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  • 1
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    SMASH: a benchmarking toolkit for human genome variant calling (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-25
    Description: Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SM a SH, a benchmarking methodology for evaluating germline variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on these benchmarking data. Moreover, we illustrate the utility of SM a SH to evaluate the performance of some leading single-nucleotide polymorphism, indel and structural variant calling algorithms. Availability and implementation: We provide free and open access online to the SM a SH tool kit, along with detailed documentation, at smash.cs.berkeley.edu Contact: ameet@cs.berkeley.edu or pattrsn@cs.berkeley.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Monoallelic expression of the interleukin-2 locus (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-04-16
    Description: The lymphokine interleukin-2 (IL-2) is responsible for autocrine cell cycle progression and regulation of immune responses. Uncontrolled secretion of IL-2 results in adverse reactions ranging from anergy, to aberrant T cell activation, to autoimmunity. With the use of fluorescent in situ hybridization and single-cell polymerase chain reaction in cells with different IL-2 alleles, IL-2 expression in mature thymocytes and T cells was found to be tightly controlled by monoallelic expression. Because IL-2 is encoded at a nonimprinted autosomal locus, this result represents an unusual regulatory mode for controlling the precise expression of a single gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hollander, G A -- Zuklys, S -- Morel, C -- Mizoguchi, E -- Mobisson, K -- Simpson, S -- Terhorst, C -- Wishart, W -- Golan, D E -- Bhan, A K -- Burakoff, S J -- P01 CA39542-09/CA/NCI NIH HHS/ -- R01 AI17258-18/AI/NIAID NIH HHS/ -- R01 DK47677/DK/NIDDK NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1998 Mar 27;279(5359):2118-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pediatric Immunology, Department of Research and Children's Hospital, Basel University Medical School, 4031 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9516115" target="_blank"〉PubMed〈/a〉
    Keywords: *Alleles ; Animals ; CD4-Positive T-Lymphocytes/cytology/*immunology ; Concanavalin A/pharmacology ; DNA Replication ; Female ; Flow Cytometry ; *Gene Expression Regulation ; Heterozygote ; In Situ Hybridization, Fluorescence ; Interleukin-2/biosynthesis/*genetics ; Lymphocyte Activation ; Male ; Mice ; Mice, Inbred C57BL ; Muridae ; Mutation ; Polymerase Chain Reaction ; S Phase ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Expression of murine CD1 on gastrointestinal epithelium (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-11-02
    Description: Cluster of differentiation 1 (CD1) in humans is a family of major histocompatibility complex (MHC) class I-like molecules expressed on the surface of immature thymocytes, Langerhans cells, and a subpopulation of B cells. The only function identified for human CD1 is as a ligand recognized by a subpopulation of T lymphocytes. In order to study the distribution and function of these molecules in the mouse, a murine CD1 complementary DNA was expressed in mouse fibroblasts and used to produce monoclonal antibodies. These antibodies revealed prominent expression of murine CD1 only on gastrointestinal tract epithelium and in the cytoplasm of hepatocytes. Low levels of expression were also detected on thymocytes and peripheral lymphocytes. The gastrointestinal distribution of murine CD1 suggests that this molecule may be important in epithelial immunity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bleicher, P A -- Balk, S P -- Hagen, S J -- Blumberg, R S -- Flotte, T J -- Terhorst, C -- AR 01805/AR/NIAMS NIH HHS/ -- CA 01310/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1990 Nov 2;250(4981):679-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, Dana-Farber Cancer Institute, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1700477" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Monoclonal ; Antigens, CD1 ; Antigens, Differentiation/*analysis/immunology/physiology ; Digestive System/*immunology ; Epithelium/immunology ; Mice ; Precipitin Tests ; T-Lymphocytes/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Reconstitution of T cell receptor zeta-mediated calcium mobilization in nonlymphoid cells (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-08-13
    Description: T cell antigen receptor (TCR) activation involves interactions between receptor subunits and nonreceptor protein tyrosine kinases (PTKs). Early steps in signaling through the zeta chain of the TCR were examined in transfected COS-1 cells. Coexpression of the PTK p59fynT, but not p56lck, with zeta or with a homodimeric TCR beta-zeta fusion protein produced tyrosine phosphorylation of both zeta and phospholipase C (PLC)-gamma 1, as well as calcium ion mobilization in response to receptor cross-linking. CD45 coexpression enhanced these effects. No requirement for the PTKZAP-70 was observed. Thus, p59fynT may link zeta directly to the PLC-gamma 1 activation pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hall, C G -- Sancho, J -- Terhorst, C -- AI 15066/AI/NIAID NIH HHS/ -- CA 01486/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 13;261(5123):915-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Immunology, Beth Israel Hospital, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8346442" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD45/analysis ; Base Sequence ; Calcium/*metabolism ; Cell Line ; Cercopithecus aethiops ; Lymphocyte Specific Protein Tyrosine Kinase p56(lck) ; Membrane Proteins/*metabolism ; Molecular Sequence Data ; Phosphorylation ; Protein-Tyrosine Kinases/*metabolism/physiology ; Proto-Oncogene Proteins/*metabolism ; Proto-Oncogene Proteins c-fyn ; Receptors, Antigen, T-Cell/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Transfection ; Type C Phospholipases/metabolism ; Tyrosine/metabolism ; ZAP-70 Protein-Tyrosine Kinase
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Biochemical analysis of human T lymphocyte differentiation antigens T4 and T5 (1980)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1980-07-25
    Description: Two major functionally distinct T cell subsets in man have been defined with heteroantiserums and monoclonal antibodies directed against stable cell surface antigens that appear during thymic ontogeny. A monoclonal antibody to T4 antigen (anti-T4) is reactive with the peripheral inducer T cell population while a monoclonal antibody to T5 antigen (anti-T5) is reactive with the cytotoxic and suppressor population. Immunoprecipitation and electrophoresis on sodium dodecyl sulfate polyacrylamide gel were used to show that on human thymocytes or peripheral T cells the T4 antigen is a single 62,000-dalton glycoprotein while the T5 antigen is a complex of two glycoproteins, one being 30,000 daltons and the other 32,000 daltons. Similar glycoproteins have been isolated with antibodies to murine Lyt 1 and Lyt 2,3 antigens. Both the antigens defining the phenotypes of inducer and suppressor populations in man and mouse are structurally homologous.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Terhorst, C -- van Agthoven, A -- Reinherz, E -- Schlossman, S -- New York, N.Y. -- Science. 1980 Jul 25;209(4455):520-1.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6967228" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies ; Antigens, Surface/*analysis ; Electrophoresis, Polyacrylamide Gel ; Glycoproteins/analysis ; Humans ; Mice ; Molecular Weight ; T-Lymphocytes/*immunology ; Thymus Gland/immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Alloantigen recognition is preceded by nonspecific adhesion of cytotoxic T cells and target cells (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-04-18
    Description: T-cell receptors bind antigens only when the antigens are exposed on the cell surface. This can be studied best in the interaction of cytolytic T lymphocytes (CTL) with target cells because the recognition and binding event can be separated from the lytic phase. Studies with CTL clones specific for HLA-A2 and HLA-B7 demonstrated that conjugates of CTL's and target cells can be formed in the absence of specific antigen recognition. Furthermore, T-cell receptor and target antigen cannot interact unless there is conjugate formation. This indicates that nonspecific conjugate formation between CTL's and target cells precedes the recognition of specific antigen by the T-cell receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spits, H -- van Schooten, W -- Keizer, H -- van Seventer, G -- van de Rijn, M -- Terhorst, C -- de Vries, J E -- AI-15066/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1986 Apr 18;232(4748):403-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3485822" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal/immunology ; Cell Adhesion ; Clone Cells ; HLA Antigens/immunology ; HLA-A2 Antigen ; HLA-B7 Antigen ; Humans ; Isoantigens/*immunology ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes, Cytotoxic/*immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Recognition of HLA-A2 by cytotoxic T lymphocytes after DNA transfer into human and murine cells (1984)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1984-11-30
    Description: A gene coding for the major histocompatibility antigen HLA-A2 was transferred into human HLA-A2 negative M1 cells and murine L cells. Following transfection, these cells expressed molecules at the cell surface that are biochemically indistinguishable from HLA-A2 antigens on the human cell line JY from which the HLA-A2 gene was isolated. The M1A2 cells were recognized and lysed by a cytolytic T-cell clone specific for HLA-A2. The transfected L cells which express HLA-A2 in association with human beta 2-microglobulin were not lysed by this T-cell clone. The specific cytolysis of M1A2 cells could be inhibited by monoclonal antibodies to HLA-A2, and monoclonal antibodies to T3, T8, and LFA-1 on cytotoxic T lymphocytes. These results suggest that killing by allospecific T cells requires HLA-A2 antigens as well as other species-specific structures on the target cell surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van de Rijn, M -- Bernabeu, C -- Royer-Pokora, B -- Weiss, J -- Seidman, J G -- de Vries, J -- Spits, H -- Terhorst, C -- AI 19148/AI/NIAID NIH HHS/ -- AI-15066/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1984 Nov 30;226(4678):1083-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6333726" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cytotoxicity, Immunologic ; *Genes ; HLA Antigens/*genetics ; HLA-A2 Antigen ; Humans ; L Cells (Cell Line)/immunology ; *Major Histocompatibility Complex ; Mice ; T-Lymphocytes, Cytotoxic/*immunology ; *Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Electronic Resource
    Electronic Resource
    T cell-specific regulation of the TCR/CD3-e gene
    Amsterdam : Elsevier
    Cell Differentiation and Development 27 (1989), S. 62 
    Details
    ISSN: 0922-3371
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0922-3371(89)90214-1
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  • 9
    Electronic Resource
    Electronic Resource
    Labeling of Adenine and Guanine Nucleotide-Binding Proteins in Permeabilized Cells with in Situ Periodate-Oxidized Nucleotides
    Amsterdam : Elsevier
    Analytical Biochemistry 210 (1993), S. 77-85 
    Details
    ISSN: 0003-2697
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1006/abio.1993.1153
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  • 10
    Electronic Resource
    Electronic Resource
    The X-linked lymphoproliferative-disease gene product SAP regulates signals induced through the co-receptor SLAM (1998)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 395 (1998), S. 462-469 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] In addition to triggering the activation of B- or T-cell antigen receptors, the binding of a ligand to its receptor at the cell surface can sometimes determine the physiological outcome of interactions between antigen-presenting cells, T and B lymphocytes. The protein SLAM (also known as CDw150), ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/26683
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