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  1. Book ; Online ; Thesis: Integration and analysis of large scale data in chemical biology

    Deghou, Samy Lyes [Verfasser] / Bork, Peer [Akademischer Betreuer]

    2016  

    Author's details Samy Lyes Deghou ; Betreuer: Peer Bork
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek Heidelberg
    Publishing place Heidelberg
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  2. Article: CART—a chemical annotation retrieval toolkit

    Deghou, Samy / Zeller, Georg / Iskar, Murat / Driessen, Marja / Castillo, Mercedes / van Noort, Vera / Bork, Peer

    Bioinformatics. 2016 Sept. 15, v. 32, no. 18

    2016  

    Abstract: Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to ... ...

    Abstract Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases. Results: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data. Availability and Implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site. Contact: bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Keywords Internet ; bioactive properties ; bioinformatics ; data collection ; databases ; pharmacology
    Language English
    Dates of publication 2016-0915
    Size p. 2869-2871.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4811 ; 1367-4803
    ISSN (online) 1460-2059 ; 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw233
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: CART-a chemical annotation retrieval toolkit.

    Deghou, Samy / Zeller, Georg / Iskar, Murat / Driessen, Marja / Castillo, Mercedes / van Noort, Vera / Bork, Peer

    Bioinformatics (Oxford, England)

    2016  Volume 32, Issue 18, Page(s) 2869–2871

    Abstract: Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to ...

    Abstract Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases.
    Results: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data.
    Availability and implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site.
    Contact: bork@embl.de
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Automatic Data Processing ; Computational Biology ; Computer Graphics ; Data Curation ; Databases, Factual ; Information Storage and Retrieval/methods ; Programming Languages ; Software
    Language English
    Publishing date 2016-09-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw233
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  4. Article ; Online: A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

    Saliba, Antoine-Emmanuel / Vonkova, Ivana / Deghou, Samy / Ceschia, Stefano / Tischer, Christian / Kugler, Karl G / Bork, Peer / Ellenberg, Jan / Gavin, Anne-Claude

    Nature protocols

    2016  Volume 11, Issue 6, Page(s) 1021–1038

    Abstract: Lipids organize the activity of the cell's proteome through a complex network of interactions. The assembly of comprehensive atlases embracing all protein-lipid interactions is an important challenge that requires innovative methods. We recently ... ...

    Abstract Lipids organize the activity of the cell's proteome through a complex network of interactions. The assembly of comprehensive atlases embracing all protein-lipid interactions is an important challenge that requires innovative methods. We recently developed a liposome-microarray-based assay (LiMA) that integrates liposomes, microfluidics and fluorescence microscopy and which is capable of measuring protein recruitment to membranes in a quantitative and high-throughput manner. Compared with previous assays that are labor-intensive and difficult to scale up, LiMA improves the protein-lipid interaction assay throughput by at least three orders of magnitude. Here we provide a step-by-step LiMA protocol that includes the following: (i) the serial and generic production of the liposome microarray; (ii) its integration into a microfluidic format; (iii) the measurement of fluorescently labeled protein (either purified proteins or from cell lysate) recruitment to liposomal membranes using high-throughput microscopy; (iv) automated image analysis pipelines to quantify protein-lipid interactions; and (v) data quality analysis. In addition, we discuss the experimental design, including the relevant quality controls. Overall, the protocol-including device preparation, assay and data analysis-takes 6-8 d. This protocol paves the way for protein-lipid interaction screens to be performed on the proteome and lipidome scales.
    MeSH term(s) Cell Line ; Humans ; Image Processing, Computer-Assisted ; Lab-On-A-Chip Devices ; Liposomes/metabolism ; Microarray Analysis/instrumentation ; Microarray Analysis/methods ; Protein Binding ; Proteins/metabolism ; Quality Control
    Chemical Substances Liposomes ; Proteins
    Language English
    Publishing date 2016
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/nprot.2016.059
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

    Vonkova, Ivana / Saliba, Antoine-Emmanuel / Deghou, Samy / Anand, Kanchan / Ceschia, Stefano / Doerks, Tobias / Galih, Augustinus / Kugler, Karl G / Maeda, Kenji / Rybin, Vladimir / van Noort, Vera / Ellenberg, Jan / Bork, Peer / Gavin, Anne-Claude

    Cell reports

    2015  Volume 12, Issue 9, Page(s) 1519–1530

    Abstract: Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We ... ...

    Abstract Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We applied a physiological, quantitative, liposome microarray-based assay to measure the membrane-binding properties of 91 pleckstrin homology (PH) domains, the most common phosphoinositide-binding target. 10,514 experiments quantified the role of phosphoinositides in membrane recruitment. For most domains examined, the observed binding specificity implied cooperativity with additional signaling lipids. Analyses of PH domains with similar lipid-binding profiles identified a conserved motif, mutations in which-including some found in human cancers-induced discrete changes in binding affinities in vitro and protein mislocalization in vivo. The data set reveals cooperativity as a key mechanism for membrane recruitment and, by enabling the interpretation of disease-associated mutations, suggests avenues for the design of small molecules targeting PH domains.
    MeSH term(s) Cell Membrane/metabolism ; Chaetomium/metabolism ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Phosphatidylinositols/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Protein Transport ; Saccharomyces cerevisiae/metabolism
    Chemical Substances Fungal Proteins ; Phosphatidylinositols
    Language English
    Publishing date 2015-09-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2015.07.054
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A quantitative liposome microarray to systematically characterize protein-lipid interactions.

    Saliba, Antoine-Emmanuel / Vonkova, Ivana / Ceschia, Stefano / Findlay, Greg M / Maeda, Kenji / Tischer, Christian / Deghou, Samy / van Noort, Vera / Bork, Peer / Pawson, Tony / Ellenberg, Jan / Gavin, Anne-Claude

    Nature methods

    2013  Volume 11, Issue 1, Page(s) 47–50

    Abstract: Lipids have a role in virtually all biological processes, acting as structural elements, scaffolds and signaling molecules, but they are still largely under-represented in known biological networks. Here we describe a liposome microarray-based assay ( ... ...

    Abstract Lipids have a role in virtually all biological processes, acting as structural elements, scaffolds and signaling molecules, but they are still largely under-represented in known biological networks. Here we describe a liposome microarray-based assay (LiMA), a method that measures protein recruitment to membranes in a quantitative, automated, multiplexed and high-throughput manner.
    MeSH term(s) Automation ; Escherichia coli/metabolism ; Green Fluorescent Proteins/metabolism ; HEK293 Cells ; Humans ; Image Processing, Computer-Assisted/methods ; Lipids/chemistry ; Liposomes/chemistry ; Microarray Analysis ; Microscopy, Fluorescence/methods ; Mutation ; Protein Binding ; Proteins/chemistry ; Recombinant Proteins/chemistry ; Saccharomyces cerevisiae/genetics ; Sepharose/chemistry ; Signal Transduction ; Systems Biology
    Chemical Substances Lipids ; Liposomes ; Proteins ; Recombinant Proteins ; Green Fluorescent Proteins (147336-22-9) ; Sepharose (9012-36-6)
    Language English
    Publishing date 2013-11-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/nmeth.2734
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6022: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains

    Ivana Vonkova / Antoine-Emmanuel Saliba / Samy Deghou / Kanchan Anand / Stefano Ceschia / Tobias Doerks / Augustinus Galih / Karl G. Kugler / Kenji Maeda / Vladimir Rybin / Vera van Noort / Jan Ellenberg / Peer Bork / Anne-Claude Gavin

    Cell Reports, Vol 12, Iss 9, Pp 1519-

    2015  Volume 1530

    Abstract: Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We ... ...

    Abstract Many cellular processes involve the recruitment of proteins to specific membranes, which are decorated with distinctive lipids that act as docking sites. The phosphoinositides form signaling hubs, and we examine mechanisms underlying recruitment. We applied a physiological, quantitative, liposome microarray-based assay to measure the membrane-binding properties of 91 pleckstrin homology (PH) domains, the most common phosphoinositide-binding target. 10,514 experiments quantified the role of phosphoinositides in membrane recruitment. For most domains examined, the observed binding specificity implied cooperativity with additional signaling lipids. Analyses of PH domains with similar lipid-binding profiles identified a conserved motif, mutations in which—including some found in human cancers—induced discrete changes in binding affinities in vitro and protein mislocalization in vivo. The data set reveals cooperativity as a key mechanism for membrane recruitment and, by enabling the interpretation of disease-associated mutations, suggests avenues for the design of small molecules targeting PH domains.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2015-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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