Bioinformatics

Article	Citations
Correction to: GTExVisualizer: a web platform for supporting ageing studies	1248
Predicting anti-cancer drug response by finding optimal subset of drugs	812
Accurate assembly of multiple RNA-seq samples with Aletsch	715
Statistical framework to determine indel-length distribution	618
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	579
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	488
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	431
Completing gene trees without species trees in sub-quadratic time	271
ATLIGATOR: editing protein interactions with an atlas-based approach	267
PsiNorm: a scalable normalization for single-cell RNA-seq data	243
Practical selection of representative sets of RNA-seq samples using a hierarchical approach	239
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	194
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	177
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	165
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	158
Integrated Genome Browser App Store	142
PANPROVA: pangenomic prokaryotic evolution of full assemblies	131
MuWU: Mutant-seq library analysis and annotation	127
Clustering single-cell RNA-seq data by rank constrained similarity learning	120
Haplotype-based membership inference from summary genomic data	117
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	116
Deep Subspace Mutual Learning for cancer subtypes prediction	111
pKPDB: a protein data bank extension database of pKa and pI theoretical values	107
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	103
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	100

MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	99
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints	97
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	95
CrossTalkeR: analysis and visualization of ligand–receptorne tworks	94
monaLisa: an R/Bioconductor package for identifying regulatory motifs	93
ELIXIR: providing a sustainable infrastructure for life science data at European scale	88
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	86
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions	82
Increasing confidence in proteomic spectral deconvolution through mass defect	81
SimPlot++: a Python application for representing sequence similarity and detecting recombination	78
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	77
Refget: standardized access to reference sequences	76
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning	76
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories	75
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing	75
The ENDS of assumptions: an online tool for the epistemic non-parametric drug–response scoring	75
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome	74
Prediction of whole-cell transcriptional response with machine learning	74
Inference of 3D genome architecture by modeling overdispersion of Hi-C data	69
GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks	69
Accurate spliced alignment of long RNA sequencing reads	67
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures	66
Decomposing mosaic tandem repeats accurately from long reads	66
Cross-species prediction of essential genes in insects	64
WMDS.net: a network control framework for identifying key players in transcriptome programs	64
Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation	63
CANTATA—prediction of missing links in Boolean networks using genetic programming	61
Hardware acceleration of genomics data analysis: challenges and opportunities	61
ProSynAR: a reference aware read merger	60
PyLiger: scalable single-cell multi-omic data integration in Python	60
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors	59
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences	58
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses	58
Exploring automatic inconsistency detection for literature-based gene ontology annotation	57
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses	57
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families	57
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci	56
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements	55
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs	55
Tysserand—fast and accurate reconstruction of spatial networks from bioimages	53
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants	53
MAT2: manifold alignment of single-cell transcriptomes with cell triplets	53
Evidential meta-model for molecular property prediction	52
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries	52
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells	52
Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis	52
The FASTQ+ format and PISA	51
Continual knowledge infusion into pre-trained biomedical language models	51
trfermikit: a tool to discover VNTR-associated deletions	51
RNAglib: a python package for RNA 2.5 D graphs	51

Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation	51
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition	51
Floria: fast and accurate strain haplotyping in metagenomes	51
Perceiver CPI: a nested cross-attention network for compound–protein interaction prediction	50
ADViSELipidomics: a workflow for analyzing lipidomics data	50
MICER: a pre-trained encoder–decoder architecture for molecular image captioning	50
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes	50
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data	49
XSI—a genotype compression tool for compressive genomics in large biobanks	49
minoTour, real-time monitoring and analysis for nanopore sequencers	49
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database	49
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning	49
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition	49
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction	48
DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks	48
Single-cell RNA sequencing data analysis based on non-uniformε−neighborhood network	48
BridgeDPI: a novel Graph Neural Network for predicting drug–protein interactions	48
EpiDope: a deep neural network for linear B-cell epitope prediction	47
hipFG: high-throughput harmonization and integration pipeline for functional genomics data	46
BATL: Bayesian annotations for targeted lipidomics	46
De novo protein design by an energy function based on series expansion in distance and orientation dependence	46
From viral evolution to spatial contagion: a biologically modulated Hawkes model	45
Hierarchical reinforcement learning for automatic disease diagnosis	45
Transfer learning for drug–target interaction prediction	45
VSS: variance-stabilized signals for sequencing-based genomic signals	44
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool	44
Adaptive digital tissue deconvolution	44
Powerful molecule generation with simple ConvNet	44
Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation	44
ViReMaShiny: an interactive application for analysis of viral recombination data	44
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines	44
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations	43
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs	43
Prediction and curation of missing biomedical identifier mappings with Biomappings	43
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds	43
Prediction of gene co-expression from chromatin contacts with graph attention network	43
2DProts: database of family-wide protein secondary structure diagrams	41
Interfacing Seurat with the R tidy universe	41
High-sensitivity pattern discovery in large, paired multiomic datasets	41
LINADMIX: evaluating the effect of ancient admixture events on modern populations	41
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario	41
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging	41
CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data	40
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl	40
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics	40
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides	40
The minimizer Jaccard estimator is biased and inconsistent	39
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph	38
RawHummus: an R Shiny app for automated raw data quality control in metabolomics	38
ECCB2022: the 21st European Conference on Computational Biology	38
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality	38
Geometry-complete perceptron networks for 3D molecular graphs	38
Functional characterization of co-phosphorylation networks	38
OMEN: network-based driver gene identification using mutual exclusivity	37
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge	37
Cell type matching across species using protein embeddings and transfer learning	37
Inferring the experimental design for accurate gene regulatory network inference	37
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties	37
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes	37
LevioSAM: fast lift-over of variant-aware reference alignments	37
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq	37
Spectral clustering of single-cell multi-omics data on multilayer graphs	36
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python	36
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network	36
Sparse allele vectors and the savvy software suite	36
PltDB: a blood platelets-based gene expression database for disease investigation	36
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence	35
On the feasibility of deep learning applications using raw mass spectrometry data	35
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures	35
LOCAN: a python library for analyzing single-molecule localization microscopy data	35
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS	35
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes	35
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis	35
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction	34
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning	34
Modified RNAs and predictions with the ViennaRNA Package	34
HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets	34
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics	34
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images	34
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction	34

scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression	34
CCIP: predicting CTCF-mediated chromatin loops with transitivity	33
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity	33
RNA threading with secondary structure and sequence profile	33
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes	33
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data	33
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets	33
tcplfit2: an R-language general purpose concentration–response modeling package	33
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers	33
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data	32
2023 ISCB Overton Prize: Jingyi Jessica Li	32
Efficient gradient boosting for prognostic biomarker discovery	32
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice	32
Scbean: a python library for single-cell multi-omics data analysis	31
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations	31
MIAMI: mutual information-based analysis of multiplex imaging data	31
The 2024 ISCB Overton Prize Award—Dr Martin Steinegger	31
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data	31
SBGNview: towards data analysis, integration and visualization on all pathways	30
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning	30
libOmexMeta: enabling semantic annotation of models to support FAIR principles	30
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data	30
Deep graph representations embed network information for robust disease marker identification	30
An automated multi-modal graph-based pipeline for mouse genetic discovery	29
iSFun: an R package for integrative dimension reduction analysis	29
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences	29
Improving dictionary-based named entity recognition with deep learning	29
An approachable, flexible and practical machine learning workshop for biologists	29
MorphoScript: a dedicated analysis to assess the morphology and contractile structures of cardiomyocytes derived from stem cells	29
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites	29
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis	29
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads	28
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency	28
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study	28
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding	28
Galaxy Helm chart: a standardized method for deploying production Galaxy servers	28
Computational modeling of mRNA degradation dynamics using deep neural networks	28
RENANO: a REference-based compressor for NANOpore FASTQ files	28
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design	28
Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation	28
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs	28
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing	28
Efficient change-points detection for genomic sequences via cumulative segmented regression	28
scDetect: a rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer	27
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides	27
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides	27
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction	27
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks	27
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline	27
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems	27
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference	27
MIO: microRNA target analysis system for immuno-oncology	27
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients	27
KCOSS: an ultra-fast k-mer counter for assembled genome analysis	26
PeakBot: machine-learning-based chromatographic peak picking	26
Liftoff: accurate mapping of gene annotations	26
Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories	26
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis	26
Fully unsupervised deep mode of action learning for phenotyping high-content cellular images	26
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning	26
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids	26
Determining epitope specificity of T-cell receptors with transformers	25
SplicingFactory—splicing diversity analysis for transcriptome data	25
CIndex: compressed indexes for fast retrieval of FASTQ files	25
HyperGraphs.jl: representing higher-order relationships in Julia	25
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data	25
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning	25
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir	25
WGA-LP: a pipeline for whole genome assembly of contaminated reads	25
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes	25
Nezzle: an interactive and programmable visualization of biological networks in Python	25
ELIXIR biovalidator for semantic validation of life science metadata	25
Oligator: a flexible interface to draw oligosaccharide structures and generate their theoretical tandem mass spectra	25
efam: an expanded, metaproteome-supported HMM profile database of viral protein families	25
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data	25
Testing microbiome association using integrated quantile regression models	25
A novel pipeline for computerized mouse spermatogenesis staging	25
Querying multiple sets ofP-values through composed hypothesis testing	25
Polyphest: fast polyploid phylogeny estimation	25
SPRISS: approximating frequentk-mers by sampling reads, and applications	25
ATHENA: analysis of tumor heterogeneity from spatial omics measurements	24
ISMB/ECCB 2021 proceedings	24
Optimal phylogenetic reconstruction of insertion and deletion events	24
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale	24
Driver gene detection through Bayesian network integration of mutation and expression profiles	24
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data	24
VisuaLife: library for interactive visualization in rich web applications	24
S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection	24
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands	24
GADGETS: a genetic algorithm for detecting epistasis using nuclear families	24
RAxML Grove: an empirical phylogenetic tree database	24
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits	24
Learning sparse log-ratios for high-throughput sequencing data	24
ORT: a workflow linking genome-scale metabolic models with reactive transport codes	24
Powerful and interpretable control of false discoveries in two-group differential expression studies	24