Bioinformatics

Article	Citations
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	1456
ATLIGATOR: editing protein interactions with an atlas-based approach	1013
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	822
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	716
Integrated Genome Browser App Store	583
PANPROVA: pangenomic prokaryotic evolution of full assemblies	562
MuWU: Mutant-seq library analysis and annotation	307
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	288
Deep Subspace Mutual Learning for cancer subtypes prediction	287
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	222
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	194
DivPro: diverse protein sequence design with direct structure recovery guidance	190
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	170
Increasing confidence in proteomic spectral deconvolution through mass defect	168
Accurate assembly of multiple RNA-seq samples with Aletsch	139
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	135
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	123
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	117
PsiNorm: a scalable normalization for single-cell RNA-seq data	116
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	112
Completing gene trees without species trees in sub-quadratic time	109
SimPlot++: a Python application for representing sequence similarity and detecting recombination	106
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	104
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	99
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	89

Correction to: GTExVisualizer: a web platform for supporting ageing studies	88
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	85
Statistical framework to determine indel-length distribution	85
monaLisa: an R/Bioconductor package for identifying regulatory motifs	84
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	83
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	81
Prediction of whole-cell transcriptional response with machine learning	80
Cross-species prediction of essential genes in insects	76
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	76
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	75
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells	75
ProSynAR: a reference aware read merger	74
Exploring automatic inconsistency detection for literature-based gene ontology annotation	73
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	73
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	71
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	71
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	71
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	69
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	68
trfermikit: a tool to discover VNTR-associated deletions	67
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	66
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	65
RNAglib: a python package for RNA 2.5 D graphs	65
PyLiger: scalable single-cell multi-omic data integration in Python	65
Continual knowledge infusion into pre-trained biomedical language models	65
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	64
CANTATA—prediction of missing links in Boolean networks using genetic programming	64
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	64
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	61
ADViSELipidomics: a workflow for analyzing lipidomics data	60
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	60
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	59
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	57
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	57
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	57
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	57
WMDS.net: a network control framework for identifying key players in transcriptome programs	56
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	56
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	56
Decomposing mosaic tandem repeats accurately from long reads	56
Evidential meta-model for molecular property prediction	56
Floria: fast and accurate strain haplotyping in metagenomes	56
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	55
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	55
The FASTQ+ format and PISA	54
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	53
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	53
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool	53
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	52
Hierarchical reinforcement learning for automatic disease diagnosis	52

HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data	51
From viral evolution to spatial contagion: a biologically modulated Hawkes model	50
De novo protein design by an energy function based on series expansion in distance and orientation dependence	50
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations	49
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs	49
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds	49
BATL: Bayesian annotations for targeted lipidomics	48
Prediction of gene co-expression from chromatin contacts with graph attention network	48
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	48
ViReMaShiny: an interactive application for analysis of viral recombination data	47
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	46
minoTour, real-time monitoring and analysis for nanopore sequencers	46
Powerful molecule generation with simple ConvNet	46
Adaptive digital tissue deconvolution	46
XSI—a genotype compression tool for compressive genomics in large biobanks	46
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	45
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	45
Prediction and curation of missing biomedical identifier mappings with Biomappings	45
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	44
High-sensitivity pattern discovery in large, paired multiomic datasets	44
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	44
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging	43
Transfer learning for drug–target interaction prediction	43
Single-cell RNA sequencing data analysis based on non-uniformε−neighborhood network	43
ECCB2022: the 21st European Conference on Computational Biology	43
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	42
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	42
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	42
OMEN: network-based driver gene identification using mutual exclusivity	42
PltDB: a blood platelets-based gene expression database for disease investigation	42
tcplfit2: an R-language general purpose concentration–response modeling package	41
RawHummus: an R Shiny app for automated raw data quality control in metabolomics	41
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction	41
Functional characterization of co-phosphorylation networks	41
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	41
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data	41
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	41
The minimizer Jaccard estimator is biased and inconsistent	41
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets	40
Cell type matching across species using protein embeddings and transfer learning	40
Spectral clustering of single-cell multi-omics data on multilayer graphs	40
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images	40
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	39
Generating synthetic genotypes using diffusion models	38
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	38
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	38
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	38
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario	38
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	38
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	37
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	37
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq	37
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	37
Geometry-complete perceptron networks for 3D molecular graphs	37
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	37
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	37
RNA threading with secondary structure and sequence profile	37
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides	37
Modified RNAs and predictions with the ViennaRNA Package	36
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	36
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	36
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	36
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning	36
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	35
Efficient gradient boosting for prognostic biomarker discovery	35
LOCAN: a python library for analyzing single-molecule localization microscopy data	35
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics	34
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	34
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	33
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	33
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data	33
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	33
2023 ISCB Overton Prize: Jingyi Jessica Li	33
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline	33
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis	33
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs	32
An approachable, flexible and practical machine learning workshop for biologists	32
Computational modeling of mRNA degradation dynamics using deep neural networks	32
iSFun: an R package for integrative dimension reduction analysis	32
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing	32

Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation	32
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	31
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	31
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study	31
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design	31
MIAMI: mutual information-based analysis of multiplex imaging data	30
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	30
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads	30
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	30
Efficient change-points detection for genomic sequences via cumulative segmented regression	30
Improving dictionary-based named entity recognition with deep learning	30
PeakBot: machine-learning-based chromatographic peak picking	30
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference	30
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding	29
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients	29
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	29
An automated multi-modal graph-based pipeline for mouse genetic discovery	29
KCOSS: an ultra-fast k-mer counter for assembled genome analysis	29
MIO: microRNA target analysis system for immuno-oncology	29
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction	29
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids	29
SBGNview: towards data analysis, integration and visualization on all pathways	29
Scbean: a python library for single-cell multi-omics data analysis	28
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	28
Deep graph representations embed network information for robust disease marker identification	28
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	28
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	28
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	28
Nezzle: an interactive and programmable visualization of biological networks in Python	27
SplicingFactory—splicing diversity analysis for transcriptome data	27
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	27
SPRISS: approximating frequentk-mers by sampling reads, and applications	27
Testing microbiome association using integrated quantile regression models	27
WGA-LP: a pipeline for whole genome assembly of contaminated reads	27
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	27
HyperGraphs.jl: representing higher-order relationships in Julia	26
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	26
Optimal phylogenetic reconstruction of insertion and deletion events	26
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias	26
ELIXIR biovalidator for semantic validation of life science metadata	26
GADGETS: a genetic algorithm for detecting epistasis using nuclear families	26
Powerful and interpretable control of false discoveries in two-group differential expression studies	26
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	26
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads	26
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	26
Polyphest: fast polyploid phylogeny estimation	26
CIndex: compressed indexes for fast retrieval of FASTQ files	26
ORT: a workflow linking genome-scale metabolic models with reactive transport codes	26
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	25
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	25
The 2025 ISCB Overton Prize Award—Dr James Zou	25
Learning sparse log-ratios for high-throughput sequencing data	25
A novel pipeline for computerized mouse spermatogenesis staging	25
Querying multiple sets ofP-values through composed hypothesis testing	25
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data	24
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	24
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data	24
ATHENA: analysis of tumor heterogeneity from spatial omics measurements	24
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	24
RAxML Grove: an empirical phylogenetic tree database	24
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	24
PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features	24
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	24
Determining epitope specificity of T-cell receptors with transformers	24
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	23
Driver gene detection through Bayesian network integration of mutation and expression profiles	23
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	23
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases	23
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	23
Phylogenetic diversity statistics for all clades in a phylogeny	23
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein–protein interaction databases	23
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	23
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	23
Comparing transmembrane protein structures with ATOLL	23
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity	23
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data	23
Biological Random Walks: multi-omics integration for disease gene prioritization	22
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data	22
IntelliPy: a GUI for analyzing IntelliCage data	22
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	22
SPEAR: Systematic ProtEin AnnotatoR	22
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	22
Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model	22
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	22
Overcoming biases in causal inference of molecular interactions	22
HOMELETTE: a unified interface to homology modelling software	22
Explainable multimodal machine learning model for classifying pregnancy drug safety	22
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	22
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics	22
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	22
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	22
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	22
A span-based joint model for extracting entities and relations of bacteria biotopes	22
BSDE: barycenter single-cell differential expression for case–control studies	22
Bayesian inference of fitness landscapes via tree-structured branching processes	22