocusZoom.js: interactive and embeddable visualization of genetic association study results	143
HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation	140
Dream: powerful differential expression analysis for repeated measures designs	134
Nebulosa recovers single-cell gene expression signals by kernel density estimation	126

scVAE: variational auto-encoders for single-cell gene expression data	126
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data	118
DeepCDA: deep cross-domain compound–protein affinity prediction through LSTM and convolutional neural networks	113
Weighted minimizer sampling improves long read mapping	110
Fast and sensitive taxonomic assignment to metagenomic contigs	108
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes	104
UCSC Cell Browser: visualize your single-cell data	104
GenMap: ultra-fast computation of genome mappability	103
COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19	100
Colour deconvolution: stain unmixing in histological imaging	98
Unsupervised topological alignment for single-cell multi-omics integration	96
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response	95
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization	89
MUFFIN: multi-scale feature fusion for drug–drug interaction prediction	88
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning	88
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects	88
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python	88
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data	84
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation	84
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit	83
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides	82
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores	80
Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus	80
ShinyCell: simple and sharable visualization of single-cell gene expression data	80
Learning context-aware structural representations to predict antigen and antibody binding interfaces	79
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees	78
DNA Features Viewer: a sequence annotation formatting and plotting library for Python	78
MGIDI: toward an effective multivariate selection in biological experiments	77
LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM	77
ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2	77
Predicting human microbe–drug associations via graph convolutional network with conditional random field	77
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control	76
HiSCF: leveraging higher-order structures for clustering analysis in biological networks	76
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation	75
Fast gap-affine pairwise alignment using the wavefront algorithm	74
Efficient toolkit implementing best practices for principal component analysis of population genetic data	74
Phigaro: high-throughput prophage sequence annotation	74
Accurate, scalable cohort variant calls using DeepVariant and GLnexus	74
TITAN: T-cell receptor specificity prediction with bimodal attention networks	72
plotsr: visualizing structural similarities and rearrangements between multiple genomes	71
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data	70
Protein interaction interface region prediction by geometric deep learning	67
methylclock: a Bioconductor package to estimate DNA methylation age	67
SoluProt: prediction of soluble protein expression in Escherichia coli	66
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function	66
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules	66
Testing hypotheses about the microbiome using the linear decomposition model (LDM)	66
PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning	66
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization	65
PyMod 3: a complete suite for structural bioinformatics in PyMOL	64

GraphQA: protein model quality assessment using graph convolutional networks	63
Structure-aware protein–protein interaction site prediction using deep graph convolutional network	63
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method	63
DELPHI: accurate deep ensemble model for protein interaction sites prediction	63
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data	62
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology	62
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis	62
CiteFuse enables multi-modal analysis of CITE-seq data	61
DeepTE: a computational method for de novo classification of transposons with convolutional neural network	61
Make Interactive Complex Heatmaps in R	61
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference	61
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs	60
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry	60
Conditional out-of-distribution generation for unpaired data using transfer VAE	60
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser	60
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery	60
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor	60
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins	60
propeller: testing for differences in cell type proportions in single cell data	59
HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism	59
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data	58
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features	57
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data	57
COVID-2019-associated overexpressed Prevotella proteins mediated host–pathogen interactions and their role in coronavirus outbreak	56
Impact of protein conformational diversity on AlphaFold predictions	56
Cellsnp-lite: an efficient tool for genotyping single cells	55
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping	54
FASPR: an open-source tool for fast and accurate protein side-chain packing	54
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts	53
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data	53
Extended connectivity interaction features: improving binding affinity prediction through chemical description	53
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	53
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing	52
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning	51
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition	51
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction	51
Automated inference of Boolean models from molecular interaction maps using CaSQ	51
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes	51
Current structure predictors are not learning the physics of protein folding	50
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction	50
Bacteriophage classification for assembled contigs using graph convolutional network	50
SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction	49
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families	49
Humanization of antibodies using a machine learning approach on large-scale repertoire data	49
MBG: Minimizer-based sparse de Bruijn Graph construction	49
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning	49
Geometric potentials from deep learning improve prediction of CDR H3 loop structures	48
Identification of sub-Golgi protein localization by use of deep representation learning features	48
eMPRess: a systematic cophylogeny reconciliation tool	48
TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding	48
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking	47
AEMDA: inferring miRNA–disease associations based on deep autoencoder	47
Evaluating single-cell cluster stability using the Jaccard similarity index	47
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor	47
EpiDope: a deep neural network for linear B-cell epitope prediction	46
BWA-MEME: BWA-MEM emulated with a machine learning approach	46
Interfacing Seurat with the R tidy universe	46
Mutalyzer 2: next generation HGVS nomenclature checker	45
Ribbon: intuitive visualization for complex genomic variation	45
Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis	45
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps	44
yacrd and fpa: upstream tools for long-read genome assembly	44
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics	44
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks	43
DLAB: deep learning methods for structure-based virtual screening of antibodies	43
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning	43
APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms	43
OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks	42
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona	42
SVIM-asm: structural variant detection from haploid and diploid genome assemblies	42
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins	42
amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool	42
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB	41
mlr3proba: an R package for machine learning in survival analysis	41
DamageProfiler: fast damage pattern calculation for ancient DNA	41
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST	41
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities	41
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery	40
Swarm v3: towards tera-scale amplicon clustering	40
AMICI: high-performance sensitivity analysis for large ordinary differential equation models	40

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction	40
ODGI: understanding pangenome graphs	40
Real-time mapping of nanopore raw signals	39
MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network	39
CoMut: visualizing integrated molecular information with comutation plots	39
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures	39
Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports	39
MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates	38
Solubility-Weighted Index: fast and accurate prediction of protein solubility	38
Plotgardener: cultivating precise multi-panel figures in R	38
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays	37
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction	37
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats	37
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences	37
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase	37
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	37
TaxoNN: ensemble of neural networks on stratified microbiome data for disease prediction	37
SHOGUN: a modular, accurate and scalable framework for microbiome quantification	36
PROSS 2: a new server for the design of stable and highly expressed protein variants	36
Improved survival analysis by learning shared genomic information from pan-cancer data	36
Fijiyama: a registration tool for 3D multimodal time-lapse imaging	36
Using drug descriptions and molecular structures for drug–drug interaction extraction from literature	36
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity	36
MAGUS: Multiple sequence Alignment using Graph clUStering	36
SCIM: universal single-cell matching with unpaired feature sets	36
OpenBioLink: a benchmarking framework for large-scale biomedical link prediction	35
VIDHOP, viral host prediction with deep learning	35
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts	35
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence	35
Deep graph learning of inter-protein contacts	35
orfipy: a fast and flexible tool for extracting ORFs	35
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions	35
Tiara: deep learning-based classification system for eukaryotic sequences	35
iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters	35
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction	34
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes	34
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR	34
ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing	34
LeafCutterMD: an algorithm for outlier splicing detection in rare diseases	34
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	34
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks	34
DTF: Deep Tensor Factorization for predicting anticancer drug synergy	34
TRTools: a toolkit for genome-wide analysis of tandem repeats	33
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information	33
DeepEventMine: end-to-end neural nested event extraction from biomedical texts	33
Advanced graph and sequence neural networks for molecular property prediction and drug discovery	33
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models	33
BERN2: an advanced neural biomedical named entity recognition and normalization tool	33
Ensembling graph attention networks for human microbe–drug association prediction	32
DNA Chisel, a versatile sequence optimizer	32
alona: a web server for single-cell RNA-seq analysis	32
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2	32
MIB2: metal ion-binding site prediction and modeling server	32
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets	32
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map	31
monaLisa: an R/Bioconductor package for identifying regulatory motifs	31
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data	31
Generating property-matched decoy molecules using deep learning	31
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers	31
Bayesian modeling of spatial molecular profiling data via Gaussian process	31
TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model	31
ELIXIR: providing a sustainable infrastructure for life science data at European scale	31
Adversarial deconfounding autoencoder for learning robust gene expression embeddings	31
Node similarity-based graph convolution for link prediction in biological networks	30
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning	30
TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data	30
MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model	30
ipDMR: identification of differentially methylated regions with interval P-values	30
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data	30
Modeling multi-scale data via a network of networks	30
Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction	30
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics	30
Identifying signaling genes in spatial single-cell expression data	30
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	29
SimPlot++: a Python application for representing sequence similarity and detecting recombination	29
Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study	29
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies	29
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction	29
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses	29
The string decomposition problem and its applications to centromere analysis and assembly	29
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers	28
Inference of gene regulatory networks based on nonlinear ordinary differential equations	28
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families	28
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy	28
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data	28
BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning	28
EpiGraphDB: a database and data mining platform for health data science	28
Blood-based multi-tissue gene expression inference with Bayesian ridge regression	28
NerLTR-DTA: drug–target binding affinity prediction based on neighbor relationship and learning to rank	28
Topsy-Turvy: integrating a global view into sequence-based PPI prediction	28
PecanPy: a fast, efficient and parallelized Python implementation of node2vec	28
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets	28
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types	28
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	27
AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics	27