Bioinformatics

Article	Citations
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	2285
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	1911
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1117
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	361
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	251
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	191
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	146
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	141
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	127
Accurate assembly of multiple RNA-seq samples with Aletsch	111
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	109
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism	108
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data	105
From genes to trajectories: mapping genetic influences on Huntington’s disease progression	92
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	91
MDCompress: better, faster compression of molecular dynamics simulation trajectories	81
ATLIGATOR: editing protein interactions with an atlas-based approach	80
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction	80
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	79
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	79
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	72
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	72
NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks	70
FUSE: data-driven functional segmentation of DNA methylation data	70
Refining sequence-to-expression modelling with chromatin accessibility	70

Diagnosing scientific replicability through probabilistic distinguishability	67
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	64
Increasing confidence in proteomic spectral deconvolution through mass defect	63
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	59
Statistical framework to determine indel-length distribution	59
CodonMoE: DNA language models for codon-dependent mRNA prediction	58
HKD-CPI: high-order knowledge distillation enhanced inductive compound-protein interaction prediction	58
ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data	58
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	58
A-liner: linear alignment visualizer for genome comparisons	57
DivPro: diverse protein sequence design with direct structure recovery guidance	57
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	56
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	55
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	53
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	53
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	52
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	51
CANTATA—prediction of missing links in Boolean networks using genetic programming	48
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs	47
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors	47
ADViSELipidomics: a workflow for analyzing lipidomics data	45
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	45
scSurv: a deep generative model for single-cell survival analysis	44
SA2E: spatial-aware auto-encoder for cell type deconvolution of spatial transcriptomics data	44
TripLexicon: prediction and analysis of gene regulatory RNA–DNA interactions	44
phylobar: an R package for multiresolution compositional barplots in omics studies	44
The FASTQ+ format and PISA	43
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	43
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement	42
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	42
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	42
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	41
Floria: fast and accurate strain haplotyping in metagenomes	41
Decomposing mosaic tandem repeats accurately from long reads	37
A novel method for across-chromosome phasing without relative data	37
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures	37
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	37
StrucPTM: a database of structurally validated protein modifications and their conformational variation	37
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	36
Finding low-complexity DNA sequences with longdust	35
WMDS.net: a network control framework for identifying key players in transcriptome programs	34
LCR-modules: a collection of workflows for cancer genome analysis	34
Evidential meta-model for molecular property prediction	34
Network methods for diagonal integration of unpaired single-cell multiomics data: a review	34
STAR-GO: improving protein function prediction by learning to hierarchically integrate ontology-informed semantic embeddings	31
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	31
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	31
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	30
EXPLANA: a user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies	30
BrainConnect: processing brain connectivity and spatial transcriptomics data for integrative analysis	30

Prediction of gene co-expression from chromatin contacts with graph attention network	30
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests	30
Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment	29
Adaptive digital tissue deconvolution	29
RAREsim2: flexible simulation of rare variant genetic data using real haplotypes	29
ViReMaShiny : an interactive application for analysis of viral recombination data	29
VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions	29
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation	29
Columba: fast approximate pattern matching with optimized search schemes	28
Hierarchical reinforcement learning for automatic disease diagnosis	28
Control-guided refinement of partially specified Boolean networks: applications to RTK signaling	27
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	27
CryoPromptSeg: prompt-guided segmentation with integrated denoising for cryo-EM particle picking	27
SEMPLR: an R package for transcription factor binding prediction	27
Functional lipid analysis via index-based lipidomics profile: a new computational module in LipidOne	27
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	27
ECCB2022: the 21st European Conference on Computational Biology	26
Prediction and curation of missing biomedical identifier mappings with Biomappings	26
ShortCake: an integrated platform for efficient and reproducible single-cell analysis	26
Transfer learning for drug–target interaction prediction	26
GraphyloVar: predicting the impact of non-coding variants using a multi-species sequence model	26
A survey of models composed of graph neural networks and large language models for molecular science	26
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	26
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	25
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	25
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	25
LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis	24
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	24
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	24
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	24
BAV-LLPS: a database of bacterial, archaea, and virus liquid–liquid phase separation proteins	24
Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications	24
Using semantic search to find publicly available gene-expression datasets	24
Cell type matching across species using protein embeddings and transfer learning	24
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	24
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE	24
Geometry-complete perceptron networks for 3D molecular graphs	24
RNA threading with secondary structure and sequence profile	23
Improving biomedical entity linking with generative relevance feedback	23
Correction to: Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker	23
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	23
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	23
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	23
Prediction of bacterial protein–compound interactions with only positive samples	23
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	23
nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction	23
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	23
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	23
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	23
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	23
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	22
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	22
Generating synthetic genotypes using diffusion models	22
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	22
Conformal inference for reliable single cell RNA-seq annotation	22
Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data	22
PULPO: pipeline of understanding large-scale patterns of oncogenomic signatures	22
NEFFy: a versatile tool for computing the number of effective sequences	22
Modified RNAs and predictions with the ViennaRNA Package	22
The cell as a token: high-dimensional geometry in language models and cell embeddings	22
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	22
DeepLMI: deep feature mining with a globally enhanced graph convolutional network for robust lncRNA–miRNA interaction prediction	21
2023 ISCB Overton Prize: Jingyi Jessica Li	21
SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset	21
Scbean: a python library for single-cell multi-omics data analysis	21
TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection	21
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	21
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	21
treestructure: an R package to detect population structure in phylogenetic trees	21
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	21
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	21
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	20
Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads	20
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	20
Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data	20
Balancing complexity and clarity—towards clinician-ready antibiotic resistance prediction models	20
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	20
Drug response profile-based machine learning enables strategic cell line and compound selection for drug development	20
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	20
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	20

PEStimate : predicting offspring disease risk after polygenic embryo screening	20
INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies	20
The 2025 ISCB Overton Prize Award—Dr James Zou	20
Polyphest: fast polyploid phylogeny estimation	20
Improving dictionary-based named entity recognition with deep learning	20
CCC-GPU: a graphics processing unit (GPU)-accelerated nonlinear correlation coefficient for large-scale transcriptomic analyses	20
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	20
Powerful and interpretable control of false discoveries in two-group differential expression studies	20
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	20
A novel pipeline for computerized mouse spermatogenesis staging	20
HyperSeg-DG: multi-scale hyper feature context for domain-generalized medical image segmentation	20
Optimal phylogenetic reconstruction of insertion and deletion events	19
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	19
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data	19
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	19
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	19
FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues	19
Integrating curation into scientific publishing to train AI models	19
Determining epitope specificity of T-cell receptors with transformers	18
Managing workflow executions with WESkit	18
TSEDTA: a transformer-based neural network with SMILES transformer and ESM2 embeddings for drug-target binding affinity prediction	18
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	18
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation	18
Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation	18
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	18
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	18
Learning drug synergy through environment-conditioned feature modulation	18
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	18
mmContext: an open framework for multimodal contrastive learning of omics and text data	18
SimBu : bias-aware simulation of bulk RNA-seq data with variable cell-type composition	18
MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing	18
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	18
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	18
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	18
Prevalence aware feature selection improves biomarker identification in microbiome studies	18
DeepProtein: deep learning library and benchmark for protein sequence learning	18
Expanding the coverage of spatial proteomics: a machine learning approach	17
Somatic mutation effects diffused over microRNA dysregulation	17
NFTest: automated testing of Nextflow pipelines	17
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	17
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	17
Biological Random Walks: multi-omics integration for disease gene prioritization	17
Phylogenetic diversity statistics for all clades in a phylogeny	17
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	17
sedimix : a workflow for the analysis of hominin nuclear DNA sequences from sediments	17
RISK: a next-generation tool for biological network annotation and visualization	17
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	17
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	16
Bayesian inference of fitness landscapes via tree-structured branching processes	16
Accurate SPARQL generation via in-context learning and schema-based query construction	16
Semantic-enhanced heterogeneous graph learning for identifying ncRNAs associated with drug resistance	16
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	16
CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types	16
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	16
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data	16
BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool	16
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	16
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	16
GLiNER-BioMed: a suite of efficient models for open biomedical named entity recognition	16
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	16
Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing	15
NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles	15
JBrowse Jupyter: a Python interface to JBrowse 2	15
Hierarchical modelling of microbial communities	15
TARO: tree-aggregated factor regression for microbiome data integration	15
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization	15
Optimal sequencing budget allocation for trajectory reconstruction of single cells	15
konnect2prot: a web application to explore the protein properties in a functional protein–protein interaction network	15
A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins	15
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction	15
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	15
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction	15
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation	15
dAMN: a genome-scale neural-mechanistic hybrid model to predict bacterial growth dynamics	15
Manifold classification of neuron types from microscopic images	15
GAN-based data augmentation for transcriptomics: survey and comparative assessment	15
Harmonization and integration of pharmacogenomics screens	14
FlowDock: Geometric flow matching for generative protein–ligand docking and affinity prediction	14
PanTools v3: functional annotation, classification and phylogenomics	14
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts	14
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction	14
Exploiting pretrained biochemical language models for targeted drug design	14
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms	14
G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration	14
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings	14
GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk	14
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning	14
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index	14
SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph	14
Efficient algorithms for simulating sequences along a phylogenetic tree	14
Closing the computational biology ‘knowledge gap’: Spanish Wikipedia as a case study	14
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer	14
chem16S: community-level chemical metrics for exploring genomic adaptation to environments	13
SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements	13
Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy	13