Bioinformatics

Article	Citations
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	1764
DivPro: diverse protein sequence design with direct structure recovery guidance	1323
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	840
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	774
Integrated Genome Browser App Store	740
PANPROVA: pangenomic prokaryotic evolution of full assemblies	439
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	341
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	304
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	267
Statistical framework to determine indel-length distribution	254
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	225
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	209
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	163
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	133
Correction to: GTExVisualizer: a web platform for supporting ageing studies	132
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	129
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	129
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	127
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	117
Completing gene trees without species trees in sub-quadratic time	115
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	105
ATLIGATOR: editing protein interactions with an atlas-based approach	104
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	101
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	99
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	93

HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	90
Increasing confidence in proteomic spectral deconvolution through mass defect	89
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	88
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	88
SimPlot++: a Python application for representing sequence similarity and detecting recombination	87
Accurate assembly of multiple RNA-seq samples with Aletsch	87
monaLisa: an R/Bioconductor package for identifying regulatory motifs	86
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	81
Cross-species prediction of essential genes in insects	79
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	76
trfermikit: a tool to discover VNTR-associated deletions	76
WMDS.net: a network control framework for identifying key players in transcriptome programs	75
Exploring automatic inconsistency detection for literature-based gene ontology annotation	74
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement	74
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	74
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	72
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	69
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	67
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	67
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	67
CANTATA—prediction of missing links in Boolean networks using genetic programming	66
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	66
Decomposing mosaic tandem repeats accurately from long reads	65
ProSynAR: a reference aware read merger	65
RNAglib: a python package for RNA 2.5 D graphs	64
ADViSELipidomics: a workflow for analyzing lipidomics data	63
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures	63
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	62
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	62
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	61
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	60
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	60
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	59
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	59
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	59
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	58
The FASTQ+ format and PISA	58
PyLiger: scalable single-cell multi-omic data integration in Python	57
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs	56
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	56
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	55
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	55
Evidential meta-model for molecular property prediction	54
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	54
Floria: fast and accurate strain haplotyping in metagenomes	54
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	53
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	52
Hierarchical reinforcement learning for automatic disease diagnosis	51
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data	51
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	51

Single-cell RNA sequencing data analysis based on non-uniformε−neighborhood network	50
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation	50
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests	49
Prediction of gene co-expression from chromatin contacts with graph attention network	49
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	48
From viral evolution to spatial contagion: a biologically modulated Hawkes model	48
XSI—a genotype compression tool for compressive genomics in large biobanks	48
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	47
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	47
Transfer learning for drug–target interaction prediction	47
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds	47
Prediction and curation of missing biomedical identifier mappings with Biomappings	46
ViReMaShiny : an interactive application for analysis of viral recombination data	46
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool	46
Adaptive digital tissue deconvolution	46
Powerful molecule generation with simple ConvNet	45
BATL: Bayesian annotations for targeted lipidomics	45
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	45
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs	45
High-sensitivity pattern discovery in large, paired multiomic datasets	44
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	44
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	44
ECCB2022: the 21st European Conference on Computational Biology	44
ShortCake: an integrated platform for efficient and reproducible single-cell analysis	44
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	43
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	43
RawHummus: an R Shiny app for automated raw data quality control in metabolomics	43
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	42
Geometry-complete perceptron networks for 3D molecular graphs	42
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE	42
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides	42
RNA threading with secondary structure and sequence profile	42
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	40
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	40
Functional characterization of co-phosphorylation networks	40
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	39
OMEN: network-based driver gene identification using mutual exclusivity	39
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	38
Conformal inference for reliable single cell RNA-seq annotation	37
The minimizer Jaccard estimator is biased and inconsistent	37
BAV-LLPS: a database of bacterial, archaea, and virus liquid–liquid phase separation proteins	37
LOCAN: a python library for analyzing single-molecule localization microscopy data	36
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning	36
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images	35
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	35
Generating synthetic genotypes using diffusion models	35
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	35
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	34
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	34
Spectral clustering of single-cell multi-omics data on multilayer graphs	34
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	33
Cell type matching across species using protein embeddings and transfer learning	33
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	33
The cell as a token: high-dimensional geometry in language models and cell embeddings	33
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	33
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario	33
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq	32
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	32
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction	32
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	32
PltDB: a blood platelets-based gene expression database for disease investigation	32
Efficient gradient boosting for prognostic biomarker discovery	32
Modified RNAs and predictions with the ViennaRNA Package	32
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	32
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	32
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	31
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	31
iSFun: an R package for integrative dimension reduction analysis	31
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	31
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	31
2023 ISCB Overton Prize: Jingyi Jessica Li	31
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	31
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	30
Scbean: a python library for single-cell multi-omics data analysis	30
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids	30
An automated multi-modal graph-based pipeline for mouse genetic discovery	30
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients	30
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference	30
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	30
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	29

Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	29
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis	29
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	29
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design	29
An approachable, flexible and practical machine learning workshop for biologists	29
MIAMI: mutual information-based analysis of multiplex imaging data	29
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing	28
Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads	28
MIO: microRNA target analysis system for immuno-oncology	28
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction	28
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	28
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	28
Improving dictionary-based named entity recognition with deep learning	28
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	28
PeakBot: machine-learning-based chromatographic peak picking	28
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	27
The 2025 ISCB Overton Prize Award—Dr James Zou	27
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	27
A novel pipeline for computerized mouse spermatogenesis staging	27
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	27
Balancing complexity and clarity—towards clinician-ready antibiotic resistance prediction models	27
Nezzle: an interactive and programmable visualization of biological networks in Python	27
Driver gene detection through Bayesian network integration of mutation and expression profiles	27
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	27
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	27
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	27
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	27
DeepProtein: deep learning library and benchmark for protein sequence learning	26
ATHENA: analysis of tumor heterogeneity from spatial omics measurements	26
SPRISS: approximating frequentk-mers by sampling reads, and applications	25
HyperGraphs.jl: representing higher-order relationships in Julia	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
ELIXIR biovalidator for semantic validation of life science metadata	25
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	25
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	25
Polyphest: fast polyploid phylogeny estimation	25
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	25
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	25
Determining epitope specificity of T-cell receptors with transformers	24
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data	24
Powerful and interpretable control of false discoveries in two-group differential expression studies	24
RAxML Grove: an empirical phylogenetic tree database	24
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads	24
Comparing transmembrane protein structures with ATOLL	24
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	24
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	24
PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features	24
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias	24
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases	23
Thermometer: a webserver to predict protein thermal stability	23
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	23
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	23
SPEAR: Systematic ProtEin AnnotatoR	23
Expanding the coverage of spatial proteomics: a machine learning approach	23
Somatic mutation effects diffused over microRNA dysregulation	23
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	23
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	23
Overcoming biases in causal inference of molecular interactions	23
Bayesian inference of fitness landscapes via tree-structured branching processes	23
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein–protein interaction databases	23
NFTest: automated testing of Nextflow pipelines	22
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	22
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	22
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	22
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation	22
BSDE: barycenter single-cell differential expression for case–control studies	22
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	21
HOMELETTE: a unified interface to homology modelling software	21
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data	21
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	21
SimBu : bias-aware simulation of bulk RNA-seq data with variable cell-type composition	21
BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction	21
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	21
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	21
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity	21
Biological Random Walks: multi-omics integration for disease gene prioritization	21
Phylogenetic diversity statistics for all clades in a phylogeny	21
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts	21
ODGI: understanding pangenome graphs	20
JBrowse Jupyter: a Python interface to JBrowse 2	20
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction	20
NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles	20
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction	20
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	20
Exploiting pretrained biochemical language models for targeted drug design	20
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer	20
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction	20
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation	20
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics	20
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms	20
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts	20
Optimal sequencing budget allocation for trajectory reconstruction of single cells	20
Hierarchical modelling of microbial communities	20
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	20