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  • 1
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    The plasticity of dendritic cell responses to pathogens and their components (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-27
    Description: Dendritic cells are involved in the initiation of both innate and adaptive immunity. To systematically explore how dendritic cells modulate the immune system in response to different pathogens, we used oligonucleotide microarrays to measure gene expression profiles of dendritic cells in response to Escherichia coli, Candida albicans, and influenza virus as well as to their molecular components. Both a shared core response and pathogen-specific programs of gene expression were observed upon exposure to each of these pathogens. These results reveal that dendritic cells sense diverse pathogens and elicit tailored pathogen-specific immune responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Q -- Liu, D -- Majewski, P -- Schulte, L C -- Korn, J M -- Young, R A -- Lander, E S -- Hacohen, N -- New York, N.Y. -- Science. 2001 Oct 26;294(5543):870-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11679675" target="_blank"〉PubMed〈/a〉
    Keywords: Antigen Presentation/genetics ; Candida albicans/*immunology ; Cells, Cultured ; Dendritic Cells/*immunology/metabolism ; Escherichia coli/*immunology ; Gene Expression Profiling ; *Gene Expression Regulation ; Humans ; Immunity, Innate ; Immunologic Factors/genetics ; Inflammation/immunology ; Influenza A virus/*immunology ; Leukocytes/immunology ; Lipopolysaccharides/immunology ; Mannans/immunology ; Oligonucleotide Array Sequence Analysis ; Phagocytosis ; RNA, Double-Stranded/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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  • 2
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    Mapping and sequencing of structural variation from eight human genomes (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-03
    Description: Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424287/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424287/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kidd, Jeffrey M -- Cooper, Gregory M -- Donahue, William F -- Hayden, Hillary S -- Sampas, Nick -- Graves, Tina -- Hansen, Nancy -- Teague, Brian -- Alkan, Can -- Antonacci, Francesca -- Haugen, Eric -- Zerr, Troy -- Yamada, N Alice -- Tsang, Peter -- Newman, Tera L -- Tuzun, Eray -- Cheng, Ze -- Ebling, Heather M -- Tusneem, Nadeem -- David, Robert -- Gillett, Will -- Phelps, Karen A -- Weaver, Molly -- Saranga, David -- Brand, Adrianne -- Tao, Wei -- Gustafson, Erik -- McKernan, Kevin -- Chen, Lin -- Malig, Maika -- Smith, Joshua D -- Korn, Joshua M -- McCarroll, Steven A -- Altshuler, David A -- Peiffer, Daniel A -- Dorschner, Michael -- Stamatoyannopoulos, John -- Schwartz, David -- Nickerson, Deborah A -- Mullikin, James C -- Wilson, Richard K -- Bruhn, Laurakay -- Olson, Maynard V -- Kaul, Rajinder -- Smith, Douglas R -- Eichler, Evan E -- 3 U54 HG002043/HG/NHGRI NIH HHS/ -- HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120-01/HG/NHGRI NIH HHS/ -- U54 HG002043-07S1/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 1;453(7191):56-64. doi: 10.1038/nature06862.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451855" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Inversion/genetics ; Continental Population Groups/genetics ; Euchromatin/genetics ; Gene Deletion ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Geography ; Haplotypes ; Humans ; Mutagenesis, Insertional/genetics ; *Physical Chromosome Mapping ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; *Sequence Analysis, DNA
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Integrating common and rare genetic variation in diverse human populations (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-09-03
    Description: Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of 〈or=5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173859/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173859/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉International HapMap 3 Consortium -- Altshuler, David M -- Gibbs, Richard A -- Peltonen, Leena -- Dermitzakis, Emmanouil -- Schaffner, Stephen F -- Yu, Fuli -- Bonnen, Penelope E -- de Bakker, Paul I W -- Deloukas, Panos -- Gabriel, Stacey B -- Gwilliam, Rhian -- Hunt, Sarah -- Inouye, Michael -- Jia, Xiaoming -- Palotie, Aarno -- Parkin, Melissa -- Whittaker, Pamela -- Chang, Kyle -- Hawes, Alicia -- Lewis, Lora R -- Ren, Yanru -- Wheeler, David -- Muzny, Donna Marie -- Barnes, Chris -- Darvishi, Katayoon -- Hurles, Matthew -- Korn, Joshua M -- Kristiansson, Kati -- Lee, Charles -- McCarrol, Steven A -- Nemesh, James -- Keinan, Alon -- Montgomery, Stephen B -- Pollack, Samuela -- Price, Alkes L -- Soranzo, Nicole -- Gonzaga-Jauregui, Claudia -- Anttila, Verneri -- Brodeur, Wendy -- Daly, Mark J -- Leslie, Stephen -- McVean, Gil -- Moutsianas, Loukas -- Nguyen, Huy -- Zhang, Qingrun -- Ghori, Mohammed J R -- McGinnis, Ralph -- McLaren, William -- Takeuchi, Fumihiko -- Grossman, Sharon R -- Shlyakhter, Ilya -- Hostetter, Elizabeth B -- Sabeti, Pardis C -- Adebamowo, Clement A -- Foster, Morris W -- Gordon, Deborah R -- Licinio, Julio -- Manca, Maria Cristina -- Marshall, Patricia A -- Matsuda, Ichiro -- Ngare, Duncan -- Wang, Vivian Ota -- Reddy, Deepa -- Rotimi, Charles N -- Royal, Charmaine D -- Sharp, Richard R -- Zeng, Changqing -- Brooks, Lisa D -- McEwen, Jean E -- 068545/Wellcome Trust/United Kingdom -- 068545/Z/02/Wellcome Trust/United Kingdom -- 076113/Wellcome Trust/United Kingdom -- 077011/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 082371/Wellcome Trust/United Kingdom -- 089061/Wellcome Trust/United Kingdom -- 089062/Wellcome Trust/United Kingdom -- 091746/Wellcome Trust/United Kingdom -- G0000934/Medical Research Council/United Kingdom -- P30 DK043351/DK/NIDDK NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Sep 2;467(7311):52-8. doi: 10.1038/nature09298.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA. altshuler@molbio.mgh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20811451" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Copy Number Variations ; *Genome, Human ; Human Genome Project ; Humans ; *Polymorphism, Single Nucleotide ; Population Groups/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Demographic history and rare allele sharing among human populations (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-07-05
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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