Bioinformatics

Generative modeling for RNA splicing predictions and design
Di Wu, Natalie Maus, Anupama Jha, Kevin Yang, Benjamin D Wales-McGrath, San Jewell, Anna Tangiyan, Peter Choi, Jake R Gardner, Yoseph Barash

bioRxiv 2025.01.20.633986; doi: https://doi.org/10.1101/2025.01.20.633986 New Results

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Sex-specific transcriptome similarity networks elucidate comorbidity relationships
Jon Sanchez-Valle, Maria Flores-Rodero, Felipe Xavier Costa, Jose Carbonell-Caballero, Iker Nunez-Carpintero, Rafael Tabares-Seisdedos, Luis Mateus Rocha, Davide Cirillo, Alfonso Valencia

bioRxiv 2025.01.22.634077; doi: https://doi.org/10.1101/2025.01.22.634077 New Results

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Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking
Pia Rautenstrauch, Uwe Ohler

bioRxiv 2025.01.21.634098; doi: https://doi.org/10.1101/2025.01.21.634098 New Results

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Targeted decontamination of sequencing data with CLEAN
Marie Lataretu, Sebastian Krautwurst, Matthew R. Huska, Mike Marquet, Adrian Viehweger, Sascha D. Braun, Christian Brandt, Martin Hölzer

bioRxiv 2023.08.05.552089; doi: https://doi.org/10.1101/2023.08.05.552089 New Results

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BiaPy: Accessible deep learning on bioimages
Daniel Franco-Barranco, Jesus Angel Andres-San Roman, Ivan Hidalgo-Cenalmor, Lenka Backova, Aitor Gonzalez-Marfil, Clement Caporal, Anatole Chessel, Pedro Gomez-Galvez, Luis M. Escudero, Donglai Wei, Arrate Munoz-Barrutia, Ignacio Arganda-Carreras

bioRxiv 2024.02.03.576026; doi: https://doi.org/10.1101/2024.02.03.576026 New Results

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A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement.
Ali Osman Berk Sapci, Siavash Mirarab

bioRxiv 2025.01.20.633730; doi: https://doi.org/10.1101/2025.01.20.633730 New Results

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Penalised regression improves imputation of cell-type specific expression using RNA-seq data from mixed cell populations compared to domain-specific methods
Wei-Yu Lin, Melissa Kartawinata, Bethany Rose Jebson, Restuadi Restuadi, Hannah Peckham, Anna Radziszewska, Claire Deakin, Coziana Ciurtin, CLUSTER Consortium, Lucy R Wedderburn, Chris Wallace

bioRxiv 2023.09.11.556650; doi: https://doi.org/10.1101/2023.09.11.556650 New Results

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Machine Learning Predictions Surpass Individual mRNAs as a Proxy of Single-cell Protein Expression
Josephine Fisher, Oliver Wood, Samuel Bullers, Lynne Murray, Li Li, Matthew Jackson-Wood

bioRxiv 2024.12.11.627925; doi: https://doi.org/10.1101/2024.12.11.627925 New Results

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Bridging polarities in metabolomics: Cross-ionization mode chemical similarity prediction between tandem mass spectra
Niek F. de Jonge, Elena Chekmeneva, Robin Schmid, David Joas, Lem-Joe Truong, Justin J.J. van der Hooft, Florian Huber

bioRxiv 2024.03.25.586580; doi: https://doi.org/10.1101/2024.03.25.586580 New Results

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Predicting antimicrobial class specificity of small molecules using machine learning
Yojana Gadiya, Olga Genilloud, Ursula Bilitewski, Mark Broenstrup, Leonie von Berlin, Marie Attwood, Philip Gribbon, Andrea Zaliani

bioRxiv 2024.12.02.626313; doi: https://doi.org/10.1101/2024.12.02.626313 New Results

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Bioinformatics

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