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  1. Book: Introduction to bioinformatics

    Attwood, Teresa K. / Parry-Smith, David J.

    (Cell and molecular biology in action series)

    1999  

    Author's details Teresa K. Attwood and David J. Parry-Smith
    Series title Cell and molecular biology in action series
    Keywords Biowissenschaften ; Informatik
    Subject Life Sciences ; Life-Sciences ; Lifesciences ; Biowissenschaft ; Lebenswissenschaften ; Computerwissenschaft
    Language English
    Size XX, 218 S. : Ill., graph. Darst.
    Publisher Longman
    Publishing place Harlow
    Publishing country Great Britain
    Document type Book
    HBZ-ID HT011128150
    ISBN 0-582-32788-1 ; 978-0-582-32788-7
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2000 A 1474 order for loan Magazin

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  2. Article: Best practice for CRISPR design using current tools and resources

    Thomas, Mark / Iyer, Vivek / Parry-Smith, David

    Methods. 2019 July 15, v. 164-165

    2019  

    Abstract: Users facing the task of designing gRNAs for a CRISPR-mutagenesis experiment are typically confronted with a large variety of possible tools and existing libraries. Here we examine the design principles for such resources, and suggest a best practice ... ...

    Abstract Users facing the task of designing gRNAs for a CRISPR-mutagenesis experiment are typically confronted with a large variety of possible tools and existing libraries. Here we examine the design principles for such resources, and suggest a best practice which allows a user to evaluate and effectively use any of the existing CRISPR design tools or genome-wide libraries.
    Keywords gene editing ; genomic libraries ; mutagenesis ; RNA
    Language English
    Dates of publication 2019-0715
    Size p. 3-17.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2019.05.019
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3239: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Best practice for CRISPR design using current tools and resources.

    Thomas, Mark / Parry-Smith, David / Iyer, Vivek

    Methods (San Diego, Calif.)

    2019  Volume 164-165, Page(s) 3–17

    Abstract: Users facing the task of designing gRNAs for a CRISPR-mutagenesis experiment are typically confronted with a large variety of possible tools and existing libraries. Here we examine the design principles for such resources, and suggest a best practice ... ...

    Abstract Users facing the task of designing gRNAs for a CRISPR-mutagenesis experiment are typically confronted with a large variety of possible tools and existing libraries. Here we examine the design principles for such resources, and suggest a best practice which allows a user to evaluate and effectively use any of the existing CRISPR design tools or genome-wide libraries.
    MeSH term(s) Algorithms ; Animals ; CRISPR-Cas Systems/genetics ; Databases, Genetic ; Gene Editing/methods ; Genomic Library ; Humans ; Mice ; RNA, Guide, CRISPR-Cas Systems/genetics ; Software
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2019-05-30
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2019.05.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3239: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Minimal genome-wide human CRISPR-Cas9 library.

    Gonçalves, Emanuel / Thomas, Mark / Behan, Fiona M / Picco, Gabriele / Pacini, Clare / Allen, Felicity / Vinceti, Alessandro / Sharma, Mamta / Jackson, David A / Price, Stacey / Beaver, Charlotte M / Dovey, Oliver / Parry-Smith, David / Iorio, Francesco / Parts, Leopold / Yusa, Kosuke / Garnett, Mathew J

    Genome biology

    2021  Volume 22, Issue 1, Page(s) 40

    Abstract: CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by ... ...

    Abstract CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.
    MeSH term(s) CRISPR-Cas Systems ; Gene Library ; Genome, Human ; Genome-Wide Association Study ; Genomic Library ; Humans ; Organoids ; RNA, Guide, CRISPR-Cas Systems/genetics
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2021-01-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02268-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Minimal genome-wide human CRISPR-Cas9 library

    Gonçalves, Emanuel / Thomas, Mark / Behan, Fiona M / Picco, Gabriele / Pacini, Clare / Allen, Felicity / Vinceti, Alessandro / Sharma, Mamta / Jackson, David A / Price, Stacey / Beaver, Charlotte M / Dovey, Oliver / Parry-Smith, David / Iorio, Francesco / Parts, Leopold / Yusa, Kosuke / Garnett, Mathew J

    Genome biology. 2021 Dec., v. 22, no. 1

    2021  

    Abstract: CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by ... ...

    Abstract CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.
    Keywords CRISPR-Cas systems ; RNA libraries ; assays ; data collection ; design ; genes ; humans ; libraries ; loss-of-function mutation ; mining ; models
    Language English
    Dates of publication 2021-12
    Size p. 40.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02268-4
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: WGE: a CRISPR database for genome engineering.

    Hodgkins, Alex / Farne, Anna / Perera, Sajith / Grego, Tiago / Parry-Smith, David J / Skarnes, William C / Iyer, Vivek

    Bioinformatics (Oxford, England)

    2015  Volume 31, Issue 18, Page(s) 3078–3080

    Abstract: Unlabelled: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome ... ...

    Abstract Unlabelled: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome.
    Availability and implementation: The WGE database is freely available at www.sanger.ac.uk/htgt/wge
    Contact: : vvi@sanger.ac.uk or skarnes@sanger.ac.uk
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Animals ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Databases, Factual ; Gene Expression Regulation ; Genetic Vectors ; Genome ; Humans ; Mice ; RNA Editing/genetics ; Software
    Language English
    Publishing date 2015-05-14
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btv308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.

    Yeung, Amy T Y / Hale, Christine / Lee, Amy H / Gill, Erin E / Bushell, Wendy / Parry-Smith, David / Goulding, David / Pickard, Derek / Roumeliotis, Theodoros / Choudhary, Jyoti / Thomson, Nick / Skarnes, William C / Dougan, Gordon / Hancock, Robert E W

    Nature communications

    2017  Volume 8, Page(s) 15013

    Abstract: Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response of macrophages to this obligate ...

    Abstract Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response of macrophages to this obligate human pathogen. Here, we describe an approach using macrophages derived from human induced pluripotent stem cells (iPSdMs) to study macrophage-Chlamydia interactions in vitro. We show that iPSdMs support the full infectious life cycle of C. trachomatis in a manner that mimics the infection of human blood-derived macrophages. Transcriptomic and proteomic profiling of the macrophage response to chlamydial infection highlighted the role of the type I interferon and interleukin 10-mediated responses. Using CRISPR/Cas9 technology, we generated biallelic knockout mutations in host genes encoding IRF5 and IL-10RA in iPSCs, and confirmed their roles in limiting chlamydial infection in macrophages. This model can potentially be extended to other pathogens and tissue systems to advance our understanding of host-pathogen interactions and the role of human genetics in influencing the outcome of infections.
    MeSH term(s) Adult ; CRISPR-Cas Systems/genetics ; Cell Differentiation ; Chlamydia Infections/genetics ; Chlamydia Infections/immunology ; Chlamydia Infections/microbiology ; Chlamydia trachomatis/immunology ; Chlamydia trachomatis/pathogenicity ; Gene Editing/methods ; Gene Expression Profiling ; Gene Knockout Techniques ; HeLa Cells ; Healthy Volunteers ; Host-Pathogen Interactions/genetics ; Host-Pathogen Interactions/immunology ; Humans ; Induced Pluripotent Stem Cells/physiology ; Interferon Regulatory Factors/genetics ; Interferon Regulatory Factors/immunology ; Interleukin-10 Receptor alpha Subunit/genetics ; Interleukin-10 Receptor alpha Subunit/immunology ; Macrophages/microbiology ; Macrophages/physiology ; Mutation ; Proteomics/methods
    Chemical Substances IRF5 protein, human ; Interferon Regulatory Factors ; Interleukin-10 Receptor alpha Subunit
    Language English
    Publishing date 2017-04-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms15013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book: Introduction to bioinformatics

    Attwood, Teresa K / Parry-Smith, David J

    (Cell and molecular biology in action series)

    1999  

    Author's details Teresa K. Attwood and David J. Parry-Smith
    Series title Cell and molecular biology in action series
    Keywords Molecular biology/Data processing.
    Language English
    Size xx, 218 p. :, ill. ;, 24 cm.
    Publisher Longman
    Publishing place Harlow, Essex, England
    Document type Book
    ISBN 0582327881 ; 9780582327887
    Database NAL-Catalogue (AGRICOLA)

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    Order via subito

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  9. Book: Introduction to bioinformatics

    Attwood, Teresa K / Parry-Smith, David J

    (Cell and molecular biology in action series)

    1999  

    Author's details Teresa K. Attwood and David J. Parry-Smith
    Series title Cell and molecular biology in action series
    MeSH term(s) Computational Biology
    Language English
    Size xx, 218 p. :, ill. ;, 24 cm.
    Publisher Longman
    Publishing place Harlow, Essex, England
    Document type Book
    ISBN 9780582327887 ; 0582327881
    Database Catalogue of the US National Library of Medicine (NLM)

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    Inter-library loan at ZB MED

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  10. Book: Introduction to bioinformatics

    Attwood, Teresa K / Parry-Smith, David J

    (Cell and molecular biology in action series)

    1999  

    Author's details Teresa K. Attwood and David J. Parry-Smith
    Series title Cell and molecular biology in action series
    Keywords Molecular biology/Data processing
    Language English
    Size XX, 218 p, graph. Darst, 24 cm
    Publisher Longman
    Publishing place Harlow
    Document type Book
    Note Includes index
    ISBN 0582327881 ; 9780582327887
    Database Former special subject collection: coastal and deep sea fishing

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    Order via subito

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    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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