Volume 39, Issue 10, October 2023

Original Paper

Genome analysis

Phables: from fragmented assemblies to high-quality bacteriophage genomes

Vijini Mallawaarachchi and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad586, https://doi.org/10.1093/bioinformatics/btad586

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SHIP: identifying antimicrobial resistance gene transfer between plasmids

Marco Teixeira and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad612, https://doi.org/10.1093/bioinformatics/btad612

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Privacy-preserving federated genome-wide association studies via dynamic sampling

Xinyue Wang and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad639, https://doi.org/10.1093/bioinformatics/btad639

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Sequence analysis

FrameD: framework for DNA-based data storage design, verification, and validation

Kevin D Volkel and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad572, https://doi.org/10.1093/bioinformatics/btad572

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HQAlign: aligning nanopore reads for SV detection using current-level modeling

Dhaivat Joshi and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad580, https://doi.org/10.1093/bioinformatics/btad580

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pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models

Kamil Kaminski and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad579, https://doi.org/10.1093/bioinformatics/btad579

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Design of optimal labeling patterns for optical genome mapping via information theory

Yevgeni Nogin and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad601, https://doi.org/10.1093/bioinformatics/btad601

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DeepPeptide predicts cleaved peptides in proteins using conditional random fields

Felix Teufel and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad616, https://doi.org/10.1093/bioinformatics/btad616

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Predicting enzymatic function of protein sequences with attention

Nicolas Buton and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad620, https://doi.org/10.1093/bioinformatics/btad620

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Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings

Yao-zhong Zhang and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad617, https://doi.org/10.1093/bioinformatics/btad617

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Structural bioinformatics

Using a novel structure/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development

Zahed Khatooni and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad590, https://doi.org/10.1093/bioinformatics/btad590

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Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction

Haifan Gong and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad589, https://doi.org/10.1093/bioinformatics/btad589

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Gene expression

ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data

Mohammad Nuwaisir Rahman and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad594, https://doi.org/10.1093/bioinformatics/btad594

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iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion

Yiming Wu and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad619, https://doi.org/10.1093/bioinformatics/btad619

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Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data

Ping-Han Hsieh and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad610, https://doi.org/10.1093/bioinformatics/btad610

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stVAE deconvolves cell-type composition in large-scale cellular resolution spatial transcriptomics

Chen Li and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad642, https://doi.org/10.1093/bioinformatics/btad642

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Systems biology

GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype

Dabin Jeong and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad582, https://doi.org/10.1093/bioinformatics/btad582

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MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing

Ali Osman Berk Şapcı and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad592, https://doi.org/10.1093/bioinformatics/btad592

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Extending protein interaction networks using proteoforms and small molecules

Luis Francisco Hernández Sánchez and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad598, https://doi.org/10.1093/bioinformatics/btad598

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Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis

Axel von Kamp and Steffen Klamt

Bioinformatics, Volume 39, Issue 10, October 2023, btad600, https://doi.org/10.1093/bioinformatics/btad600

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An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells

Shabnam Sahay and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad602, https://doi.org/10.1093/bioinformatics/btad602

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Scalable inference of cell differentiation networks in gene therapy clonal tracking studies of haematopoiesis

Luca Del Core and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad605, https://doi.org/10.1093/bioinformatics/btad605

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Constructing maps between distinct cell fates and parametric conditions by systematic perturbations

Ruoyu Tang and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad624, https://doi.org/10.1093/bioinformatics/btad624

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Data and text mining

DeepCCI: a deep learning framework for identifying cell–cell interactions from single-cell RNA sequencing data

Wenyi Yang and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad596, https://doi.org/10.1093/bioinformatics/btad596

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A machine learning-based quantitative model (LogBB_Pred) to predict the blood–brain barrier permeability (logBB value) of drug compounds

Bilal Shaker and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad577, https://doi.org/10.1093/bioinformatics/btad577

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A cell-level discriminative neural network model for diagnosis of blood cancers

Edgar E Robles and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad585, https://doi.org/10.1093/bioinformatics/btad585

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SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra

Xu Han and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad593, https://doi.org/10.1093/bioinformatics/btad593

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Evidential meta-model for molecular property prediction

Kyung Pyo Ham and Lee Sael

Bioinformatics, Volume 39, Issue 10, October 2023, btad604, https://doi.org/10.1093/bioinformatics/btad604

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Predicting synergistic anticancer drug combination based on low-rank global attention mechanism and bilinear predictor

Yanglan Gan and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad607, https://doi.org/10.1093/bioinformatics/btad607

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Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information

Peishun Jiao and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad637, https://doi.org/10.1093/bioinformatics/btad637

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Bioimage informatics

Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks

Kwan-Ling Wu and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad584, https://doi.org/10.1093/bioinformatics/btad584

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Simulating structurally variable nuclear pore complexes for microscopy

Maria Theiss and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad587, https://doi.org/10.1093/bioinformatics/btad587

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Applications Note

Genome analysis

compleasm: a faster and more accurate reimplementation of BUSCO

Neng Huang and Heng Li

Bioinformatics, Volume 39, Issue 10, October 2023, btad595, https://doi.org/10.1093/bioinformatics/btad595

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scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data

Huiling Liu and Wenxiu Ma

Bioinformatics, Volume 39, Issue 10, October 2023, btad625, https://doi.org/10.1093/bioinformatics/btad625

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PanKmer: k-mer-based and reference-free pangenome analysis

Anthony J Aylward and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad621, https://doi.org/10.1093/bioinformatics/btad621

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Sequence analysis

phippery: a software suite for PhIP-Seq data analysis

Jared G Galloway and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad583, https://doi.org/10.1093/bioinformatics/btad583

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simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry

Dongze He and Rob Patro

Bioinformatics, Volume 39, Issue 10, October 2023, btad614, https://doi.org/10.1093/bioinformatics/btad614

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CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions

Fabio Barteri and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad623, https://doi.org/10.1093/bioinformatics/btad623

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Evaluation of haplotype-aware long-read error correction with hifieval

Yujie Guo and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad631, https://doi.org/10.1093/bioinformatics/btad631

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Structural bioinformatics

DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes

Jun Liu and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad591, https://doi.org/10.1093/bioinformatics/btad591

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Surfaces: a software to quantify and visualize interactions within and between proteins and ligands

Natália Teruel and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad608, https://doi.org/10.1093/bioinformatics/btad608

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cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling

Michal Wlasnowolski and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad588, https://doi.org/10.1093/bioinformatics/btad588

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UDock2: interactive real-time multi-body protein–protein docking software

Cyprien Plateau-Holleville and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad609, https://doi.org/10.1093/bioinformatics/btad609

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SBILib: a handle for protein modeling and engineering

Patrick Gohl and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad613, https://doi.org/10.1093/bioinformatics/btad613

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Gene expression

optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis

Dong Pei and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad611, https://doi.org/10.1093/bioinformatics/btad611

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Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization

Ludvig Larsson and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad626, https://doi.org/10.1093/bioinformatics/btad626

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Genetics and population analysis

SCORPIO: a utility for defining and classifying mutation constellations of virus genomes

Rachel Colquhoun and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad575, https://doi.org/10.1093/bioinformatics/btad575

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Systems biology

BondGraphs.jl: composable energy-based modelling in systems biology

Joshua Forrest and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad578, https://doi.org/10.1093/bioinformatics/btad578

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ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics

Noriaki Sato and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad622, https://doi.org/10.1093/bioinformatics/btad622

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Data and text mining

Aliro: an automated machine learning tool leveraging large language models

Hyunjun Choi and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad606, https://doi.org/10.1093/bioinformatics/btad606

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MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data

Thomas Naake and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad618, https://doi.org/10.1093/bioinformatics/btad618

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GNorm2: an improved gene name recognition and normalization system

Chih-Hsuan Wei and others

Bioinformatics, Volume 39, Issue 10, October 2023, btad599, https://doi.org/10.1093/bioinformatics/btad599

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Correction

Correction to: BIODICA: a computational environment for Independent Component Analysis of omics data

Bioinformatics, Volume 39, Issue 10, October 2023, btad597, https://doi.org/10.1093/bioinformatics/btad597

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