Bioinformatics

Article	Citations
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks	2387
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1990
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins	374
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment	282
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline	199
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT	151
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics	132
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data	116
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism	116
From genes to trajectories: mapping genetic influences on Huntington’s disease progression	111
MDCompress: better, faster compression of molecular dynamics simulation trajectories	110
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction	96
ATLIGATOR: editing protein interactions with an atlas-based approach	93
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	85
The 2025 ISCB Accomplishments by a Senior Scientist Award—Dr Amos Bairoch	84
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	81
FUSE: data-driven functional segmentation of DNA methylation data	80
NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks	73
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	73
Diagnosing scientific replicability through probabilistic distinguishability	73
DivPro: diverse protein sequence design with direct structure recovery guidance	72
A-liner: linear alignment visualizer for genome comparisons	70
CodonMoE: DNA language models for codon-dependent mRNA prediction	66
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs	66
ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data	65

Increasing confidence in proteomic spectral deconvolution through mass defect	60
HKD-CPI: high-order knowledge distillation enhanced inductive compound-protein interaction prediction	60
LoMuS: low-rank adaptation with sequence multi-representation improves protein stability prediction	60
Statistical framework to determine indel-length distribution	59
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection	59
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples	59
Accurate assembly of multiple RNA-seq samples with Aletsch	58
3DICE: interpretable 3D cross-modal learning for drug–target interaction prediction and large-scale drug discovery	55
ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics	54
NPBIP: predicting binding preferences of uncharacterized nucleic-acid-binding proteins	53
Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data	53
DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing	50
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	49
Refining sequence-to-expression modelling with chromatin accessibility	49
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	46
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	46
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes	46
CANTATA—prediction of missing links in Boolean networks using genetic programming	45
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs	45
ADViSELipidomics: a workflow for analyzing lipidomics data	44
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	44
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors	44
SA2E: spatial-aware auto-encoder for cell type deconvolution of spatial transcriptomics data	43
TripLexicon: prediction and analysis of gene regulatory RNA–DNA interactions	43
phylobar: an R package for multiresolution compositional barplots in omics studies	43
scSurv: a deep generative model for single-cell survival analysis	42
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement	42
Floria: fast and accurate strain haplotyping in metagenomes	39
Decomposing mosaic tandem repeats accurately from long reads	39
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures	39
A novel method for across-chromosome phasing without relative data	38
StrucPTM: a database of structurally validated protein modifications and their conformational variation	38
Finding low-complexity DNA sequences with longdust	35
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	35
LCR-modules: a collection of workflows for cancer genome analysis	34
Network methods for diagonal integration of unpaired single-cell multiomics data: a review	34
WMDS.net: a network control framework for identifying key players in transcriptome programs	33
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	32
GT-Mamba: a Topology-Aware Graph-State space model for robust and interpretable epigenetic age prediction	32
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	32
The 2026 ISCB Overton Prize Award—Dr Marinka Zitnik	31
DeepSynBa: actionable drug combination prediction with complete dose-response profiles	31
R4ST: a reference-guided graph-generative model for robust reconstruction of spatial transcriptomic profiles	31
Evidential meta-model for molecular property prediction	31
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs	30
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	30
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	30
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	30
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	30
SegJointGene: joint cell segmentation and spatial gene prioritization by information entropy guided convolutional neural networks	30

The FASTQ+ format and PISA	30
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification	29
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model	29
GraphyloVar: predicting the impact of non-coding variants using a multi-species sequence model	28
Robust prioritization of genomic features with stability selection	28
ShortCake: an integrated platform for efficient and reproducible single-cell analysis	28
VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion	28
A survey of models composed of graph neural networks and large language models for molecular science	28
BrainConnect: processing brain connectivity and spatial transcriptomics data for integrative analysis	27
Prediction of gene co-expression from chromatin contacts with graph attention network	27
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests	27
EXPLANA: a user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies	27
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	27
STAR-GO: improving protein function prediction by learning to hierarchically integrate ontology-informed semantic embeddings	27
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation	26
Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment	26
RAREsim2: flexible simulation of rare variant genetic data using real haplotypes	26
VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions	26
Columba: fast approximate pattern matching with optimized search schemes	26
SpaBiT: enhancing spatial transcriptomics resolution via bidirectional attention transformers	25
Transfer learning for drug–target interaction prediction	25
Control-guided refinement of partially specified Boolean networks: applications to RTK signaling	25
Prediction and curation of missing biomedical identifier mappings with Biomappings	25
Functional lipid analysis via index-based lipidomics profile: a new computational module in LipidOne	25
CryoPromptSeg: prompt-guided segmentation with integrated denoising for cryo-EM particle picking	25
Enhancing cross-context generalization in drug perturbation prediction with a multimodal conditional diffusion framework	25
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	25
SEMPLR: an R package for transcription factor binding prediction	25
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	24
Adaptive digital tissue deconvolution	24
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	24
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	24
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	24
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	24
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	24
Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications	23
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	23
Prediction of bacterial protein–compound interactions with only positive samples	23
Using semantic search to find publicly available gene-expression datasets	23
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	23
Correction to: Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker	23
LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis	23
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	23
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	23
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	23
PULPO: pipeline of understanding large-scale patterns of oncogenomic signatures	22
VIJB: a companion of the JBROWSE genome browser for the visually impaired people	22
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	22
The cell as a token: high-dimensional geometry in language models and cell embeddings	22
Cell type matching across species using protein embeddings and transfer learning	22
Movi 2: fast and space-efficient queries on pangenomes	22
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	22
Improving biomedical entity linking with generative relevance feedback	22
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	22
Protein–nucleic acid binding site prediction using interpretable Kolmogorov–Arnold networks with hypergraph representation learning	21
Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity	21
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE	21
Geometry-complete perceptron networks for 3D molecular graphs	21
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	21
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	21
Deciphering key factors of active learning performance in biomolecular design	21
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	21
NEFFy: a versatile tool for computing the number of effective sequences	20
BAV-LLPS: a database of bacterial, archaea, and virus liquid–liquid phase separation proteins	20
ECCB2022: the 21st European Conference on Computational Biology	20
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach	20
Conformal inference for reliable single cell RNA-seq annotation	20
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	20
RNA threading with secondary structure and sequence profile	20
Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data	19
Modified RNAs and predictions with the ViennaRNA Package	19
DeepLMI: deep feature mining with a globally enhanced graph convolutional network for robust lncRNA–miRNA interaction prediction	19
2023 ISCB Overton Prize: Jingyi Jessica Li	19
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	19
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	19
treestructure: an R package to detect population structure in phylogenetic trees	19
Generating synthetic genotypes using diffusion models	19
nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction	19
TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection	19
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	19

PU-GRAIL: residue-level graph learning for identifying protective bacterial antigens under positive-unlabeled supervision	18
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	18
Drug response profile-based machine learning enables strategic cell line and compound selection for drug development	18
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	18
Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads	18
SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset	18
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks	18
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	18
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction	18
Bridging ancestry gaps in genomic risk prediction with tabular foundation models	18
Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data	18
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	18
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	18
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	18
Improving dictionary-based named entity recognition with deep learning	18
Scbean: a python library for single-cell multi-omics data analysis	18
The 2025 ISCB Overton Prize Award—Dr James Zou	18
HyperSeg-DG: multi-scale hyper feature context for domain-generalized medical image segmentation	18
CCC-GPU: a graphics processing unit (GPU)-accelerated nonlinear correlation coefficient for large-scale transcriptomic analyses	18
INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies	18
PEStimate : predicting offspring disease risk after polygenic embryo screening	18
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	17
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences	17
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	17
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	17
FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues	17
Powerful and interpretable control of false discoveries in two-group differential expression studies	17
Managing workflow executions with WESkit	17
Polyphest: fast polyploid phylogeny estimation	17
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server	16
Integrating curation into scientific publishing to train AI models	16
Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation	16
MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing	16
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	16
Learning drug synergy through environment-conditioned feature modulation	16
TSEDTA: a transformer-based neural network with SMILES transformer and ESM2 embeddings for drug-target binding affinity prediction	16
mmContext: an open framework for multimodal contrastive learning of omics and text data	16
Determining epitope specificity of T-cell receptors with transformers	16
MixingDTA: improved drug–target affinity prediction by extending mixup with guilt-by-association	16
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data	16
Prevalence aware feature selection improves biomarker identification in microbiome studies	16
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	16
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	15
CAMUS: scalable phylogenetic network estimation	15
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	15
Expanding the coverage of spatial proteomics: a machine learning approach	15
RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing	15
Benchmarking AI scientists for omics data–driven biological discovery	15
The 2026 ISCB Outstanding Service Award—Dr Philip E. Bourne	15
Optimal phylogenetic reconstruction of insertion and deletion events	15
A novel pipeline for computerized mouse spermatogenesis staging	15
CATH-ddG: towards robust mutation effect prediction on protein–protein interactions out of CATH homologous superfamily	15
Balancing complexity and clarity—towards clinician-ready antibiotic resistance prediction models	15
DeepProtein: deep learning library and benchmark for protein sequence learning	15
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation	15
CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types	14
Somatic mutation effects diffused over microRNA dysregulation	14
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	14
Accurate SPARQL generation via in-context learning and schema-based query construction	14
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	14
RISK: a next-generation tool for biological network annotation and visualization	14
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	14
sedimix : a workflow for the analysis of hominin nuclear DNA sequences from sediments	14
Phylogenetic diversity statistics for all clades in a phylogeny	14
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	14
SimBu : bias-aware simulation of bulk RNA-seq data with variable cell-type composition	13
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	13
Hotgenes: an R package for reducing bottlenecks in bulk omics data exploration and collaboration	13
ADAMIXTURE: adaptive first-order optimization for biobank-scale genetic clustering	13
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction	13
Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing	13
Bayesian inference of fitness landscapes via tree-structured branching processes	13
GLiNER-BioMed: a suite of efficient models for open biomedical named entity recognition	13
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	13
Semantic-enhanced heterogeneous graph learning for identifying ncRNAs associated with drug resistance	13
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation	13
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	13
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	13
BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool	13
NFTest: automated testing of Nextflow pipelines	13
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data	13
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	13
Optimal sequencing budget allocation for trajectory reconstruction of single cells	13
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	13
Inferring and evaluating network medicine-based disease modules with nextflow	12
Efficient algorithms for simulating sequences along a phylogenetic tree	12
TARO: tree-aggregated factor regression for microbiome data integration	12
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts	12
CPS: mapping physical coordinates to high-fidelity spatial transcriptomics via privileged multi-scale context distillation	12
A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins	12
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction	12
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer	12
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization	12
Manifold classification of neuron types from microscopic images	12
G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration	12