Bioinformatics

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment
Noor Pratap Singh, Jamshed Khan, Rob Patro

bioRxiv 2024.11.27.625771; doi: https://doi.org/10.1101/2024.11.27.625771 New Results

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InSituPy – A framework for histology-guided, multi-sample analysis of single-cell spatial transcriptomics data
Johannes Wirth, Anna Chernysheva, Birthe Lemke, Isabel Giray, Aitana Egea Lavandera, Katja Steiger

bioRxiv 2025.03.07.641860; doi: https://doi.org/10.1101/2025.03.07.641860 New Results

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Dynamic mode decomposition for analysis and prediction of metabolic oscillations from time-lapse imaging of cellular autofluorescence
Daniel Wüstner, Henrik Helge Gundestrup, Katja Thaysen

bioRxiv 2025.03.06.641958; doi: https://doi.org/10.1101/2025.03.06.641958 New Results

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Single cell transcriptomic analyses of human heart failure with preserved ejection fraction
Virginia S. Hahn, Mark Chaffin, Bridget Simonson, Sydney C. Jenkin, Abigail S. Mulligan, Kenneth C. Bedi Jr, Kenneth B. Margulies, Carla A Klattenhoff, Kavita Sharma, David A. Kass, Patrick T. Ellinor

bioRxiv 2025.03.06.641949; doi: https://doi.org/10.1101/2025.03.06.641949 New Results

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Likelihood of social-ecological genetic model
Stéphane Dupas, Camilo Patarroyo

bioRxiv 2025.03.06.641298; doi: https://doi.org/10.1101/2025.03.06.641298 New Results

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rplec: An R package of placental epigenetic clock to estimate aging by DNA-methylation-based gestational age
Herdiantri Sufriyana, Emily Chia-Yu Su

bioRxiv 2025.02.04.636367; doi: https://doi.org/10.1101/2025.02.04.636367 New Results

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Delineating inter- and intra-antibody repertoire evolution with AntibodyForests
Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T. Reddy, Alexander Yermanos

bioRxiv 2025.03.11.642619; doi: https://doi.org/10.1101/2025.03.11.642619 New Results

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Bimodality in pan-cancer proteomics reveals new opportunities for biomarker discovery
Wen Jiang, Damian Bikiel, Jan Zaucha, Jixin Wang, Sanddhya Jayabalan, Yongjin Li, Matthew Sung, James Harper, Jimmy Zhao, Krishna Bulusu, Wenyan Zhong

bioRxiv 2025.03.03.641218; doi: https://doi.org/10.1101/2025.03.03.641218 New Results

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TISCalling: Leveraging Machine Learning to Identify Translational Initiation Sites in Plants and Viruses
Ming-Ren Yen, Chia-Yi Cheng, Ting-Ying Wu, Ming-Jung Liu

bioRxiv 2025.03.06.641763; doi: https://doi.org/10.1101/2025.03.06.641763 New Results

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MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration
Simo Inkala, Michele Fratello, Giusy del Giudice, Giorgia Migliaccio, Angela Serra, Dario Greco, Antonio Federico

bioRxiv 2025.03.10.642416; doi: https://doi.org/10.1101/2025.03.10.642416 New Results

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Bioinformatics

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