Bioinformatics

Article	Citations
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	1517
ATLIGATOR: editing protein interactions with an atlas-based approach	1079
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	856
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	742
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	617
Integrated Genome Browser App Store	613
PANPROVA: pangenomic prokaryotic evolution of full assemblies	335
MuWU: Mutant-seq library analysis and annotation	302
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	291
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	232
Accurate assembly of multiple RNA-seq samples with Aletsch	204
Deep Subspace Mutual Learning for cancer subtypes prediction	203
Completing gene trees without species trees in sub-quadratic time	182
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	177
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	144
Statistical framework to determine indel-length distribution	135
Correction to: GTExVisualizer: a web platform for supporting ageing studies	126
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	120
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	118
DivPro: diverse protein sequence design with direct structure recovery guidance	114
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	112
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	108
Increasing confidence in proteomic spectral deconvolution through mass defect	107
SimPlot++: a Python application for representing sequence similarity and detecting recombination	99
monaLisa: an R/Bioconductor package for identifying regulatory motifs	90

TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	90
PsiNorm: a scalable normalization for single-cell RNA-seq data	88
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	88
MRDagent: Iterative and Adaptive Parameter Optimisation for stable ctDNA-Based MRD Detection in Heterogeneous Samples	87
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	84
Prediction of whole-cell transcriptional response with machine learning	83
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	82
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	81
Cross-species prediction of essential genes in insects	81
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	81
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	81
The FASTQ+ format and PISA	80
ADViSELipidomics: a workflow for analyzing lipidomics data	80
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	78
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	78
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	76
ProSynAR: a reference aware read merger	73
Exploring automatic inconsistency detection for literature-based gene ontology annotation	71
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	71
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	70
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	69
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	69
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	67
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	66
trfermikit: a tool to discover VNTR-associated deletions	66
RNAglib: a python package for RNA 2.5 D graphs	65
Continual knowledge infusion into pre-trained biomedical language models	65
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	64
PyLiger: scalable single-cell multi-omic data integration in Python	63
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	61
CANTATA—prediction of missing links in Boolean networks using genetic programming	61
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	60
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	60
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	59
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	58
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	58
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	57
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	57
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	57
Decomposing mosaic tandem repeats accurately from long reads	56
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	56
Evidential meta-model for molecular property prediction	56
Floria: fast and accurate strain haplotyping in metagenomes	55
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	54
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	54
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	53
WMDS.net: a network control framework for identifying key players in transcriptome programs	53
From viral evolution to spatial contagion: a biologically modulated Hawkes model	52
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data	52
Powerful molecule generation with simple ConvNet	52

COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool	52
Prediction of gene co-expression from chromatin contacts with graph attention network	51
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds	51
ViReMaShiny: an interactive application for analysis of viral recombination data	50
BATL: Bayesian annotations for targeted lipidomics	50
Hierarchical reinforcement learning for automatic disease diagnosis	50
XSI—a genotype compression tool for compressive genomics in large biobanks	49
Adaptive digital tissue deconvolution	49
minoTour, real-time monitoring and analysis for nanopore sequencers	49
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	48
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	48
Single-cell RNA sequencing data analysis based on non-uniformε−neighborhood network	48
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	48
Prediction and curation of missing biomedical identifier mappings with Biomappings	48
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs	47
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	46
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	46
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	45
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging	44
scPOEM: Robust Co-embedding of Peaks and Genes Revealing Peak-Gene Regulation	44
High-sensitivity pattern discovery in large, paired multiomic datasets	44
Transfer learning for drug–target interaction prediction	44
Cell type matching across species using protein embeddings and transfer learning	43
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	43
ECCB2022: the 21st European Conference on Computational Biology	43
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data	43
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	43
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	43
OMEN: network-based driver gene identification using mutual exclusivity	43
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	42
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario	42
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction	42
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides	41
RawHummus: an R Shiny app for automated raw data quality control in metabolomics	41
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq	41
The minimizer Jaccard estimator is biased and inconsistent	41
LOCAN: a python library for analyzing single-molecule localization microscopy data	41
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	41
Functional characterization of co-phosphorylation networks	41
Generating synthetic genotypes using diffusion models	40
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	40
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	40
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	39
Efficient gradient boosting for prognostic biomarker discovery	39
Geometry-complete perceptron networks for 3D molecular graphs	39
RNA threading with secondary structure and sequence profile	39
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images	39
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	38
Spectral clustering of single-cell multi-omics data on multilayer graphs	38
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	38
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	38
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	37
Modified RNAs and predictions with the ViennaRNA Package	37
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	37
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	37
PltDB: a blood platelets-based gene expression database for disease investigation	37
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	37
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	36
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	36
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	36
tcplfit2: an R-language general purpose concentration–response modeling package	36
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning	36
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	36
2023 ISCB Overton Prize: Jingyi Jessica Li	35
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline	35
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	35
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	35
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	34
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	33
iSFun: an R package for integrative dimension reduction analysis	33
Scbean: a python library for single-cell multi-omics data analysis	33
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	33
An approachable, flexible and practical machine learning workshop for biologists	32
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs	32
Computational modeling of mRNA degradation dynamics using deep neural networks	32
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing	32
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	31
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	31
MIO: microRNA target analysis system for immuno-oncology	31
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference	31

MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study	31
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction	31
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	31
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis	30
MIAMI: mutual information-based analysis of multiplex imaging data	30
Efficient change-points detection for genomic sequences via cumulative segmented regression	30
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids	30
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads	30
PeakBot: machine-learning-based chromatographic peak picking	30
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	30
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding	29
KCOSS: an ultra-fast k-mer counter for assembled genome analysis	29
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	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
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design	29
An automated multi-modal graph-based pipeline for mouse genetic discovery	29
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	29
Deep graph representations embed network information for robust disease marker identification	29
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data	28
SBGNview: towards data analysis, integration and visualization on all pathways	28
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	28
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	28
Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation	28
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	27
ELIXIR biovalidator for semantic validation of life science metadata	27
WGA-LP: a pipeline for whole genome assembly of contaminated reads	27
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	27
Improving dictionary-based named entity recognition with deep learning	27
GADGETS: a genetic algorithm for detecting epistasis using nuclear families	27
SplicingFactory—splicing diversity analysis for transcriptome data	27
Testing microbiome association using integrated quantile regression models	27
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	27
Polyphest: fast polyploid phylogeny estimation	27
SPRISS: approximating frequentk-mers by sampling reads, and applications	27
Nezzle: an interactive and programmable visualization of biological networks in Python	27
The 2025 ISCB Overton Prize Award—Dr James Zou	26
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data	26
A novel pipeline for computerized mouse spermatogenesis staging	26
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	26
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	26
Learning sparse log-ratios for high-throughput sequencing data	26
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	26
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads	26
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias	25
ORT: a workflow linking genome-scale metabolic models with reactive transport codes	25
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	25
PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features	25
Powerful and interpretable control of false discoveries in two-group differential expression studies	25
Optimal phylogenetic reconstruction of insertion and deletion events	25
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	25
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	25
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	25
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	25
CIndex: compressed indexes for fast retrieval of FASTQ files	24
Driver gene detection through Bayesian network integration of mutation and expression profiles	24
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics	24
RAxML Grove: an empirical phylogenetic tree database	24
ATHENA: analysis of tumor heterogeneity from spatial omics measurements	24
Phylogenetic diversity statistics for all clades in a phylogeny	24
Determining epitope specificity of T-cell receptors with transformers	24
Querying multiple sets ofP-values through composed hypothesis testing	24
HyperGraphs.jl: representing higher-order relationships in Julia	24
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data	24
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	24
Comparing transmembrane protein structures with ATOLL	23
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases	23
IntelliPy: a GUI for analyzing IntelliCage data	23
BSDE: barycenter single-cell differential expression for case–control studies	23
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	23
Bayesian inference of fitness landscapes via tree-structured branching processes	23
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	23
SPEAR: Systematic ProtEin AnnotatoR	23
SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition	23
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity	23
Thermometer: a webserver to predict protein thermal stability	23
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts	23
Overcoming biases in causal inference of molecular interactions	23
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	22
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	22
NFTest: automated testing of Nextflow pipelines	22
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	22
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	22
Explainable multimodal machine learning model for classifying pregnancy drug safety	22
Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model	22
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	22
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	22
Expanding the coverage of spatial proteomics: a machine learning approach	22
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	22
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	22
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	22
HOMELETTE: a unified interface to homology modelling software	22
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	22
Somatic mutation effects diffused over microRNA dysregulation	22
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations	21