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Systems & Computational Biology

  • A new metabolic model of <em>Drosophila melanogaster</em> and the integrative analysis of Parkinson’s disease
    Open Access
    A new metabolic model of Drosophila melanogaster and the integrative analysis of Parkinson’s disease

    Müberra Fatma Cesur, Arianna Basile, Kiran Raosaheb Patil, Tunahan Çakır

    Müberra Fatma Cesur ... Tunahan Çakır

    Published 26 May 2023

    The reconstruction of a comprehensive and literature-curated Drosophila metabolic model, iDrosophila1, provided a powerful platform for studying metabolism with systems medicine perspective.

  • Evaluation of genetic demultiplexing of single-cell sequencing data from model species
    Open Access
    Evaluation of genetic demultiplexing of single-cell sequencing data from model species

    Joseph F Cardiello, Alberto Joven Araus, Sarantis Giatrellis, Clement Helsens, András Simon, Nicholas D Leigh

    Joseph F Cardiello ... Nicholas D Leigh

    Published 17 May 2023

    The authors demonstrate that scRNA-seq sample pooling followed by genetics-based separation of individuals is an effective means to identify individual samples in a variety of commonly studied species.

  • Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network
    Open Access
    Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network

    Jacqueline S Gerritsen, Joseph S Faraguna, Rudy Bonavia, Frank B Furnari, Forest M White

    Jacqueline S Gerritsen ... Forest M White

    Published 11 May 2023

    The site-specific function of EGFR’s C-terminal tyrosines is interrogated by phosphotyrosine phosphoproteomics to build a data-driven model that links cell response to signaling nodes and elucidates novel associations in the EGFR signaling network.

  • Antibody reliability influences observed mRNA–protein correlations in tumour samples
    Open Access
    Antibody reliability influences observed mRNA–protein correlations in tumour samples

    Swathi Ramachandra Upadhya, Colm J Ryan

    Swathi Ramachandra Upadhya ... Colm J Ryan

    Published 11 May 2023

    Upadhya and Ryan show that the reliability of antibodies used for RPPA profiling influences the mRNA-protein correlations observed in tumour cohorts.

  • Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease
    Open Access
    Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease

    Dmitry Umerenkov, Alan Herbert, Dmitrii Konovalov, Anna Danilova, Nazar Beknazarov, Vladimir Kokh, Aleksandr Fedorov, Maria Poptsova

    Dmitry Umerenkov ... Maria Poptsova

    Published 10 May 2023

    Z-DNABERT uses the transformer algorithm to map genomic Z-DNA. We validate the approach using chemical footprinting data from live cells. We show the utility of the approach by mapping the Z-flipons discovered to Mendelian disease variants and various quantitative traits.

  • Gapless provides combined scaffolding, gap filling, and assembly correction with long reads
    Open Access
    Gapless provides combined scaffolding, gap filling, and assembly correction with long reads

    Stephan Schmeing, Mark D Robinson

    Stephan Schmeing ... Mark D Robinson

    Published 4 May 2023

    gapless is a new tool for combined execution of correction, scaffolding and gap filling using PacBio or Oxford Nanopore reads.

  • Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma
    Open Access
    Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma

    Elena Panizza, Brandon D Regalado, Fangyu Wang, Ichiro Nakano, Nathaniel M Vacanti, Richard A Cerione, Marc A Antonyak

    Elena Panizza ... Marc A Antonyak

    Published 10 April 2023

    Glioma patients often relapse because of resistance to radiation therapy. The transfer of the metabolic enzyme NAMPT via microvesicles and the accompanying elevated levels of NAD are found to be a mechanism by which glioma cells become resistant to radiation.

  • Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cells
    Open Access
    Analysis of context-specific KRAS–effector (sub)complexes in Caco-2 cells

    Camille Ternet, Philipp Junk, Thomas Sevrin, Simona Catozzi, Erik Wåhlén, Johan Heldin, Giorgio Oliviero, Kieran Wynne, Christina Kiel

    Camille Ternet ... Christina Kiel

    Published 9 March 2023

    We used affinity purification of KRAS in different genetic and growth contexts to determine KRAS-mediated complexes, their rewiring in specific contexts, and their link to functional outcomes.

  • RAS and PP2A activities converge on epigenetic gene regulation
    Open Access
    RAS and PP2A activities converge on epigenetic gene regulation

    Anna Aakula, Mukund Sharma, Francesco Tabaro, Reetta Nätkin, Jesse Kamila, Henrik Honkanen, Matthieu Schapira, Cheryl Arrowsmith, Matti Nykter, Jukka Westermarck

    Anna Aakula ... Jukka Westermarck

    Published 1 March 2023

    This study reveals a hidden regulatory layer in epigenetic gene expression in cancer by co-operative phosphoregulation by RAS and tumor suppressor phosphatase PP2A.

  • Assessing the impacts of various factors on circular RNA reliability
    Open Access
    Assessing the impacts of various factors on circular RNA reliability

    Trees-Juen Chuang, Tai-Wei Chiang, Chia-Ying Chen

    Trees-Juen Chuang ... Chia-Ying Chen

    Published 27 February 2023

    This study systematically assesses the impacts of numerous factors related to circRNA identification, conservation, biogenesis, and function on circRNA reliability, providing a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations.

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