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  • 1
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    European science (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-06-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mewes, H W -- Oliver, S -- Goffeau, A -- New York, N.Y. -- Science. 1992 Jun 5;256(5062):1378-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17791593" target="_blank"〉PubMed〈/a〉
    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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    Illuminating the evolutionary history of chlamydiae (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-10
    Description: Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Horn, Matthias -- Collingro, Astrid -- Schmitz-Esser, Stephan -- Beier, Cora L -- Purkhold, Ulrike -- Fartmann, Berthold -- Brandt, Petra -- Nyakatura, Gerald J -- Droege, Marcus -- Frishman, Dmitrij -- Rattei, Thomas -- Mewes, Hans-Werner -- Wagner, Michael -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):728-30. Epub 2004 Apr 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. horn@microbial-ecology.net〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15073324" target="_blank"〉PubMed〈/a〉
    Keywords: Acanthamoeba/microbiology ; Animals ; Bacterial Proteins/analysis/genetics/metabolism ; *Biological Evolution ; Cell Membrane/chemistry ; Cell Wall/chemistry ; Chlamydia/classification/genetics/metabolism/pathogenicity ; Chlamydiales/*classification/*genetics/metabolism/pathogenicity ; Chlamydophila/classification/genetics/metabolism/pathogenicity ; Electron Transport ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Nucleotide Transport Proteins/metabolism ; Phylogeny ; Symbiosis ; Virulence ; Virulence Factors/genetics/metabolism
    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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    Human metabolic individuality in biomedical and pharmaceutical research (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-09-03
    Description: Genome-wide association studies (GWAS) have identified many risk loci for complex diseases, but effect sizes are typically small and information on the underlying biological processes is often lacking. Associations with metabolic traits as functional intermediates can overcome these problems and potentially inform individualized therapy. Here we report a comprehensive analysis of genotype-dependent metabolic phenotypes using a GWAS with non-targeted metabolomics. We identified 37 genetic loci associated with blood metabolite concentrations, of which 25 show effect sizes that are unusually high for GWAS and account for 10-60% differences in metabolite levels per allele copy. Our associations provide new functional insights for many disease-related associations that have been reported in previous studies, including those for cardiovascular and kidney disorders, type 2 diabetes, cancer, gout, venous thromboembolism and Crohn's disease. The study advances our knowledge of the genetic basis of metabolic individuality in humans and generates many new hypotheses for biomedical and pharmaceutical research.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832838/" 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/PMC3832838/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suhre, Karsten -- Shin, So-Youn -- Petersen, Ann-Kristin -- Mohney, Robert P -- Meredith, David -- Wagele, Brigitte -- Altmaier, Elisabeth -- CARDIoGRAM -- Deloukas, Panos -- Erdmann, Jeanette -- Grundberg, Elin -- Hammond, Christopher J -- de Angelis, Martin Hrabe -- Kastenmuller, Gabi -- Kottgen, Anna -- Kronenberg, Florian -- Mangino, Massimo -- Meisinger, Christa -- Meitinger, Thomas -- Mewes, Hans-Werner -- Milburn, Michael V -- Prehn, Cornelia -- Raffler, Johannes -- Ried, Janina S -- Romisch-Margl, Werner -- Samani, Nilesh J -- Small, Kerrin S -- Wichmann, H-Erich -- Zhai, Guangju -- Illig, Thomas -- Spector, Tim D -- Adamski, Jerzy -- Soranzo, Nicole -- Gieger, Christian -- 091746/Wellcome Trust/United Kingdom -- 091746/Z/10/Z/Wellcome Trust/United Kingdom -- 1R01HL103931-01/HL/NHLBI NIH HHS/ -- HL087647/HL/NHLBI NIH HHS/ -- MOP172605/Canadian Institutes of Health Research/Canada -- MOP77682/Canadian Institutes of Health Research/Canada -- MOP-82810/Canadian Institutes of Health Research/Canada -- N01-AG-12100/AG/NIA NIH HHS/ -- N01-HC-55015/HC/NHLBI NIH HHS/ -- N01-HC-55016/HC/NHLBI NIH HHS/ -- N01-HC-55018/HC/NHLBI NIH HHS/ -- N01-HC-55019/HC/NHLBI NIH HHS/ -- N01-HC-55020/HC/NHLBI NIH HHS/ -- N01-HC-55021/HC/NHLBI NIH HHS/ -- N01-HC-55022/HC/NHLBI NIH HHS/ -- P01 HL098055/HL/NHLBI NIH HHS/ -- P01HL076491-06/HL/NHLBI NIH HHS/ -- P01HL087018/HL/NHLBI NIH HHS/ -- R01 HL087647/HL/NHLBI NIH HHS/ -- R01 HL087676/HL/NHLBI NIH HHS/ -- R01DK080732/DK/NIDDK NIH HHS/ -- R01HL089650-02/HL/NHLBI NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- British Heart Foundation/United Kingdom -- Cancer Research UK/United Kingdom -- Intramural NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2011 Aug 31;477(7362):54-60. doi: 10.1038/nature10354.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany. karsten@suhre.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21886157" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Biomedical Research ; Blood/metabolism ; Child ; Chronic Disease ; Coronary Artery Disease/genetics ; Diabetes Mellitus/genetics ; *Drug Industry ; Female ; Genetic Loci/genetics ; *Genetic Variation ; *Genome-Wide Association Study ; Genotype ; Humans ; Male ; Metabolism/*genetics ; Metabolomics ; Middle Aged ; Pharmacogenetics ; Renal Insufficiency/genetics ; Risk Factors ; Venous Thromboembolism/genetics ; Young Adult
    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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    Life with 6000 genes (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-10-25
    Description: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goffeau, A -- Barrell, B G -- Bussey, H -- Davis, R W -- Dujon, B -- Feldmann, H -- Galibert, F -- Hoheisel, J D -- Jacq, C -- Johnston, M -- Louis, E J -- Mewes, H W -- Murakami, Y -- Philippsen, P -- Tettelin, H -- Oliver, S G -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 1996 Oct 25;274(5287):546, 563-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite Catholique de Louvain, Unite de Biochimie Physiologique, Place Croix du Sud, 2/20, 1348 Louvain-la-Neuve, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8849441" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; *Chromosome Mapping ; Chromosomes, Fungal/genetics ; Computer Communication Networks ; DNA, Fungal/genetics ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/physiology ; Gene Library ; *Genes, Fungal ; *Genome, Fungal ; International Cooperation ; Multigene Family ; Open Reading Frames ; RNA, Fungal/genetics ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA
    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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    The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-08
    Description: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuomo, Christina A -- Guldener, Ulrich -- Xu, Jin-Rong -- Trail, Frances -- Turgeon, B Gillian -- Di Pietro, Antonio -- Walton, Jonathan D -- Ma, Li-Jun -- Baker, Scott E -- Rep, Martijn -- Adam, Gerhard -- Antoniw, John -- Baldwin, Thomas -- Calvo, Sarah -- Chang, Yueh-Long -- Decaprio, David -- Gale, Liane R -- Gnerre, Sante -- Goswami, Rubella S -- Hammond-Kosack, Kim -- Harris, Linda J -- Hilburn, Karen -- Kennell, John C -- Kroken, Scott -- Magnuson, Jon K -- Mannhaupt, Gertrud -- Mauceli, Evan -- Mewes, Hans-Werner -- Mitterbauer, Rudolf -- Muehlbauer, Gary -- Munsterkotter, Martin -- Nelson, David -- O'donnell, Kerry -- Ouellet, Therese -- Qi, Weihong -- Quesneville, Hadi -- Roncero, M Isabel G -- Seong, Kye-Yong -- Tetko, Igor V -- Urban, Martin -- Waalwijk, Cees -- Ward, Todd J -- Yao, Jiqiang -- Birren, Bruce W -- Kistler, H Corby -- U54 HG003067/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1400-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823352" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Fungal ; Evolution, Molecular ; Fusarium/*genetics/physiology ; *Genome, Fungal ; Hordeum/microbiology ; Molecular Sequence Data ; Plant Diseases/microbiology ; Point Mutation ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA
    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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  • 6
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    Large-scale modeling of condition-specific gene regulatory networks by information integration and inference (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-28
    Description: Understanding how regulatory networks globally coordinate the response of a cell to changing conditions, such as perturbations by shifting environments, is an elementary challenge in systems biology which has yet to be met. Genome-wide gene expression measurements are high dimensional as these are reflecting the condition-specific interplay of thousands of cellular components. The integration of prior biological knowledge into the modeling process of systems-wide gene regulation enables the large-scale interpretation of gene expression signals in the context of known regulatory relations. We developed COGERE ( http://mips.helmholtz-muenchen.de/cogere ), a method for the inference of condition-specific gene regulatory networks in human and mouse. We integrated existing knowledge of regulatory interactions from multiple sources to a comprehensive model of prior information. COGERE infers condition-specific regulation by evaluating the mutual dependency between regulator (transcription factor or miRNA) and target gene expression using prior information. This dependency is scored by the non-parametric, nonlinear correlation coefficient 2 (eta squared) that is derived by a two-way analysis of variance. We show that COGERE significantly outperforms alternative methods in predicting condition-specific gene regulatory networks on simulated data sets. Furthermore, by inferring the cancer-specific gene regulatory network from the NCI-60 expression study, we demonstrate the utility of COGERE to promote hypothesis-driven clinical research.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    EXPANDS: expanding ploidy and allele frequency on nested subpopulations (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-19
    Description: Motivation:  Several cancer types consist of multiple genetically and phenotypically distinct subpopulations. The underlying mechanism for this intra-tumoral heterogeneity can be explained by the clonal evolution model, whereby growth advantageous mutations cause the expansion of cancer cell subclones. The recurrent phenotype of many cancers may be a consequence of these coexisting subpopulations responding unequally to therapies. Methods to computationally infer tumor evolution and subpopulation diversity are emerging and they hold the promise to improve the understanding of genetic and molecular determinants of recurrence. Results:  To address cellular subpopulation dynamics within human tumors, we developed a bioinformatic method, EXPANDS. It estimates the proportion of cells harboring specific mutations in a tumor. By modeling cellular frequencies as probability distributions, EXPANDS predicts mutations that accumulate in a cell before its clonal expansion. We assessed the performance of EXPANDS on one whole genome sequenced breast cancer and performed SP analyses on 118 glioblastoma multiforme samples obtained from TCGA. Our results inform about the extent of subclonal diversity in primary glioblastoma, subpopulation dynamics during recurrence and provide a set of candidate genes mutated in the most well-adapted subpopulations. In summary, EXPANDS predicts tumor purity and subclonal composition from sequencing data. Availability and implementation:  EXPANDS is available for download at http://code.google.com/p/expands (matlab version - used in this manuscript) and http://cran.r-project.org/web/packages/expands (R version). Contact :  claudia.petritsch@ucsf.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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  • 8
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    SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-29
    Description: The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/ ) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains 〉163 million proteins corresponding to ~70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    The MIPS mammalian protein-protein interaction database (2004)
    Oxford University Press
    Details
    Publication Date: 2004-11-05
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Optimization models for cancer classification: extracting gene interaction information from microarray expression data (2004)
    Oxford University Press
    Details
    Publication Date: 2004-01-22
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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