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Systems & Computational Biology

  • Convergent evolution and B-cell recirculation in germinal centers in a human lymph node
    Open Access
    Convergent evolution and B-cell recirculation in germinal centers in a human lymph node

    Aurelien Pelissier, Maria Stratigopoulou, Naomi Donner, Evangelos Dimitriadis, Richard J Bende, Jeroen E Guikema, Maria Rodriguez Martinez, Carel JM van Noesel

    Aurelien Pelissier ... Carel JM van Noesel

    Published 28 August 2023

    The study characterizes an ongoing immune response by sequencing B-cells from 10 germinal centers and finds diverse clonal patterns and convergent evolution, indicating re-engagement and rediversification of B-cell clones across GCs.

  • De novo network analysis reveals autism causal genes and developmental links to co-occurring traits
    Open Access
    De novo network analysis reveals autism causal genes and developmental links to co-occurring traits

    Catriona J Miller, Evgeniia Golovina, Joerg S Wicker, Jessie C Jacobsen, Justin M O’Sullivan

    Catriona J Miller ... Justin M O’Sullivan

    Published 8 August 2023

    In this study, we provide a biological argument for looking at an autistic individual’s phenotype as being related to their combined genetic risk for different clusters of traits.

  • Basonuclin-2 regulates extracellular matrix production and degradation
    Open Access
    Basonuclin-2 regulates extracellular matrix production and degradation

    Ayla Orang, B Kate Dredge, Chi Yau Liu, Julie M Bracken, Chun-Hsien Chen, Laura Sourdin, Holly J Whitfield, Rachael Lumb, Sarah T Boyle, Melissa J Davis, Michael S Samuel, Philip A Gregory, Yeesim Khew-Goodall, Gregory J Goodall, Katherine A Pillman, Cameron P Bracken

    Ayla Orang ... Cameron P Bracken

    Published 3 August 2023

    Basonuclin-2 (BNC2) is identified as a novel regulator of genes associated with the extracellular matrix and cytokines in fibroblasts. BNC2 is thereby identified as a novel regulator of the tumour microenvironment where its high expression correlates with poor prognosis.

  • PASCAR: a multiscale framework to explore the design space of constitutive and inducible CAR T cells
    Open Access
    PASCAR: a multiscale framework to explore the design space of constitutive and inducible CAR T cells

    Harshana Rajakaruna, Milie Desai, Jayajit Das

    Harshana Rajakaruna ... Jayajit Das

    Published 28 July 2023

    An experimentally validated protein abundance structured population dynamic model for CAR T cells (PASCAR) that integrates processes from molecules to single cells to cell populations and systematically explores the design space of constitutive and tunable CAR T cells.

  • A network embedding approach to identify active modules in biological interaction networks
    Open Access
    A network embedding approach to identify active modules in biological interaction networks

    Claude Pasquier, Vincent Guerlais, Denis Pallez, Raphaël Rapetti-Mauss, Olivier Soriani

    Claude Pasquier ... Olivier Soriani

    Published 20 June 2023

    This study proposes the AMINE method as a flexible and efficient approach to identify active modules from a data embedding combining gene expression and interaction data.

  • Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and function
    Open Access
    Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and function

    Christina S Moesslacher, Elisabeth Auernig, Jonathan Woodsmith, Andreas Feichtner, Evelyne Jany-Luig, Stefanie Jehle, Josephine M Worseck, Christian L Heine, Eduard Stefan, Ulrich Stelzl

    Christina S Moesslacher ... Ulrich Stelzl

    Published 6 June 2023

    Deep mutational interaction perturbation scanning of NF2 with conformation-dependent interaction partners KDM1A, EMILIN, and PIK3R3 revealed two regions critical for NF2 tumor suppressor function.

  • 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.

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