Bioinformatics

Article	Citations
clinker & clustermap.js: automatic generation of gene cluster comparison figures	624
YaHS: yet another Hi-C scaffolding tool	582
GraphDTA: predicting drug–target binding affinity with graph neural networks	408
Analysing high-throughput sequencing data in Python with HTSeq 2.0	401
New strategies to improve minimap2 alignment accuracy	388
GTDB-Tk v2: memory friendly classification with the genome taxonomy database	379
Liftoff: accurate mapping of gene annotations	371
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome	339
LDpred2: better, faster, stronger	291
CoV-AbDab: the coronavirus antibody database	276
STREME: accurate and versatile sequence motif discovery	267
CAFE 5 models variation in evolutionary rates among gene families	264
pyGenomeTracks: reproducible plots for multivariate genomic datasets	262
ProteinBERT: a universal deep-learning model of protein sequence and function	258
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants	212
MolTrans: Molecular Interaction Transformer for drug–target interaction prediction	193
DeepPurpose: a deep learning library for drug–target interaction prediction	180
fastsimcoal2: demographic inference under complex evolutionary scenarios	173
LocusZoom.js: interactive and embeddable visualization of genetic association study results	159
Dream: powerful differential expression analysis for repeated measures designs	152
Nebulosa recovers single-cell gene expression signals by kernel density estimation	144
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data	138
Fast and sensitive taxonomic assignment to metagenomic contigs	126
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization	126
UCSC Cell Browser: visualize your single-cell data	125

Weighted minimizer sampling improves long read mapping	118
Colour deconvolution: stain unmixing in histological imaging	113
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response	110
ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2	108
COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19	107
ShinyCell: simple and sharable visualization of single-cell gene expression data	103
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit	101
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning	100
MGIDI: toward an effective multivariate selection in biological experiments	100
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation	100
Unsupervised topological alignment for single-cell multi-omics integration	98
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
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides	97
MUFFIN: multi-scale feature fusion for drug–drug interaction prediction	95
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data	93
plotsr: visualizing structural similarities and rearrangements between multiple genomes	93
propeller: testing for differences in cell type proportions in single cell data	92
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees	91
TITAN: T-cell receptor specificity prediction with bimodal attention networks	90
LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM	89
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores	88
DNA Features Viewer: a sequence annotation formatting and plotting library for Python	86
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation	86
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data	86
Accurate, scalable cohort variant calls using DeepVariant and GLnexus	84
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control	84
methylclock: a Bioconductor package to estimate DNA methylation age	83
HiSCF: leveraging higher-order structures for clustering analysis in biological networks	83
Fast gap-affine pairwise alignment using the wavefront algorithm	82
Make Interactive Complex Heatmaps in R	80
SoluProt: prediction of soluble protein expression in Escherichia coli	80
Impact of protein conformational diversity on AlphaFold predictions	77
Structure-aware protein–protein interaction site prediction using deep graph convolutional network	74
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules	74
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization	74
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis	72
Protein interaction interface region prediction by geometric deep learning	72
HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism	71
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function	71
PyMod 3: a complete suite for structural bioinformatics in PyMOL	71
DELPHI: accurate deep ensemble model for protein interaction sites prediction	70
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data	70
Cellsnp-lite: an efficient tool for genotyping single cells	69
GraphQA: protein model quality assessment using graph convolutional networks	68
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping	67
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	65
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data	65
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery	65
BWA-MEME: BWA-MEM emulated with a machine learning approach	64

Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry	64
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method	64
Conditional out-of-distribution generation for unpaired data using transfer VAE	64
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins	63
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor	63
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning	63
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data	63
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts	62
TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding	61
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology	61
Bacteriophage classification for assembled contigs using graph convolutional network	60
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction	59
Extended connectivity interaction features: improving binding affinity prediction through chemical description	59
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features	59
Mutalyzer 2: next generation HGVS nomenclature checker	59
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction	58
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing	58
Humanization of antibodies using a machine learning approach on large-scale repertoire data	58
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor	57
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families	56
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data	56
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics	55
eMPRess: a systematic cophylogeny reconciliation tool	54
Current structure predictors are not learning the physics of protein folding	54
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks	54
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition	54
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning	54
Evaluating single-cell cluster stability using the Jaccard similarity index	53
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes	53
MBG: Minimizer-based sparse de Bruijn Graph construction	53
Geometric potentials from deep learning improve prediction of CDR H3 loop structures	52
ODGI: understanding pangenome graphs	52
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps	51
Identification of sub-Golgi protein localization by use of deep representation learning features	50
Interfacing Seurat with the R tidy universe	50
DamageProfiler: fast damage pattern calculation for ancient DNA	50
AEMDA: inferring miRNA–disease associations based on deep autoencoder	50
amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool	50
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST	49
Ribbon: intuitive visualization for complex genomic variation	49
EpiDope: a deep neural network for linear B-cell epitope prediction	49
SVIM-asm: structural variant detection from haploid and diploid genome assemblies	48
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins	48
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning	48
DLAB: deep learning methods for structure-based virtual screening of antibodies	48
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona	47
Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis	47
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB	47
Swarm v3: towards tera-scale amplicon clustering	47
MIB2: metal ion-binding site prediction and modeling server	47
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction	47
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	46
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities	45
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery	45
mlr3proba: an R package for machine learning in survival analysis	45
OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks	44
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity	43
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences	43
Plotgardener: cultivating precise multi-panel figures in R	43
AMICI: high-performance sensitivity analysis for large ordinary differential equation models	43
Real-time mapping of nanopore raw signals	43
Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports	42
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures	42
MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network	42
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats	42
Using drug descriptions and molecular structures for drug–drug interaction extraction from literature	42
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	41
MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates	41
Fijiyama: a registration tool for 3D multimodal time-lapse imaging	41
PROSS 2: a new server for the design of stable and highly expressed protein variants	41
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR	41
Tiara: deep learning-based classification system for eukaryotic sequences	41
SCIM: universal single-cell matching with unpaired feature sets	41
Ensembling graph attention networks for human microbe–drug association prediction	41
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction	40
Deep graph learning of inter-protein contacts	40
MAGUS: Multiple sequence Alignment using Graph clUStering	40
BERN2: an advanced neural biomedical named entity recognition and normalization tool	39
monaLisa: an R/Bioconductor package for identifying regulatory motifs	39
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models	39

orfipy: a fast and flexible tool for extracting ORFs	39
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts	39
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets	39
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	38
Generating property-matched decoy molecules using deep learning	38
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions	38
Improved survival analysis by learning shared genomic information from pan-cancer data	38
Predicting protein–peptide binding residues via interpretable deep learning	38
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction	38
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data	38
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies	37
ELIXIR: providing a sustainable infrastructure for life science data at European scale	37
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map	37
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays	37
Modeling multi-scale data via a network of networks	37
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets	37
SimPlot++: a Python application for representing sequence similarity and detecting recombination	37
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes	36
VIDHOP, viral host prediction with deep learning	36
Advanced graph and sequence neural networks for molecular property prediction and drug discovery	36
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families	36
Bayesian modeling of spatial molecular profiling data via Gaussian process	36
Topsy-Turvy: integrating a global view into sequence-based PPI prediction	36
iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters	36
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction	36
Adversarial deconfounding autoencoder for learning robust gene expression embeddings	36
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information	35
BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning	35
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks	35
MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model	34
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy	34
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides	34
TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model	34
Multi-omics data integration by generative adversarial network	34
DNA Chisel, a versatile sequence optimizer	34
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers	33
TRTools: a toolkit for genome-wide analysis of tandem repeats	33
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2	33
Inference of gene regulatory networks based on nonlinear ordinary differential equations	33
Pre-training graph neural networks for link prediction in biomedical networks	33
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data	33
Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction	33
Node similarity-based graph convolution for link prediction in biological networks	32
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning	32
Sparse and skew hashing of K-mers	32
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	32
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data	32
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling	32
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types	31
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses	31
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework	31
ipDMR: identification of differentially methylated regions with interval P-values	31
A mixture model for determining SARS-Cov-2 variant composition in pooled samples	31
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers	31
Methylartist: tools for visualizing modified bases from nanopore sequence data	31
Identifying signaling genes in spatial single-cell expression data	31
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis	31
Supervised graph co-contrastive learning for drug–target interaction prediction	31
EpiGraphDB: a database and data mining platform for health data science	31
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction	30
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity	30
Cooperative sequence clustering and decoding for DNA storage system with fountain codes	30
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms	30
PecanPy: a fast, efficient and parallelized Python implementation of node2vec	30
AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics	30
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0	30
Improved design and analysis of practical minimizers	30
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics	30
Statistical approaches for differential expression analysis in metatranscriptomics	30
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug–drug links based on graph neural network	29
Annotating high-impact 5′untranslated region variants with the UTRannotator	29
TransformerGO: predicting protein–protein interactions by modelling the attention between sets of gene ontology terms	29
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis	29
CrossTalkeR: analysis and visualization of ligand–receptorne tworks	29
SMILE: mutual information learning for integration of single-cell omics data	29
NerLTR-DTA: drug–target binding affinity prediction based on neighbor relationship and learning to rank	29
The string decomposition problem and its applications to centromere analysis and assembly	29
Clustering spatial transcriptomics data	29
Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation	29
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	29
Accurate spliced alignment of long RNA sequencing reads	29
Effective drug–target interaction prediction with mutual interaction neural network	29
Federated Random Forests can improve local performance of predictive models for various healthcare applications	28
CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function	28
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model	28
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations	28
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development	28
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification	28
Cross-dependent graph neural networks for molecular property prediction	28
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	28
panRGP: a pangenome-based method to predict genomic islands and explore their diversity	28
LLPSDB v2.0: an updated database of proteins undergoing liquid–liquid phase separation in vitro	28
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning	28
Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation	28
GNN-based embedding for clustering scRNA-seq data	28