Bioinformatics

Article	Citations
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1317
Predicting anti-cancer drug response by finding optimal subset of drugs	861
Accurate assembly of multiple RNA-seq samples with Aletsch	751
Statistical framework to determine indel-length distribution	647
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	517
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	473
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	278
Completing gene trees without species trees in sub-quadratic time	272
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	260
ATLIGATOR: editing protein interactions with an atlas-based approach	260
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	206
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	184
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	177
Integrated Genome Browser App Store	167
PANPROVA: pangenomic prokaryotic evolution of full assemblies	148
MuWU: Mutant-seq library analysis and annotation	145
Haplotype-based membership inference from summary genomic data	131
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	130
pKPDB: a protein data bank extension database of pKa and pI theoretical values	123
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	114
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	113
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	106
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	103
Practical selection of representative sets of RNA-seq samples using a hierarchical approach	102
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints	99

DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions	97
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	97
Deep Subspace Mutual Learning for cancer subtypes prediction	95
SimPlot++: a Python application for representing sequence similarity and detecting recombination	94
monaLisa: an R/Bioconductor package for identifying regulatory motifs	89
Increasing confidence in proteomic spectral deconvolution through mass defect	88
PsiNorm: a scalable normalization for single-cell RNA-seq data	83
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	81
ELIXIR: providing a sustainable infrastructure for life science data at European scale	80
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	79
Refget: standardized access to reference sequences	79
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	78
Prediction of whole-cell transcriptional response with machine learning	76
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	76
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	75
Cross-species prediction of essential genes in insects	73
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	70
WMDS.net: a network control framework for identifying key players in transcriptome programs	69
PyLiger: scalable single-cell multi-omic data integration in Python	67
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	67
CANTATA—prediction of missing links in Boolean networks using genetic programming	67
ProSynAR: a reference aware read merger	67
Exploring automatic inconsistency detection for literature-based gene ontology annotation	65
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	64
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	64
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	62
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	62
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	61
Tysserand—fast and accurate reconstruction of spatial networks from bioimages	60
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	59
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries	59
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells	58
trfermikit: a tool to discover VNTR-associated deletions	58
Evidential meta-model for molecular property prediction	58
Continual knowledge infusion into pre-trained biomedical language models	57
Floria: fast and accurate strain haplotyping in metagenomes	57
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	57
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	56
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	56
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	56
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	56
RNAglib: a python package for RNA 2.5 D graphs	56
ADViSELipidomics: a workflow for analyzing lipidomics data	54
Accurate spliced alignment of long RNA sequencing reads	54
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	54
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	54
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	54
The FASTQ+ format and PISA	53
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	53
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	53

hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	52
Decomposing mosaic tandem repeats accurately from long reads	52
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	52
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	52
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data	51
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	51
De novo protein design by an energy function based on series expansion in distance and orientation dependence	50
VSS: variance-stabilized signals for sequencing-based genomic signals	50
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	50
From viral evolution to spatial contagion: a biologically modulated Hawkes model	50
EpiDope: a deep neural network for linear B-cell epitope prediction	50
Hierarchical reinforcement learning for automatic disease diagnosis	50
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds	49
Powerful molecule generation with simple ConvNet	49
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	49
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs	49
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations	48
Prediction and curation of missing biomedical identifier mappings with Biomappings	48
ViReMaShiny: an interactive application for analysis of viral recombination data	48
2DProts: database of family-wide protein secondary structure diagrams	47
Prediction of gene co-expression from chromatin contacts with graph attention network	47
BATL: Bayesian annotations for targeted lipidomics	46
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	46
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	46
Adaptive digital tissue deconvolution	46
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool	46
minoTour, real-time monitoring and analysis for nanopore sequencers	46
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	45
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database	45
Single-cell RNA sequencing data analysis based on non-uniformε−neighborhood network	45
Transfer learning for drug–target interaction prediction	44
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging	44
XSI—a genotype compression tool for compressive genomics in large biobanks	44
High-sensitivity pattern discovery in large, paired multiomic datasets	44
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics	42
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides	42
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl	42
LINADMIX: evaluating the effect of ancient admixture events on modern populations	42
The minimizer Jaccard estimator is biased and inconsistent	42
Functional characterization of co-phosphorylation networks	41
RawHummus: an R Shiny app for automated raw data quality control in metabolomics	41
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	41
Geometry-complete perceptron networks for 3D molecular graphs	40
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq	40
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	40
ECCB2022: the 21st European Conference on Computational Biology	40
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	39
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	39
OMEN: network-based driver gene identification using mutual exclusivity	39
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	39
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	38
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	38
LOCAN: a python library for analyzing single-molecule localization microscopy data	38
PltDB: a blood platelets-based gene expression database for disease investigation	38
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	38
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	38
Modified RNAs and predictions with the ViennaRNA Package	37
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction	37
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	37
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	37
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	37
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	37
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning	37
RNA threading with secondary structure and sequence profile	37
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images	36
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets	36
Cell type matching across species using protein embeddings and transfer learning	36
Spectral clustering of single-cell multi-omics data on multilayer graphs	36
CCIP: predicting CTCF-mediated chromatin loops with transitivity	36
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	35
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	35
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	35
CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data	35
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario	35
tcplfit2: an R-language general purpose concentration–response modeling package	34
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity	34
HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets	34
On the feasibility of deep learning applications using raw mass spectrometry data	34
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	34
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	34

Efficient gradient boosting for prognostic biomarker discovery	34
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	34
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data	34
Scbean: a python library for single-cell multi-omics data analysis	33
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	33
2023 ISCB Overton Prize: Jingyi Jessica Li	33
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	33
An approachable, flexible and practical machine learning workshop for biologists	32
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	32
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads	32
iSFun: an R package for integrative dimension reduction analysis	32
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	32
Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation	32
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis	32
libOmexMeta: enabling semantic annotation of models to support FAIR principles	32
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs	31
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	31
Computational modeling of mRNA degradation dynamics using deep neural networks	31
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	31
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding	31
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference	30
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design	30
RENANO: a REference-based compressor for NANOpore FASTQ files	30
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study	30
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing	30
Efficient change-points detection for genomic sequences via cumulative segmented regression	30
MIAMI: mutual information-based analysis of multiplex imaging data	29
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline	29
Fully unsupervised deep mode of action learning for phenotyping high-content cellular images	29
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data	29
An automated multi-modal graph-based pipeline for mouse genetic discovery	29
Deep graph representations embed network information for robust disease marker identification	29
MIO: microRNA target analysis system for immuno-oncology	29
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis	28
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	28
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids	28
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	28
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems	28
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	28
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	28
PeakBot: machine-learning-based chromatographic peak picking	28
Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories	28
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients	28
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	28
KCOSS: an ultra-fast k-mer counter for assembled genome analysis	28
Improving dictionary-based named entity recognition with deep learning	27
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction	27
WGA-LP: a pipeline for whole genome assembly of contaminated reads	27
SplicingFactory—splicing diversity analysis for transcriptome data	27
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides	27
Testing microbiome association using integrated quantile regression models	27
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	27
SBGNview: towards data analysis, integration and visualization on all pathways	27
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	27
SPRISS: approximating frequentk-mers by sampling reads, and applications	27
ISMB/ECCB 2021 proceedings	26
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data	26
Polyphest: fast polyploid phylogeny estimation	26
S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection	26
Querying multiple sets ofP-values through composed hypothesis testing	26
ELIXIR biovalidator for semantic validation of life science metadata	26
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	26
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	26
HyperGraphs.jl: representing higher-order relationships in Julia	26
Nezzle: an interactive and programmable visualization of biological networks in Python	26
GADGETS: a genetic algorithm for detecting epistasis using nuclear families	25
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	25
CIndex: compressed indexes for fast retrieval of FASTQ files	25
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias	25
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads	25
ORT: a workflow linking genome-scale metabolic models with reactive transport codes	25
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	25
AQUARIUM: accurate quantification of circular isoforms using model-based strategy	25
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	25
Optimal phylogenetic reconstruction of insertion and deletion events	25
Powerful and interpretable control of false discoveries in two-group differential expression studies	25
Driver gene detection through Bayesian network integration of mutation and expression profiles	25
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution	25
A novel pipeline for computerized mouse spermatogenesis staging	24
PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features	24
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	24
Determining epitope specificity of T-cell receptors with transformers	24
ATHENA: analysis of tumor heterogeneity from spatial omics measurements	24
RAxML Grove: an empirical phylogenetic tree database	24
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	24
Learning sparse log-ratios for high-throughput sequencing data	24
efam: an expanded, metaproteome-supported HMM profile database of viral protein families	24
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	24
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics	24
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data	23
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	23
BSDE: barycenter single-cell differential expression for case–control studies	23
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein–protein interaction databases	23
A variant selection framework for genome graphs	23
GdClean: removal of Gadolinium contamination in mass cytometry data	23