Bioinformatics

Article	Citations
clinker & clustermap.js: automatic generation of gene cluster comparison figures	577
YaHS: yet another Hi-C scaffolding tool	479
GraphDTA: predicting drug–target binding affinity with graph neural networks	363
Analysing high-throughput sequencing data in Python with HTSeq 2.0	355
Liftoff: accurate mapping of gene annotations	339
New strategies to improve minimap2 alignment accuracy	330
GTDB-Tk v2: memory friendly classification with the genome taxonomy database	311
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome	294
CoV-AbDab: the coronavirus antibody database	265
LDpred2: better, faster, stronger	261
STREME: accurate and versatile sequence motif discovery	249
pyGenomeTracks: reproducible plots for multivariate genomic datasets	237
CAFE 5 models variation in evolutionary rates among gene families	230
ProteinBERT: a universal deep-learning model of protein sequence and function	217
A multimodal deep learning framework for predicting drug–drug interaction events	199
TransformerCPI: improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments	194
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants	191
MolTrans: Molecular Interaction Transformer for drug–target interaction prediction	175
DeepPurpose: a deep learning library for drug–target interaction prediction	171
fastsimcoal2: demographic inference under complex evolutionary scenarios	160
Metaviral SPAdes: assembly of viruses from metagenomic data	148
LocusZoom.js: interactive and embeddable visualization of genetic association study results	148
Dream: powerful differential expression analysis for repeated measures designs	139
scVAE: variational auto-encoders for single-cell gene expression data	133
Nebulosa recovers single-cell gene expression signals by kernel density estimation	132

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data	125
DeepCDA: deep cross-domain compound–protein affinity prediction through LSTM and convolutional neural networks	118
Fast and sensitive taxonomic assignment to metagenomic contigs	114
UCSC Cell Browser: visualize your single-cell data	114
Weighted minimizer sampling improves long read mapping	112
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes	106
Colour deconvolution: stain unmixing in histological imaging	104
COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19	103
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response	100
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization	98
Unsupervised topological alignment for single-cell multi-omics integration	96
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects	96
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning	93
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python	93
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit	91
MUFFIN: multi-scale feature fusion for drug–drug interaction prediction	89
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data	88
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation	88
ShinyCell: simple and sharable visualization of single-cell gene expression data	87
MGIDI: toward an effective multivariate selection in biological experiments	86
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides	85
ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2	84
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores	83
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees	82
DNA Features Viewer: a sequence annotation formatting and plotting library for Python	82
Predicting human microbe–drug associations via graph convolutional network with conditional random field	82
TITAN: T-cell receptor specificity prediction with bimodal attention networks	80
Accurate, scalable cohort variant calls using DeepVariant and GLnexus	80
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control	79
LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM	79
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation	78
HiSCF: leveraging higher-order structures for clustering analysis in biological networks	77
Fast gap-affine pairwise alignment using the wavefront algorithm	77
Efficient toolkit implementing best practices for principal component analysis of population genetic data	77
plotsr: visualizing structural similarities and rearrangements between multiple genomes	75
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data	73
methylclock: a Bioconductor package to estimate DNA methylation age	69
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules	68
SoluProt: prediction of soluble protein expression in Escherichia coli	68
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization	68
Protein interaction interface region prediction by geometric deep learning	68
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function	68
Structure-aware protein–protein interaction site prediction using deep graph convolutional network	67
Make Interactive Complex Heatmaps in R	66
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser	66
PyMod 3: a complete suite for structural bioinformatics in PyMOL	66
GraphQA: protein model quality assessment using graph convolutional networks	65
propeller: testing for differences in cell type proportions in single cell data	65
DELPHI: accurate deep ensemble model for protein interaction sites prediction	65
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis	64

NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data	64
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery	64
DeepTE: a computational method for de novo classification of transposons with convolutional neural 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
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference	63
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs	63
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology	62
HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism	62
Impact of protein conformational diversity on AlphaFold predictions	61
Conditional out-of-distribution generation for unpaired data using transfer VAE	61
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor	61
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry	60
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins	60
Cellsnp-lite: an efficient tool for genotyping single cells	60
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data	60
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data	59
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping	58
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features	58
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning	57
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts	56
COVID-2019-associated overexpressed Prevotella proteins mediated host–pathogen interactions and their role in coronavirus outbreak	56
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	56
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing	56
Extended connectivity interaction features: improving binding affinity prediction through chemical description	55
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction	54
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data	53
TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding	53
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction	53
Mutalyzer 2: next generation HGVS nomenclature checker	52
MBG: Minimizer-based sparse de Bruijn Graph construction	52
Current structure predictors are not learning the physics of protein folding	52
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor	51
SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction	51
Bacteriophage classification for assembled contigs using graph convolutional network	51
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families	51
Automated inference of Boolean models from molecular interaction maps using CaSQ	51
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning	51
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes	51
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition	51
eMPRess: a systematic cophylogeny reconciliation tool	51
Geometric potentials from deep learning improve prediction of CDR H3 loop structures	50
Humanization of antibodies using a machine learning approach on large-scale repertoire data	50
EpiDope: a deep neural network for linear B-cell epitope prediction	49
BWA-MEME: BWA-MEM emulated with a machine learning approach	49
Evaluating single-cell cluster stability using the Jaccard similarity index	49
Identification of sub-Golgi protein localization by use of deep representation learning features	48
AEMDA: inferring miRNA–disease associations based on deep autoencoder	48
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks	47
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics	47
Interfacing Seurat with the R tidy universe	47
DamageProfiler: fast damage pattern calculation for ancient DNA	46
Ribbon: intuitive visualization for complex genomic variation	46
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning	46
Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis	46
DLAB: deep learning methods for structure-based virtual screening of antibodies	45
SVIM-asm: structural variant detection from haploid and diploid genome assemblies	45
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins	45
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps	45
OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks	44
amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool	44
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB	43
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona	43
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST	43
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities	42
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	42
Swarm v3: towards tera-scale amplicon clustering	42
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery	42
CoMut: visualizing integrated molecular information with comutation plots	41
ODGI: understanding pangenome graphs	41
Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports	41
mlr3proba: an R package for machine learning in survival analysis	41
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction	41
AMICI: high-performance sensitivity analysis for large ordinary differential equation models	41
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity	40
TaxoNN: ensemble of neural networks on stratified microbiome data for disease prediction	40
Solubility-Weighted Index: fast and accurate prediction of protein solubility	40
Plotgardener: cultivating precise multi-panel figures in R	40
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats	40
Real-time mapping of nanopore raw signals	40
MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network	40

Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures	39
Using drug descriptions and molecular structures for drug–drug interaction extraction from literature	39
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase	38
MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates	38
Fijiyama: a registration tool for 3D multimodal time-lapse imaging	38
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences	38
Deep graph learning of inter-protein contacts	37
PROSS 2: a new server for the design of stable and highly expressed protein variants	37
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction	37
MAGUS: Multiple sequence Alignment using Graph clUStering	37
DTF: Deep Tensor Factorization for predicting anticancer drug synergy	37
DeepEventMine: end-to-end neural nested event extraction from biomedical texts	37
orfipy: a fast and flexible tool for extracting ORFs	37
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays	37
Tiara: deep learning-based classification system for eukaryotic sequences	36
SCIM: universal single-cell matching with unpaired feature sets	36
SHOGUN: a modular, accurate and scalable framework for microbiome quantification	36
MIB2: metal ion-binding site prediction and modeling server	36
iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters	36
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	36
VIDHOP, viral host prediction with deep learning	36
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction	36
Improved survival analysis by learning shared genomic information from pan-cancer data	36
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR	36
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction	35
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks	35
Advanced graph and sequence neural networks for molecular property prediction and drug discovery	35
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions	35
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models	35
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes	35
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence	35
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts	35
Generating property-matched decoy molecules using deep learning	35
monaLisa: an R/Bioconductor package for identifying regulatory motifs	35
TRTools: a toolkit for genome-wide analysis of tandem repeats	34
BERN2: an advanced neural biomedical named entity recognition and normalization tool	34
Ensembling graph attention networks for human microbe–drug association prediction	34
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information	34
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map	33
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2	33
ELIXIR: providing a sustainable infrastructure for life science data at European scale	33
SimPlot++: a Python application for representing sequence similarity and detecting recombination	33
Bayesian modeling of spatial molecular profiling data via Gaussian process	33
TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data	33
DNA Chisel, a versatile sequence optimizer	33
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	33
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy	33
Multi-omics data integration by generative adversarial network	32
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets	32
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data	32
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies	32
Modeling multi-scale data via a network of networks	32
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data	32
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning	31
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families	31
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers	31
Inference of gene regulatory networks based on nonlinear ordinary differential equations	31
Adversarial deconfounding autoencoder for learning robust gene expression embeddings	31
TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model	31
MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model	31
Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction	31
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets	31
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers	30
EpiGraphDB: a database and data mining platform for health data science	30
Pre-training graph neural networks for link prediction in biomedical networks	30
Identifying signaling genes in spatial single-cell expression data	30
Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study	30
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses	30
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling	30
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics	30
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data	30
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides	30
Node similarity-based graph convolution for link prediction in biological networks	30
Predicting protein–peptide binding residues via interpretable deep learning	30
ipDMR: identification of differentially methylated regions with interval P-values	30
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types	30
Topsy-Turvy: integrating a global view into sequence-based PPI prediction	29
The string decomposition problem and its applications to centromere analysis and assembly	29
BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning	29
Accurate spliced alignment of long RNA sequencing reads	29
A mixture model for determining SARS-Cov-2 variant composition in pooled samples	28
Improved design and analysis of practical minimizers	28
PecanPy: a fast, efficient and parallelized Python implementation of node2vec	28
NerLTR-DTA: drug–target binding affinity prediction based on neighbor relationship and learning to rank	28
Supervised graph co-contrastive learning for drug–target interaction prediction	28
AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics	28
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction	28
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	28
Statistical approaches for differential expression analysis in metatranscriptomics	28
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model	27
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	27
Cross-dependent graph neural networks for molecular property prediction	27
CrossTalkeR: analysis and visualization of ligand–receptorne tworks	27
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis	27
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	27