Bioinformatics

Article	Citations
Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data	1179
2023 ISCB innovator award: Dana Pe’er	773
qTeller: a tool for comparative multi-genomic gene expression analysis	686
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts	587
webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration	554
The 2024 Outstanding Contributions to ISCB Award—Dr Scott Markel	463
Disease gene prediction with privileged information and heteroscedastic dropout	389
SPDE: a multi-functional software for sequence processing and data extraction	265
Embeddings of genomic region sets capture rich biological associations in lower dimensions	252
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information	229
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia	222
HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations	180
Biomedical evidence engineering for data-driven discovery	175
Correction to: GTExVisualizer: a web platform for supporting ageing studies	156
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs	147
ISMB 2022 proceedings	135
Current structure predictors are not learning the physics of protein folding	134
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing	127
MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA	125
Deep structure integrative representation of multi-omics data for cancer subtyping	117
CLIN-X: pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domain	116
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs	113
Computing optimal factories in metabolic networks with negative regulation	106
Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data	100
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data	100

Looking at the BiG picture: incorporating bipartite graphs in drug response prediction	95
MultiBaC: an R package to remove batch effects in multi-omic experiments	94
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution	93
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction	93
SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug–drug interactions	91
Fine-tuning protein embeddings for functional similarity evaluation	89
DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma	84
Biological Random Walks: multi-omics integration for disease gene prioritization	82
On the feasibility of dynamical analysis of network models of biochemical regulation	80
Clustering single-cell RNA-seq data by rank constrained similarity learning	79
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization	74
HPOFiller: identifying missing protein–phenotype associations by graph convolutional network	74
REALGAR: a web app of integrated respiratory omics data	74
DrugCVar: a platform for evidence-based drug annotation for genetic variants in cancer	74
SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition	73
I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform	73
MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data	72
massDatabase: utilities for the operation of the public compound and pathway database	71
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes	70
GLIDER: function prediction from GLIDE-based neighborhoods	70
teff: estimation of Treatment EFFects on transcriptomic data using causal random forest	68
Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures	67
medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata	65
Overcoming selection bias in synthetic lethality prediction	64
Phylogenetic diversity statistics for all clades in a phylogeny	63
A weighted distance-based approach for deriving consensus tumor evolutionary trees	63
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data	63
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations	61
Haplotype-based membership inference from summary genomic data	60
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images	59
Practical selection of representative sets of RNA-seq samples using a hierarchical approach	57
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data	56
tSFM 1.0: tRNA Structure–Function Mapper	56
PrISM: precision for integrative structural models	56
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments	55
scWMC: weighted matrix completion-based imputation of scRNA-seq data via prior subspace information	55
scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation	55
Study of real-valued distance prediction for protein structure prediction with deep learning	54
Systematic replication enables normalization of high-throughput imaging assays	54
DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia	54
Discovering drug–target interaction knowledge from biomedical literature	53
wenda_gpu: fast domain adaptation for genomic data	52
Utilizing image and caption information for biomedical document classification	52
Optimization of drug–target affinity prediction methods through feature processing schemes	52
SpaceX: gene co-expression network estimation for spatial transcriptomics	51
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers	51
Fec: a fast error correction method based on two-rounds overlapping and caching	51
MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences	50
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG	50
CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction	50

CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks	49
Rapid T-cell receptor interaction grouping with ting	49
Predicting anti-cancer drug response by finding optimal subset of drugs	49
3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax	48
TimiRGeN: R/Bioconductor package for time series microRNA–mRNA integration and analysis	48
PaIntDB: network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa	48
SimService: a lightweight library for building simulation services in Python	47
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design	47
Statistical framework to determine indel-length distribution	47
GdClean: removal of Gadolinium contamination in mass cytometry data	47
SPOT: a web-tool enabling swift profiling of transcriptomes	47
ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes	47
DMIL-IsoFun: predicting isoform function using deep multi-instance learning	47
CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype–genotype interaction	47
Phytest: quality control for phylogenetic analyses	47
DeepSec: a deep learning framework for secreted protein discovery in human body fluids	46
Organism-specific training improves performance of linear B-cell epitope prediction	46
Joint eQTL mapping and inference of gene regulatory network improves power of detecting bothcis- andtrans-eQTLs	45
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images	45
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype	45
ATLIGATOR: editing protein interactions with an atlas-based approach	44
ConsensuSV—from the whole-genome sequencing data to the complete variant list	44
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data	44
PsiNorm: a scalable normalization for single-cell RNA-seq data	44
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data	43
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network	43
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS	43
RCandy: an R package for visualizing homologous recombinations in bacterial genomes	43
COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases	43
An empirical study on KDIGO-defined acute kidney injury prediction in the intensive care unit	43
Accurate large-scale phylogeny-aware alignment using BAli-Phy	42
HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer	42
CAMML with the Integration of Marker Proteins (ChIMP)	42
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets	42
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification	41
learnMSA2: deep protein multiple alignments with large language and hidden Markov models	41
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation	41
Comparing transmembrane protein structures with ATOLL	40
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein–protein interaction databases	40
PANPROVA: pangenomic prokaryotic evolution of full assemblies	40
Deciphering associations between gut microbiota and clinical factors using microbial modules	39
CIBRA identifies genomic alterations with a system-wide impact on tumor biology	39
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity	39
Completing gene trees without species trees in sub-quadratic time	39
A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors	39
Integrated Genome Browser App Store	39
LPTD: a novel linear programming-based topology determination method for cryo-EM maps	38
fastISM: performantin silicosaturation mutagenesis for convolutional neural networks	38
An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation	38
Chromosomal imbalances detected via RNA-sequencing in 28 cancers	38
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem	37
TMQuery: a database of precomputed template modeling scores for assessment of protein structural similarity	37
Steer’n’Detect: fast 2D template detection with accurate orientation estimation	36
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach	36
Biomarker identification by interpretable maximum mean discrepancy	36
maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines	36
StAmP-DB: a platform for structures of polymorphic amyloid fibril cores	36
BSDE: barycenter single-cell differential expression for case–control studies	36
Synthetic-to-real: instance segmentation of clinical cluster cells with unlabeled synthetic training	35
KIMGENS: a novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure	35
Scoring protein sequence alignments using deep learning	35
Mian: interactive web-based microbiome data table visualization and machine learning platform	35
Seeding with minimized subsequence	35
seqgra: principled selection of neural network architectures for genomics prediction tasks	35
MOJITOO: a fast and universal method for integration of multimodal single-cell data	34
POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching	34
OMAMO: orthology-based alternative model organism selection	34
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses	34
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities	33
SPEAR: Systematic ProtEin AnnotatoR	33
The DOMINO web-server for active module identification analysis	33
Deep Subspace Mutual Learning for cancer subtypes prediction	33
Median and small parsimony problems on RNA trees	33
Trap spaces of multi-valued networks: definition, computation, and applications	33
scKINETICS: inference of regulatory velocity with single-cell transcriptomics data	33
Overcoming biases in causal inference of molecular interactions	33
RoDiCE: robust differential protein co-expression analysis for cancer complexome	33
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases	33
Phylogenomic branch length estimation using quartets	33
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion	33

CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis	33
SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks	32
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology	32
Explainable multimodal machine learning model for classifying pregnancy drug safety	32
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores	32
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations	32
MuWU: Mutant-seq library analysis and annotation	32
Toward the assessment of predicted inter-residue distance	32
Multi-instance learning of graph neural networks for aqueous pKa prediction	32
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions	32
ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR	32
NetControl4BioMed: a web-based platform for controllability analysis of protein–protein interaction networks	32
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves	31
Learning locality-sensitive bucketing functions	31
ACES: Analysis of Conservation with an Extensive list of Species	31
Clustering spatial transcriptomics data	30
Accurate assembly of multiple RNA-seq samples with Aletsch	30
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA	30
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria	30
MS1Connect: a mass spectrometry run similarity measure	30
TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs	30
An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics	29
A count-based model for delineating cell–cell interactions in spatial transcriptomics data	29
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations	29
SigTools: exploratory visualization for genomic signals	29
Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model	29
On the stability of log-rank test under labeling errors	29
dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA–protein binding	28
BioCCP.jl: collecting coupons in combinatorial biotechnology	28
On the relation between input and output distributions of scRNA-seq experiments	28
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations	28
Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets	28
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects	28
A heuristic algorithm solving the mutual-exclusivity-sorting problem	28
Predicting protein functions using positive-unlabeled ranking with ontology-based priors	28
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures	28
DULoc: quantitatively unmixing protein subcellular location patterns in immunofluorescence images based on deep learning features	28
ChromDL: a next-generation regulatory DNA classifier	27
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics	27
AMC: accurate mutation clustering from single-cell DNA sequencing data	27
HOMELETTE: a unified interface to homology modelling software	27
Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions	27
CACONET: a novel classification framework for microbial correlation networks	27
MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm	27
Target–Decoy MineR for determining the biological relevance of variables in noisy datasets	26
VeTra: a tool for trajectory inference based on RNA velocity	26
NeoFox: annotating neoantigen candidates with neoantigen features	26
An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells	26
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models	26
Identification of cell-type-specific spatially variable genes accounting for excess zeros	26
Comparison of structural variants detected by optical mapping with long-read next-generation sequencing	26
XRRpred: accurate predictor of crystal structure quality from protein sequence	26
Topology-based sparsification of graph annotations	26
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX	26
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics	26
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis	26
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores	26
MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data	25
ASHLEYS: automated quality control for single-cell Strand-seq data	25
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments	25
methyLImp2: faster missing value estimation for DNA methylation data	25
RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset	25
On the stability of log-rank test under labeling errors	25
IIFDTI: predicting drug–target interactions through interactive and independent features based on attention mechanism	25
3D GAN image synthesis and dataset quality assessment for bacterial biofilm	25
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry	25
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow	24
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation	24
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data	24
pKPDB: a protein data bank extension database of pKa and pI theoretical values	24
Isoform function prediction by Gene Ontology embedding	24
Correction to: GSpace: an exact coalescence simulator of recombining genomes under isolation by distance	24
GBZ file format for pangenome graphs	24
GEInter: an R package for robust gene–environment interaction analysis	24
Improving deep learning-based protein distance prediction in CASP14	24
Somatic mutation effects diffused over microRNA dysregulation	24
pycofitness—Evaluating the fitness landscape of RNA and protein sequences	24
Statistical approaches for differential expression analysis in metatranscriptomics	24
Automated exploitation of deep learning for cancer patient stratification across multiple types	24
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data	24
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules	24
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties	24
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment	24
CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations	24
A graph neural network approach for molecule carcinogenicity prediction	24
Metagenomic functional profiling: to sketch or not to sketch?	23
DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction	23
The topology of data: opportunities for cancer research	23
IntelliPy: a GUI for analyzing IntelliCage data	23
GNN-based embedding for clustering scRNA-seq data	23
Expanding the coverage of spatial proteomics: a machine learning approach	23
RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks	23
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints	23
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure	23
On the reliability and the limits of inference of amino acid sequence alignments	23