Bioinformatics

Article	Citations
DivPro: diverse protein sequence design with direct structure recovery guidance	2121
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	1739
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	988
Correction to: GTExVisualizer: a web platform for supporting ageing studies	603
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	400
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	336
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	207
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	171
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	165
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	134
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	129
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	116
Accurate assembly of multiple RNA-seq samples with Aletsch	101
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	100
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism	98
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data	96
From genes to trajectories: mapping genetic influences on Huntington’s disease progression	90
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	87
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction	85
Statistical framework to determine indel-length distribution	80
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	79
ATLIGATOR: editing protein interactions with an atlas-based approach	77
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	76
Increasing confidence in proteomic spectral deconvolution through mass defect	74
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	74

Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	74
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	73
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	72
MDCompress: better, faster compression of molecular dynamics simulation trajectories	71
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	69
ADViSELipidomics: a workflow for analyzing lipidomics data	68
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	67
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	67
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	65
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	65
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	64
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	62
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	61
Decomposing mosaic tandem repeats accurately from long reads	60
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	58
Exploring automatic inconsistency detection for literature-based gene ontology annotation	57
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	57
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	57
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	56
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	56
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	54
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors	54
CANTATA—prediction of missing links in Boolean networks using genetic programming	54
Evidential meta-model for molecular property prediction	52
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures	52
TripLexicon: prediction and analysis of gene regulatory RNA–DNA interactions	52
WMDS.net: a network control framework for identifying key players in transcriptome programs	51
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	50
scSurv: a deep generative model for single-cell survival analysis	50
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement	50
Finding low-complexity DNA sequences with longdust	48
Floria: fast and accurate strain haplotyping in metagenomes	46
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	46
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	45
The FASTQ+ format and PISA	45
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs	45
phylobar: an R package for multiresolution compositional barplots in omics studies	43
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	43
SA2E: spatial-aware auto-encoder for cell type deconvolution of spatial transcriptomics data	43
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	42
ShortCake: an integrated platform for efficient and reproducible single-cell analysis	41
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	41
Powerful molecule generation with simple ConvNet	41
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests	41
EXPLANA: a user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies	39
ViReMaShiny : an interactive application for analysis of viral recombination data	38
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	38
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation	38
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	38
Prediction and curation of missing biomedical identifier mappings with Biomappings	38

Columba: fast approximate pattern matching with optimized search schemes	37
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	37
BrainConnect: processing brain connectivity and spatial transcriptomics data for integrative analysis	37
Prediction of gene co-expression from chromatin contacts with graph attention network	36
Hierarchical reinforcement learning for automatic disease diagnosis	36
High-sensitivity pattern discovery in large, paired multiomic datasets	36
Functional lipid analysis via index-based lipidomics profile: a new computational module in LipidOne	36
VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions	35
Transfer learning for drug–target interaction prediction	35
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	35
XSI—a genotype compression tool for compressive genomics in large biobanks	35
Adaptive digital tissue deconvolution	35
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	34
ECCB2022: the 21st European Conference on Computational Biology	34
STAR-GO: improving protein function prediction by learning to hierarchically integrate ontology-informed semantic embeddings	34
OMEN: network-based driver gene identification using mutual exclusivity	33
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	33
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	33
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	33
Prediction of bacterial protein–compound interactions with only positive samples	33
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	33
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE	33
LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis	32
Conformal inference for reliable single cell RNA-seq annotation	32
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	31
The cell as a token: high-dimensional geometry in language models and cell embeddings	31
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	30
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	30
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	30
BAV-LLPS: a database of bacterial, archaea, and virus liquid–liquid phase separation proteins	30
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	29
Generating synthetic genotypes using diffusion models	29
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	29
Spectral clustering of single-cell multi-omics data on multilayer graphs	29
Improving biomedical entity linking with generative relevance feedback	29
Using semantic search to find publicly available gene-expression datasets	28
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	28
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	28
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	28
Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications	28
The minimizer Jaccard estimator is biased and inconsistent	28
RNA threading with secondary structure and sequence profile	27
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	27
Geometry-complete perceptron networks for 3D molecular graphs	27
Modified RNAs and predictions with the ViennaRNA Package	27
Functional characterization of co-phosphorylation networks	27
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	27
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	27
Cell type matching across species using protein embeddings and transfer learning	26
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	26
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	26
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	26
2023 ISCB Overton Prize: Jingyi Jessica Li	25
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	25
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	25
MIAMI: mutual information-based analysis of multiplex imaging data	25
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	25
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	25
An automated multi-modal graph-based pipeline for mouse genetic discovery	25
Scbean: a python library for single-cell multi-omics data analysis	24
MIO: microRNA target analysis system for immuno-oncology	24
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	24
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	24
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	24
SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset	24
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients	24
PeakBot: machine-learning-based chromatographic peak picking	23
An approachable, flexible and practical machine learning workshop for biologists	23
TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection	23
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	23
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	23
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	23
CCC-GPU: a graphics processing unit (GPU)-accelerated nonlinear correlation coefficient for large-scale transcriptomic analyses	23
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	23
Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads	23
Improving dictionary-based named entity recognition with deep learning	23
Nezzle: an interactive and programmable visualization of biological networks in Python	22
SPRISS: approximating frequentk-mers by sampling reads, and applications	22
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	22
DeepLMI: deep feature mining with a globally enhanced graph convolutional network for robust lncRNA–miRNA interaction prediction	22

2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	22
Powerful and interpretable control of false discoveries in two-group differential expression studies	22
The 2025 ISCB Overton Prize Award—Dr James Zou	22
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	22
Balancing complexity and clarity—towards clinician-ready antibiotic resistance prediction models	22
A novel pipeline for computerized mouse spermatogenesis staging	22
DeepProtein: deep learning library and benchmark for protein sequence learning	21
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data	21
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	21
Optimal phylogenetic reconstruction of insertion and deletion events	21
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	21
FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues	21
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias	21
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads	21
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	21
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	21
HyperGraphs.jl: representing higher-order relationships in Julia	21
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	21
Integrating curation into scientific publishing to train AI models	21
Managing workflow executions with WESkit	21
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	21
Polyphest: fast polyploid phylogeny estimation	21
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	20
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	20
SimBu : bias-aware simulation of bulk RNA-seq data with variable cell-type composition	20
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation	20
Somatic mutation effects diffused over microRNA dysregulation	20
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	20
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	20
Determining epitope specificity of T-cell receptors with transformers	20
SPEAR: Systematic ProtEin AnnotatoR	20
Expanding the coverage of spatial proteomics: a machine learning approach	20
sedimix : a workflow for the analysis of hominin nuclear DNA sequences from sediments	20
Phylogenetic diversity statistics for all clades in a phylogeny	20
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	20
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	20
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	20
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	20
Semantic-enhanced heterogeneous graph learning for identifying ncRNAs associated with drug resistance	20
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	20
CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types	20
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	19
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	19
ODGI: understanding pangenome graphs	19
Biological Random Walks: multi-omics integration for disease gene prioritization	19
NFTest: automated testing of Nextflow pipelines	19
Bayesian inference of fitness landscapes via tree-structured branching processes	19
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	19
G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration	19
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	19
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	19
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	19
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	19
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data	19
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts	19
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	19
RISK: a next-generation tool for biological network annotation and visualization	19
Hierarchical modelling of microbial communities	18
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization	18
Exploiting pretrained biochemical language models for targeted drug design	18
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning	18
konnect2prot: a web application to explore the protein properties in a functional protein–protein interaction network	18
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer	18
Efficient algorithms for simulating sequences along a phylogenetic tree	18
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation	18
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction	18
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms	18
GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk	18
JBrowse Jupyter: a Python interface to JBrowse 2	18
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction	18
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction	18
Optimal sequencing budget allocation for trajectory reconstruction of single cells	18
Closing the computational biology ‘knowledge gap’: Spanish Wikipedia as a case study	18
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index	18
SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph	18
Manifold classification of neuron types from microscopic images	18
A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins	18
Common data model for COVID-19 datasets	17
chem16S: community-level chemical metrics for exploring genomic adaptation to environments	17
CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS	17
PanTools v3: functional annotation, classification and phylogenomics	17
Probabilistic pathway-based multimodal factor analysis	17
CREMSA: compressed indexing of (ultra) large multiple sequence alignments	17
Assembly and reasoning over semantic mappings at scale for biomedical data integration	17
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings	17
Joint registration of multiple point clouds for fast particle fusion in localization microscopy	17
GAN-based data augmentation for transcriptomics: survey and comparative assessment	17
HNOXPred: a web tool for the prediction of gas-sensing H-NOX proteins from amino acid sequence	17
HCS—hierarchical algorithm for simulation of omics datasets	17
TARO: tree-aggregated factor regression for microbiome data integration	17
NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles	17
FlowDock: Geometric flow matching for generative protein–ligand docking and affinity prediction	17
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks	16
Drug–Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information	16
The 2024 ISCB Accomplishments by a Senior Scientist Award—Dr Tandy Warnow	16