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  1. Article ; Online: Antibody-secreting plasma cells persist for decades in human intestine.

    Landsverk, Ole J B / Snir, Omri / Casado, Raquel Bartolomé / Richter, Lisa / Mold, Jeff E / Réu, Pedro / Horneland, Rune / Paulsen, Vemund / Yaqub, Sheraz / Aandahl, Einar Martin / Øyen, Ole M / Thorarensen, Hildur Sif / Salehpour, Mehran / Possnert, Göran / Frisén, Jonas / Sollid, Ludvig M / Baekkevold, Espen S / Jahnsen, Frode L

    The Journal of experimental medicine

    2017  Volume 214, Issue 2, Page(s) 309–317

    Abstract: Plasma cells (PCs) produce antibodies that mediate immunity after infection or vaccination. In contrast to PCs in the bone marrow, PCs in the gut have been considered short lived. In this study, we studied PC dynamics in the human small intestine by cell- ...

    Abstract Plasma cells (PCs) produce antibodies that mediate immunity after infection or vaccination. In contrast to PCs in the bone marrow, PCs in the gut have been considered short lived. In this study, we studied PC dynamics in the human small intestine by cell-turnover analysis in organ transplants and by retrospective cell birth dating measuring carbon-14 in genomic DNA. We identified three distinct PC subsets: a CD19
    MeSH term(s) Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antibody-Producing Cells/immunology ; Antigens, CD19/analysis ; Child ; Female ; Humans ; Intestines/immunology ; Leukocyte Common Antigens/analysis ; Male ; Middle Aged ; Plasma Cells/immunology
    Chemical Substances Antigens, CD19 ; CD19 molecule, human ; Leukocyte Common Antigens (EC 3.1.3.48) ; PTPRC protein, human (EC 3.1.3.48)
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218343-2
    ISSN 1540-9538 ; 0022-1007
    ISSN (online) 1540-9538
    ISSN 0022-1007
    DOI 10.1084/jem.20161590
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.

    Simovski, Boris / Vodák, Daniel / Gundersen, Sveinung / Domanska, Diana / Azab, Abdulrahman / Holden, Lars / Holden, Marit / Grytten, Ivar / Rand, Knut / Drabløs, Finn / Johansen, Morten / Mora, Antonio / Lund-Andersen, Christin / Fromm, Bastian / Eskeland, Ragnhild / Gabrielsen, Odd Stokke / Ferkingstad, Egil / Nakken, Sigve / Bengtsen, Mads /
    Nederbragt, Alexander Johan / Thorarensen, Hildur Sif / Akse, Johannes Andreas / Glad, Ingrid / Hovig, Eivind / Sandve, Geir Kjetil

    GigaScience

    2017  Volume 6, Issue 7, Page(s) 1–12

    Abstract: Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell ... ...

    Abstract Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation.
    Findings: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered.
    Conclusions: Through a combination of streamlined data acquisition, interoperable representation of dataset collections, and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no.
    MeSH term(s) Datasets as Topic/standards ; Epigenesis, Genetic ; Epigenomics/methods ; Epigenomics/standards ; Genome, Human ; Humans ; Software ; Whole Genome Sequencing/methods ; Whole Genome Sequencing/standards
    Language English
    Publishing date 2017-04-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/gix032
    Database MEDical Literature Analysis and Retrieval System OnLINE

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