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  1. Article ; Online: A Graph Based Framework to Model Virus Integration Sites

    Raffaele Fronza / Alessandro Vasciaveo / Alfredo Benso / Manfred Schmidt

    Computational and Structural Biotechnology Journal, Vol 14, Iss C, Pp 69-

    2016  Volume 77

    Abstract: With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may ... ...

    Abstract With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related genomic features such as oncogenes. Here, we addressed the challenge to: 1) define the notion of CIS on graph models, 2) demonstrate that the structure of CIS enters in the category of scale-free networks and 3) show that our network approach analyzes CIS dynamically in an integrated systems biology framework using the Retroviral Transposon Tagged Cancer Gene Database (RTCGD) as a testing dataset.
    Keywords Gene therapy ; Systems biology ; Genomics ; Insertional mutagenesis ; Biotechnology ; TP248.13-248.65
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation

    Michael E. Stokes / Jonnell Candice Small / Alessandro Vasciaveo / Kenichi Shimada / Tal Hirschhorn / Andrea Califano / Brent R. Stockwell

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Abstract The identification of targeted agents with high therapeutic index is a major challenge for cancer drug discovery. We found that screening chemical libraries across neuroblastoma (NBL) tumor subtypes for selectively-lethal compounds revealed ... ...

    Abstract Abstract The identification of targeted agents with high therapeutic index is a major challenge for cancer drug discovery. We found that screening chemical libraries across neuroblastoma (NBL) tumor subtypes for selectively-lethal compounds revealed metabolic dependencies that defined each subtype. Bioactive compounds were screened across cell models of mesenchymal (MESN) and MYCN-amplified (MYCNA) NBL subtypes, which revealed the mevalonate and folate biosynthetic pathways as MESN-selective dependencies. Treatment with lovastatin, a mevalonate biosynthesis inhibitor, selectively inhibited protein prenylation and induced apoptosis in MESN cells, while having little effect in MYCNA lines. Statin sensitivity was driven by HMGCR expression, the rate-limiting enzyme for cholesterol synthesis, which correlated with statin sensitivity across NBL cell lines, thus providing a drug sensitivity biomarker. Comparing expression profiles from sensitive and resistant cell lines revealed a TGFBR2 signaling axis that regulates HMGCR, defining an actionable addiction in that leads to MESN-subtype-dependent apoptotic cell death.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  3. Article ; Online: Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow

    Vartika Mishra / Diane B. Re / Virginia Le Verche / Mariano J. Alvarez / Alessandro Vasciaveo / Arnaud Jacquier / Paschalis-Tomas Doulias / Todd M. Greco / Monica Nizzardo / Dimitra Papadimitriou / Tetsuya Nagata / Paola Rinchetti / Eduardo J. Perez-Torres / Kristin A. Politi / Burcin Ikiz / Kevin Clare / Manuel E. Than / Stefania Corti / Harry Ischiropoulos /
    Francesco Lotti / Andrea Califano / Serge Przedborski

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 20

    Abstract: Neuron-astrocyte communication plays a key role in pathophysiology, however systematic approaches to unveil it are limited. Here, the authors propose SEARCHIN, a multi-modal integrated workflow, as a tool to identify cross-compartment ligand-receptor ... ...

    Abstract Neuron-astrocyte communication plays a key role in pathophysiology, however systematic approaches to unveil it are limited. Here, the authors propose SEARCHIN, a multi-modal integrated workflow, as a tool to identify cross-compartment ligand-receptor interactions, applied to ALS models.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  4. Article ; Online: Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow

    Vartika Mishra / Diane B. Re / Virginia Le Verche / Mariano J. Alvarez / Alessandro Vasciaveo / Arnaud Jacquier / Paschalis-Tomas Doulias / Todd M. Greco / Monica Nizzardo / Dimitra Papadimitriou / Tetsuya Nagata / Paola Rinchetti / Eduardo J. Perez-Torres / Kristin A. Politi / Burcin Ikiz / Kevin Clare / Manuel E. Than / Stefania Corti / Harry Ischiropoulos /
    Francesco Lotti / Andrea Califano / Serge Przedborski

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 20

    Abstract: Neuron-astrocyte communication plays a key role in pathophysiology, however systematic approaches to unveil it are limited. Here, the authors propose SEARCHIN, a multi-modal integrated workflow, as a tool to identify cross-compartment ligand-receptor ... ...

    Abstract Neuron-astrocyte communication plays a key role in pathophysiology, however systematic approaches to unveil it are limited. Here, the authors propose SEARCHIN, a multi-modal integrated workflow, as a tool to identify cross-compartment ligand-receptor interactions, applied to ALS models.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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