Volume 40, Issue 6, June 2024

Review

Gene expression

Interpretable deep learning in single-cell omics

Manoj M Wagle and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae374, https://doi.org/10.1093/bioinformatics/btae374

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Original Paper

Genome analysis

SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings

Aysun Urhan and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae328, https://doi.org/10.1093/bioinformatics/btae328

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AmplificationTimeR: an R package for timing sequential amplification events

G Maria Jakobsdottir and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae281, https://doi.org/10.1093/bioinformatics/btae281

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Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation

Minzhu Xie and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae360, https://doi.org/10.1093/bioinformatics/btae360

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RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads

Peng Ni and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae375, https://doi.org/10.1093/bioinformatics/btae375

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Sequence analysis

Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy’s outcome for HIV-1

Giulia Di Teodoro and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae327, https://doi.org/10.1093/bioinformatics/btae327

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MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data

Marjan Faizi and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae335, https://doi.org/10.1093/bioinformatics/btae335

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Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data

Siang Chen and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae336, https://doi.org/10.1093/bioinformatics/btae336

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HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer

Xiaopeng Xu and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae364, https://doi.org/10.1093/bioinformatics/btae364

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Phylogenetics

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach

Yueyu Jiang and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae361, https://doi.org/10.1093/bioinformatics/btae361

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Structural bioinformatics

FMCA-DTI: a fragment-oriented method based on a multihead cross attention mechanism to improve drug–target interaction prediction

Qi Zhang and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae347, https://doi.org/10.1093/bioinformatics/btae347

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OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs

Yueming Yin and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae365, https://doi.org/10.1093/bioinformatics/btae365

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Gene expression

Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation

Ziheng Duan and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae339, https://doi.org/10.1093/bioinformatics/btae339

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HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data

Xingjian Chen and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae343, https://doi.org/10.1093/bioinformatics/btae343

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Supervised learning of enhancer–promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning

Dylan Barth and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae367, https://doi.org/10.1093/bioinformatics/btae367

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scCross: efficient search for rare subpopulations across multiple single-cell samples

Alexander Gerniers and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae371, https://doi.org/10.1093/bioinformatics/btae371

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Genetics and population analysis

SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts

Nianqiao Ju and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae344, https://doi.org/10.1093/bioinformatics/btae344

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Systems biology

Drug–target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism

Wei Song and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae346, https://doi.org/10.1093/bioinformatics/btae346

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spillR: spillover compensation in mass cytometry data

Marco Guazzini and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae337, https://doi.org/10.1093/bioinformatics/btae337

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Data and text mining

Improving the performance and interpretability on medical datasets using graphical ensemble feature selection

Enzo Battistella and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae341, https://doi.org/10.1093/bioinformatics/btae341

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TARO: tree-aggregated factor regression for microbiome data integration

Aditya K Mishra and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae321, https://doi.org/10.1093/bioinformatics/btae321

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DEAttentionDTA: protein–ligand binding affinity prediction based on dynamic embedding and self-attention

Xiying Chen and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae319, https://doi.org/10.1093/bioinformatics/btae319

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MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis

Lexiang Wang and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae362, https://doi.org/10.1093/bioinformatics/btae362

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Computing linkage disequilibrium aware genome embeddings using autoencoders

Gizem Taş and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae326, https://doi.org/10.1093/bioinformatics/btae326

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Bioimage informatics

CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm

Teng-Yu Lin and Szu-Chi Chung

Bioinformatics, Volume 40, Issue 6, June 2024, btae345, https://doi.org/10.1093/bioinformatics/btae345

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GammaGateR: semi-automated marker gating for single-cell multiplexed imaging

Jiangmei Xiong and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae356, https://doi.org/10.1093/bioinformatics/btae356

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Applications Note

Genome analysis

SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models

Ketrin Gjoni and Katherine S Pollard

Bioinformatics, Volume 40, Issue 6, June 2024, btae340, https://doi.org/10.1093/bioinformatics/btae340

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Mariner: explore the Hi-Cs

Eric S Davis and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae352, https://doi.org/10.1093/bioinformatics/btae352

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Figeno: multi-region genomic figures with long-read support

Etienne Sollier and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae354, https://doi.org/10.1093/bioinformatics/btae354

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Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases

Francesco Gualdi and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae379, https://doi.org/10.1093/bioinformatics/btae379

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Sequence analysis

SWGTS—a platform for stream-based host DNA depletion

Philipp Spohr and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae332, https://doi.org/10.1093/bioinformatics/btae332

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Flexible parsing, interpretation, and editing of technical sequences with splitcode

Delaney K Sullivan and Lior Pachter

Bioinformatics, Volume 40, Issue 6, June 2024, btae331, https://doi.org/10.1093/bioinformatics/btae331

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GenoFig: a user-friendly application for the visualization and comparison of genomic regions

Maxime Branger and Sébastien O Leclercq

Bioinformatics, Volume 40, Issue 6, June 2024, btae372, https://doi.org/10.1093/bioinformatics/btae372

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Structural bioinformatics

MolDy: molecular dynamics simulation made easy

Mohd Imran Khan and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae313, https://doi.org/10.1093/bioinformatics/btae313

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MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2

Ho Yeung Chim and Arne Elofsson

Bioinformatics, Volume 40, Issue 6, June 2024, btae329, https://doi.org/10.1093/bioinformatics/btae329

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RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments

Sebastian Bittrich and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae370, https://doi.org/10.1093/bioinformatics/btae370

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Gene expression

RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution

Jonathan Chacko and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae369, https://doi.org/10.1093/bioinformatics/btae369

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Ragas: integration and enhanced visualization for single cell subcluster analysis

Uthra Balaji and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae366, https://doi.org/10.1093/bioinformatics/btae366

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Genetics and population analysis

snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics

Kim L Vertacnik and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae377, https://doi.org/10.1093/bioinformatics/btae377

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tstrait: a quantitative trait simulator for ancestral recombination graphs

Daiki Tagami and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae334, https://doi.org/10.1093/bioinformatics/btae334

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Systems biology

ReactomeGSA: new features to simplify public data reuse

Alexander Grentner and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae338, https://doi.org/10.1093/bioinformatics/btae338

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PathwayNexus: a tool for interactive metabolic data analysis

Philipp Eberhard and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae310, https://doi.org/10.1093/bioinformatics/btae310

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bnglViz: online visualization of rule-based models

Noah Liguori-Bills and Michael L Blinov

Bioinformatics, Volume 40, Issue 6, June 2024, btae351, https://doi.org/10.1093/bioinformatics/btae351

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gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python

Carlos J Rodriguez-Flores and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae318, https://doi.org/10.1093/bioinformatics/btae318

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MetaboReport: from metabolomics data analysis to comprehensive reporting

Yonghui Dong and Sergey Malitsky

Bioinformatics, Volume 40, Issue 6, June 2024, btae373, https://doi.org/10.1093/bioinformatics/btae373

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Data and text mining

Bigtools: a high-performance BigWig and BigBed library in Rust

Jack D Huey and Nezar Abdennur

Bioinformatics, Volume 40, Issue 6, June 2024, btae350, https://doi.org/10.1093/bioinformatics/btae350

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biotextgraph: graphical summarization of functional similarities from textual information

Noriaki Sato and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae357, https://doi.org/10.1093/bioinformatics/btae357

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DDN3.0: determining significant rewiring of biological network structure with differential dependency networks

Yi Fu and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae376, https://doi.org/10.1093/bioinformatics/btae376

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Databases and ontologies

KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models

Nicholas Matsumoto and others

Bioinformatics, Volume 40, Issue 6, June 2024, btae353, https://doi.org/10.1093/bioinformatics/btae353

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Correction

Correction to: For antibody sequence generative modeling, mixture models may be all you need

Bioinformatics, Volume 40, Issue 6, June 2024, btae407, https://doi.org/10.1093/bioinformatics/btae407

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