Volume 39, Issue 9, September 2023

Original Paper

Genome analysis

Joint embedding of biological networks for cross-species functional alignment

Lechuan Li and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad529, https://doi.org/10.1093/bioinformatics/btad529

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Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

Wuwei Tan and Yang Shen

Bioinformatics, Volume 39, Issue 9, September 2023, btad541, https://doi.org/10.1093/bioinformatics/btad541

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μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data

Davide Cozzi and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad552, https://doi.org/10.1093/bioinformatics/btad552

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INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA

Jace Webster and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad569, https://doi.org/10.1093/bioinformatics/btad569

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GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs

Yuzhong Deng and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad533, https://doi.org/10.1093/bioinformatics/btad533

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Automated machine learning for genome wide association studies

Kleanthi Lakiotaki and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad545, https://doi.org/10.1093/bioinformatics/btad545

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Sequence analysis

MSDRP: a deep learning model based on multisource data for predicting drug response

Haochen Zhao and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad514, https://doi.org/10.1093/bioinformatics/btad514

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DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors

Anna Paola Muntoni and Andrea Pagnani

Bioinformatics, Volume 39, Issue 9, September 2023, btad537, https://doi.org/10.1093/bioinformatics/btad537

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Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads

Seong-Joon Park and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad548, https://doi.org/10.1093/bioinformatics/btad548

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Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation

Bryce Kille and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad512, https://doi.org/10.1093/bioinformatics/btad512

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DataDTA: a multi-feature and dual-interaction aggregation framework for drug–target binding affinity prediction

Yan Zhu and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad560, https://doi.org/10.1093/bioinformatics/btad560

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Phylogenetics

DecentTree: scalable Neighbour-Joining for the genomic era

Weiwen Wang and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad536, https://doi.org/10.1093/bioinformatics/btad536

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Phylogenetic inference using generative adversarial networks

Megan L Smith and Matthew W Hahn

Bioinformatics, Volume 39, Issue 9, September 2023, btad543, https://doi.org/10.1093/bioinformatics/btad543

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Structural bioinformatics

Optimal selection of suitable templates in protein interface prediction

Steven Grudman and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad510, https://doi.org/10.1093/bioinformatics/btad510

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Gene expression

Cell-connectivity-guided trajectory inference from single-cell data

Johannes Smolander and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad515, https://doi.org/10.1093/bioinformatics/btad515

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The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data

Viktoria Schuster and Anders Krogh

Bioinformatics, Volume 39, Issue 9, September 2023, btad497, https://doi.org/10.1093/bioinformatics/btad497

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IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions

Yiwei Liu and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad530, https://doi.org/10.1093/bioinformatics/btad530

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scAce: an adaptive embedding and clustering method for single-cell gene expression data

Xinwei He and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad546, https://doi.org/10.1093/bioinformatics/btad546

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ActivePPI: quantifying protein–protein interaction network activity with Markov random fields

Chuanyuan Wang and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad567, https://doi.org/10.1093/bioinformatics/btad567

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Genetics and population analysis

HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes

Sophie Wharrie and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad535, https://doi.org/10.1093/bioinformatics/btad535

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Genome-wide multimediator analyses using the generalized Berk–Jones statistics with the composite test

En-Yu Lai and Yen-Tsung Huang

Bioinformatics, Volume 39, Issue 9, September 2023, btad544, https://doi.org/10.1093/bioinformatics/btad544

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Systems biology

metGWAS 1.0: an R workflow for network-driven over-representation analysis between independent metabolomic and meta-genome-wide association studies

Saifur R Khan and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad523, https://doi.org/10.1093/bioinformatics/btad523

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A neighborhood-regularization method leveraging multiview data for predicting the frequency of drug–side effects

Lin Wang and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad532, https://doi.org/10.1093/bioinformatics/btad532

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Cardinality optimization in constraint-based modelling: application to human metabolism

Ronan M T Fleming and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad450, https://doi.org/10.1093/bioinformatics/btad450

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Data and text mining

Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data

Matthew D Smith and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad446, https://doi.org/10.1093/bioinformatics/btad446

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Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach

Yan Hu and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad542, https://doi.org/10.1093/bioinformatics/btad542

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DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction

Wei Qu and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad551, https://doi.org/10.1093/bioinformatics/btad551

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Accessibility of covariance information creates vulnerability in Federated Learning frameworks

Manuel Huth and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad531, https://doi.org/10.1093/bioinformatics/btad531

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An extensive benchmark study on biomedical text generation and mining with ChatGPT

Qijie Chen and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad557, https://doi.org/10.1093/bioinformatics/btad557

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Databases and ontologies

Somatic mutation effects diffused over microRNA dysregulation

Hui Yu and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad520, https://doi.org/10.1093/bioinformatics/btad520

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CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server

Pin Lyu and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad521, https://doi.org/10.1093/bioinformatics/btad521

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FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms

Federico Bianca and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad549, https://doi.org/10.1093/bioinformatics/btad549

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Applications Note

Genome analysis

iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences

Pablo Millan Arias and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad508, https://doi.org/10.1093/bioinformatics/btad508

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Tracking and curating putative SARS-CoV-2 recombinants with RIVET

Kyle Smith and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad538, https://doi.org/10.1093/bioinformatics/btad538

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mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation

Mercedeh Movassagh and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad565, https://doi.org/10.1093/bioinformatics/btad565

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Structural bioinformatics

RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints

Grzegorz Chojnowski and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad527, https://doi.org/10.1093/bioinformatics/btad527

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DrForna: visualization of cotranscriptional folding

Anda Ramona Tănasie and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad555, https://doi.org/10.1093/bioinformatics/btad555

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Gene expression

PyDESeq2: a python package for bulk RNA-seq differential expression analysis

Boris Muzellec and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad547, https://doi.org/10.1093/bioinformatics/btad547

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MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor

Bárbara Zita Peters Couto and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad550, https://doi.org/10.1093/bioinformatics/btad550

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Genetics and population analysis

diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype

Daoyi Huang and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad517, https://doi.org/10.1093/bioinformatics/btad517

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Data and text mining

MuTATE—an R package for comprehensive multi-objective molecular modeling

Sarah G Ayton and Víctor Treviño

Bioinformatics, Volume 39, Issue 9, September 2023, btad507, https://doi.org/10.1093/bioinformatics/btad507

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chem16S: community-level chemical metrics for exploring genomic adaptation to environments

Jeffrey M Dick and Xun Kang

Bioinformatics, Volume 39, Issue 9, September 2023, btad564, https://doi.org/10.1093/bioinformatics/btad564

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Bioimage informatics

VoDEx: a Python library for time annotation and management of volumetric functional imaging data

Anna Nadtochiy and others

Bioinformatics, Volume 39, Issue 9, September 2023, btad568, https://doi.org/10.1093/bioinformatics/btad568

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Message from ISCB

Systems biology

Advancements in computational modelling of biological systems: seventh annual SysMod meeting

Bhanwar Lal Puniya and Andreas Dräger

Bioinformatics, Volume 39, Issue 9, September 2023, btad539, https://doi.org/10.1093/bioinformatics/btad539

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Correction

Correction to: Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization

Bioinformatics, Volume 39, Issue 9, September 2023, btad554, https://doi.org/10.1093/bioinformatics/btad554

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Correction to: Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

Bioinformatics, Volume 39, Issue 9, September 2023, btad559, https://doi.org/10.1093/bioinformatics/btad559

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Correction to: “Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency”

Bioinformatics, Volume 39, Issue 9, September 2023, btad562, https://doi.org/10.1093/bioinformatics/btad562

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Correction to: Online bias-aware disease module mining with ROBUST-Web

Bioinformatics, Volume 39, Issue 9, September 2023, btad566, https://doi.org/10.1093/bioinformatics/btad566

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Correction to: Clustering spatial transcriptomics data

Bioinformatics, Volume 39, Issue 9, September 2023, btad574, https://doi.org/10.1093/bioinformatics/btad574

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