Bioinformatics

Article	Citations
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	1692
DivPro: diverse protein sequence design with direct structure recovery guidance	1228
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	808
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	735
Integrated Genome Browser App Store	706
PANPROVA: pangenomic prokaryotic evolution of full assemblies	395
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	329
ATLIGATOR: editing protein interactions with an atlas-based approach	298
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	247
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	234
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	218
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	199
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	157
Increasing confidence in proteomic spectral deconvolution through mass defect	128
monaLisa: an R/Bioconductor package for identifying regulatory motifs	127
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	123
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	120
Statistical framework to determine indel-length distribution	116
Correction to: GTExVisualizer: a web platform for supporting ageing studies	111
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	106
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	100
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	99
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	94
Accurate assembly of multiple RNA-seq samples with Aletsch	94
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	91

Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	86
Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data	86
Completing gene trees without species trees in sub-quadratic time	86
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	85
SimPlot++: a Python application for representing sequence similarity and detecting recombination	84
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	82
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	81
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	76
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	75
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	74
Cross-species prediction of essential genes in insects	74
trfermikit: a tool to discover VNTR-associated deletions	74
Exploring automatic inconsistency detection for literature-based gene ontology annotation	73
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	73
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	70
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	70
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	66
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	66
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	65
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	65
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	64
Floria: fast and accurate strain haplotyping in metagenomes	64
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	64
CANTATA—prediction of missing links in Boolean networks using genetic programming	64
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	63
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	63
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	62
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	61
ADViSELipidomics: a workflow for analyzing lipidomics data	59
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	59
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	59
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	58
ProSynAR: a reference aware read merger	58
PyLiger: scalable single-cell multi-omic data integration in Python	58
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	58
Decomposing mosaic tandem repeats accurately from long reads	57
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	57
RNAglib: a python package for RNA 2.5 D graphs	57
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	56
The FASTQ+ format and PISA	55
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	55
Evidential meta-model for molecular property prediction	54
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	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
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	53
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	52
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool	52
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data	51
minoTour, real-time monitoring and analysis for nanopore sequencers	50

Hierarchical reinforcement learning for automatic disease diagnosis	50
Adaptive digital tissue deconvolution	50
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	49
Single-cell RNA sequencing data analysis based on non-uniformε−neighborhood network	49
Powerful molecule generation with simple ConvNet	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
XSI—a genotype compression tool for compressive genomics in large biobanks	48
BATL: Bayesian annotations for targeted lipidomics	48
From viral evolution to spatial contagion: a biologically modulated Hawkes model	48
ViReMaShiny: an interactive application for analysis of viral recombination data	47
Prediction and curation of missing biomedical identifier mappings with Biomappings	46
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs	46
Transfer learning for drug–target interaction prediction	45
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	45
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation	45
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests	45
Prediction of gene co-expression from chromatin contacts with graph attention network	45
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds	44
High-sensitivity pattern discovery in large, paired multiomic datasets	44
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	44
ECCB2022: the 21st European Conference on Computational Biology	44
RawHummus: an R Shiny app for automated raw data quality control in metabolomics	43
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	43
The minimizer Jaccard estimator is biased and inconsistent	43
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	43
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	42
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	42
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	42
Geometry-complete perceptron networks for 3D molecular graphs	42
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq	41
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	41
Spectral clustering of single-cell multi-omics data on multilayer graphs	41
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	41
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	40
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides	40
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	40
Functional characterization of co-phosphorylation networks	39
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	39
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	38
OMEN: network-based driver gene identification using mutual exclusivity	38
Cell type matching across species using protein embeddings and transfer learning	38
Modified RNAs and predictions with the ViennaRNA Package	38
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction	37
RNA threading with secondary structure and sequence profile	37
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario	37
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	36
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	34
Generating synthetic genotypes using diffusion models	34
Conformal inference for reliable single cell RNA-seq annotation	34
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE	34
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	33
BAV-LLPS: a database of bacterial, archaea, and virus liquid–liquid phase separation proteins	33
LOCAN: a python library for analyzing single-molecule localization microscopy data	33
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	33
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images	33
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	33
tcplfit2: an R-language general purpose concentration–response modeling package	32
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	32
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	32
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	32
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning	32
PltDB: a blood platelets-based gene expression database for disease investigation	32
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	32
Efficient gradient boosting for prognostic biomarker discovery	31
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	31
Scbean: a python library for single-cell multi-omics data analysis	31
2023 ISCB Overton Prize: Jingyi Jessica Li	31
Computational modeling of mRNA degradation dynamics using deep neural networks	31
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	31
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing	31
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data	30
iSFun: an R package for integrative dimension reduction analysis	30
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	30
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	30
PeakBot: machine-learning-based chromatographic peak picking	30
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads	30
Improving dictionary-based named entity recognition with deep learning	30
An automated multi-modal graph-based pipeline for mouse genetic discovery	30
MIAMI: mutual information-based analysis of multiplex imaging data	30
Deep graph representations embed network information for robust disease marker identification	29

ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	29
MIO: microRNA target analysis system for immuno-oncology	29
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis	29
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	29
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	29
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	29
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference	28
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	28
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	28
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients	28
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	28
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids	28
An approachable, flexible and practical machine learning workshop for biologists	28
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design	28
SBGNview: towards data analysis, integration and visualization on all pathways	27
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction	27
Nezzle: an interactive and programmable visualization of biological networks in Python	27
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	27
KCOSS: an ultra-fast k-mer counter for assembled genome analysis	27
ELIXIR biovalidator for semantic validation of life science metadata	27
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	27
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	27
SPRISS: approximating frequentk-mers by sampling reads, and applications	27
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	27
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	26
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	26
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	26
The 2025 ISCB Overton Prize Award—Dr James Zou	26
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	26
Powerful and interpretable control of false discoveries in two-group differential expression studies	26
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	26
GADGETS: a genetic algorithm for detecting epistasis using nuclear families	26
Balancing complexity and clarity—towards clinician-ready antibiotic resistance prediction models	25
HyperGraphs.jl: representing higher-order relationships in Julia	25
A novel pipeline for computerized mouse spermatogenesis staging	25
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	25
ORT: a workflow linking genome-scale metabolic models with reactive transport codes	25
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data	25
Optimal phylogenetic reconstruction of insertion and deletion events	25
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	25
Polyphest: fast polyploid phylogeny estimation	24
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	24
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data	24
DeepProtein: deep learning library and benchmark for protein sequence learning	24
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	24
Driver gene detection through Bayesian network integration of mutation and expression profiles	24
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	24
PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features	24
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads	24
Determining epitope specificity of T-cell receptors with transformers	24
RAxML Grove: an empirical phylogenetic tree database	24
Comparing transmembrane protein structures with ATOLL	23
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases	23
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias	23
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	23
SPEAR: Systematic ProtEin AnnotatoR	23
ATHENA: analysis of tumor heterogeneity from spatial omics measurements	23
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity	23
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	23
Explainable multimodal machine learning model for classifying pregnancy drug safety	22
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	22
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	22
Thermometer: a webserver to predict protein thermal stability	22
Bayesian inference of fitness landscapes via tree-structured branching processes	22
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	22
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein–protein interaction databases	22
Expanding the coverage of spatial proteomics: a machine learning approach	22
Overcoming biases in causal inference of molecular interactions	22
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	22
Somatic mutation effects diffused over microRNA dysregulation	22
Biological Random Walks: multi-omics integration for disease gene prioritization	22
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	22
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	22
BSDE: barycenter single-cell differential expression for case–control studies	21
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics	21
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	21
NFTest: automated testing of Nextflow pipelines	21
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction	21
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	21
HOMELETTE: a unified interface to homology modelling software	21
ODGI: understanding pangenome graphs	21
SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition	21
Phylogenetic diversity statistics for all clades in a phylogeny	21
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	21
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction	20
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	20
konnect2prot: a web application to explore the protein properties in a functional protein–protein interaction network	20
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings	20
End-to-end learning of evolutionary models to find coding regions in genome alignments	20
scGAC: a graph attentional architecture for clustering single-cell RNA-seq data	20
HiCARN: resolution enhancement of Hi-C data using cascading residual networks	20
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction	20
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts	20
massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation	20
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction	20