Bioinformatics

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
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data	168
Nebulosa recovers single-cell gene expression signals by kernel density estimation	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

ShinyCell: simple and sharable visualization of single-cell gene expression data	122
plotsr: visualizing structural similarities and rearrangements between multiple genomes	122
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects	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
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization	84
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning	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
Protein interaction interface region prediction by geometric deep learning	76
Conditional out-of-distribution generation for unpaired data using transfer VAE	76
Bacteriophage classification for assembled contigs using graph convolutional network	75
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data	75
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps	74
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry	73
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping	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
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor	65
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method	64
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning	62
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families	62
SVIM-asm: structural variant detection from haploid and diploid genome assemblies	62
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction	62
MBG: Minimizer-based sparse de Bruijn Graph construction	61
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor	61

MIB2: metal ion-binding site prediction and modeling server	61
ODGI: understanding pangenome graphs	61
Extended connectivity interaction features: improving binding affinity prediction through chemical description	61
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics	60
Evaluating single-cell cluster stability using the Jaccard similarity index	60
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology	59
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition	59
Current structure predictors are not learning the physics of protein folding	59
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning	58
Interfacing Seurat with the R tidy universe	58
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks	57
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST	57
Plotgardener: cultivating precise multi-panel figures in R	57
eMPRess: a systematic cophylogeny reconciliation tool	57
amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool	57
Tiara: deep learning-based classification system for eukaryotic sequences	56
DamageProfiler: fast damage pattern calculation for ancient DNA	55
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona	55
Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis	54
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	54
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	53
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins	52
Identification of sub-Golgi protein localization by use of deep representation learning features	51
BERN2: an advanced neural biomedical named entity recognition and normalization tool	51
Swarm v3: towards tera-scale amplicon clustering	50
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	50
DLAB: deep learning methods for structure-based virtual screening of antibodies	50
PROSS 2: a new server for the design of stable and highly expressed protein variants	49
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB	49
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction	49
Real-time mapping of nanopore raw signals	48
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction	48
Generating property-matched decoy molecules using deep learning	48
Predicting protein–peptide binding residues via interpretable deep learning	48
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR	47
Ensembling graph attention networks for human microbe–drug association prediction	47
mlr3proba: an R package for machine learning in survival analysis	47
Supervised graph co-contrastive learning for drug–target interaction prediction	46
MAGUS: Multiple sequence Alignment using Graph clUStering	46
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery	46
SCIM: universal single-cell matching with unpaired feature sets	45
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts	45
SimPlot++: a Python application for representing sequence similarity and detecting recombination	45
MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network	45
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies	44
monaLisa: an R/Bioconductor package for identifying regulatory motifs	44
Topsy-Turvy: integrating a global view into sequence-based PPI prediction	44
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling	44
Advanced graph and sequence neural networks for molecular property prediction and drug discovery	44
AMICI: high-performance sensitivity analysis for large ordinary differential equation models	44
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map	43
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures	43
orfipy: a fast and flexible tool for extracting ORFs	43
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data	42
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays	42
Modeling multi-scale data via a network of networks	42
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models	42
Deep graph learning of inter-protein contacts	41
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families	41
Federated Random Forests can improve local performance of predictive models for various healthcare applications	41
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets	41
BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning	40
Cross-dependent graph neural networks for molecular property prediction	40
Bayesian modeling of spatial molecular profiling data via Gaussian process	40
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides	39
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information	39
Multi-omics data integration by generative adversarial network	39
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data	39
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework	39
Adversarial deconfounding autoencoder for learning robust gene expression embeddings	39
ELIXIR: providing a sustainable infrastructure for life science data at European scale	38
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types	38
Pre-training graph neural networks for link prediction in biomedical networks	38
GNN-based embedding for clustering scRNA-seq data	38
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction	38
Effective drug–target interaction prediction with mutual interaction neural network	38
Node similarity-based graph convolution for link prediction in biological networks	38
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics	37
scGAC: a graph attentional architecture for clustering single-cell RNA-seq data	37
A mixture model for determining SARS-Cov-2 variant composition in pooled samples	37

TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model	37
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes	36
Clustering spatial transcriptomics data	36
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms	36
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	36
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers	36
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis	36
Statistical approaches for differential expression analysis in metatranscriptomics	36
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification	35
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	35
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations	35
Sparse and skew hashing of K-mers	35
Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction	35
Methylartist: tools for visualizing modified bases from nanopore sequence data	35
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model	35
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0	34
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity	34
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data	34
Identifying signaling genes in spatial single-cell expression data	34
Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation	33
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information	33
ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing	33
EpiGraphDB: a database and data mining platform for health data science	33
GNN-SubNet: disease subnetwork detection with explainable graph neural networks	33
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2	33
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning	33
PecanPy: a fast, efficient and parallelized Python implementation of node2vec	32
CrossTalkeR: analysis and visualization of ligand–receptorne tworks	32
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development	32
Cooperative sequence clustering and decoding for DNA storage system with fountain codes	32
panRGP: a pangenome-based method to predict genomic islands and explore their diversity	31
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers	31
HFBSurv: hierarchical multimodal fusion with factorized bilinear models for cancer survival prediction	31
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug–drug links based on graph neural network	31
LLPSDB v2.0: an updated database of proteins undergoing liquid–liquid phase separation in vitro	31
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	31
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction	31
Quantification of aneuploidy in targeted sequencing data using ASCETS	31
Autoencoder-based drug–target interaction prediction by preserving the consistency of chemical properties and functions of drugs	30
NerLTR-DTA: drug–target binding affinity prediction based on neighbor relationship and learning to rank	30
TransformerGO: predicting protein–protein interactions by modelling the attention between sets of gene ontology terms	30
Annotating high-impact 5′untranslated region variants with the UTRannotator	30
CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function	30
Accurate spliced alignment of long RNA sequencing reads	30
Scaling multi-instance support vector machine to breast cancer detection on the BreaKHis dataset	30
BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer	30
i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites	29
iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization	29
DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction	29
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants	29
SMILE: mutual information learning for integration of single-cell omics data	29
Recognition of small molecule–RNA binding sites using RNA sequence and structure	29
CBNplot: Bayesian network plots for enrichment analysis	29
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA	29
Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing	29
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning	29
DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research	29
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data	29
EPSOL: sequence-based protein solubility prediction using multidimensional embedding	28
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology	28
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations	28
phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data	28
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions	28
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis	28
NetSolP: predicting protein solubility in Escherichia coli using language models	28
PICS2: next-generation fine mapping via probabilistic identification of causal SNPs	28
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	27
Multi-instance learning of graph neural networks for aqueous pKa prediction	27
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees	27
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs	27
Graph contextualized attention network for predicting synthetic lethality in human cancers	27
Virtifier: a deep learning-based identifier for viral sequences from metagenomes	27
Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data	27
Neuron tracing from light microscopy images: automation, deep learning and bench testing	27
APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data	27
A span-graph neural model for overlapping entity relation extraction in biomedical texts	27
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression	27
Improving circRNA–disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks	27
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction	27
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x)	27
Viral Host Range database, an online tool for recording, analyzing and disseminating virus–host interactions	27
MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction	27
The COVID-19 Ontology	27
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	27
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study	26
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps	26
PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods	26
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled	26
Deep feature extraction of single-cell transcriptomes by generative adversarial network	26
Random forest of perfect trees: concept, performance, applications and perspectives	26
Genozip: a universal extensible genomic data compressor	26
BioDynaMo: a modular platform for high-performance agent-based simulation	26
High-sensitivity pattern discovery in large, paired multiomic datasets	26
PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma	26
The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators	26