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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Wednesday, 2014 October 15
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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PubMed Results

Items 1 - 3 of 3

1.	Nature. 2014 Sep 18;513(7518):445-8. doi: 10.1038/513445a. When disease strikes from nowhere. Marx V. Author information: Nature and Nature Methods.
	PMID: 25230666 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Sep 18;513(7518):375-81. doi: 10.1038/nature13726. Epub 2014 Sep 3. The genomic substrate for adaptive radiation in African cichlid fish. Brawand D1, Wagner CE2, Li YI3, Malinsky M4, Keller I5, Fan S6, Simakov O7, Ng AY8, Lim ZW8, Bezault E9, Turner-Maier J10, Johnson J10, Alcazar R11, Noh HJ10, Russell P12, Aken B13, Alföldi J10, Amemiya C14, Azzouzi N15, Baroiller JF16, Barloy-Hubler F15, Berlin A10, Bloomquist R17, Carleton KL18, Conte MA18, D'Cotta H16, Eshel O19, Gaffney L10, Galibert F15, Gante HF20, Gnerre S10, Greuter L21, Guyon R15, Haddad NS17, Haerty W22, Harris RM23, Hofmann HA23, Hourlier T13, Hulata G19, Jaffe DB10, Lara M10, Lee AP8, MacCallum I10, Mwaiko S24, Nikaido M25, Nishihara H25, Ozouf-Costaz C26, Penman DJ27, Przybylski D10, Rakotomanga M15, Renn SC9, Ribeiro FJ10, Ron M19, Salzburger W20, Sanchez-Pulido L22, Santos ME20, Searle S13, Sharpe T10, Swofford R10, Tan FJ28, Williams L10, Young S10, Yin S10, Okada N29, Kocher TD18, Miska EA30, Lander ES10, Venkatesh B8, Fernald RD11, Meyer A6, Ponting CP22, Streelman JT17, Lindblad-Toh K31, Seehausen O21, Di Palma F32. Author information: 11] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [3]. 21] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland [3]. 31] MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK [2]. 41] Gurdon Institute, Cambridge CB2 1QN, UK [2] Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. 5Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. 6Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. 71] Department of Biology, University of Konstanz, D-78457 Konstanz, Germany [2] European Molecular Biology Laboratory, 69117 Heidelberg, Germany. 8Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore. 9Department of Biology, Reed College, Portland, Oregon 97202, USA. 10Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. 11Biology Department, Stanford University, Stanford, California 94305-5020, USA. 12Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA. 13Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. 14Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA. 15Institut Génétique et Développement, CNRS/University of Rennes, 35043 Rennes, France. 16CIRAD, Campus International de Baillarguet, TA B-110/A, 34398 Montpellier cedex 5, France. 17School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA. 18Department of Biology, University of Maryland, College Park, Maryland 20742, USA. 19Animal Genetics, Institute of Animal Science, ARO, The Volcani Center, Bet-Dagan, 50250 Israel. 20Zoological Institute, University of Basel, CH-4051 Basel, Switzerland. 211] Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland [2] Division of Aquatic Ecology, Institute of Ecology &Evolution, University of Bern, CH-3012 Bern, Switzerland. 22MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK. 23Department of Integrative Biology, Center for Computational Biology and Bioinformatics; The University of Texas at Austin, Austin, Texas 78712, USA. 24Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution &Biogeochemistry, CH-6047 Kastanienbaum, Switzerland. 25Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan. 26Systématique, Adaptation, Evolution, National Museum of Natural History, 75005 Paris, France. 27Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK. 28Carnegie Institution of Washington, Department of Embryology, 3520 San Martin Drive Baltimore, Maryland 21218, USA. 291] Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 226-8501 Yokohama, Japan [2] National Cheng Kung University, Tainan City, 704 Taiwan. 30Gurdon Institute, Cambridge CB2 1QN, UK. 311] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden. 321] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich NR18 7UH, UK. Comment in Evolutionary biology: Radiating genomes. [Nature. 2014] Evolutionary biology: Radiating genomes.Jiggins CD. Nature. 2014 Sep 18; 513(7518):318-9. Epub 2014 Sep 3. Abstract Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
	PMID: 25186727 [PubMed - indexed for MEDLINE]
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3.	Nature. 2014 Sep 18;513(7518):382-7. doi: 10.1038/nature13438. Epub 2014 Jul 20. Proteogenomic characterization of human colon and rectal cancer. Zhang B1, Wang J2, Wang X2, Zhu J2, Liu Q2, Shi Z3, Chambers MC2, Zimmerman LJ4, Shaddox KF5, Kim S6, Davies SR7, Wang S8, Wang P9, Kinsinger CR10, Rivers RC10, Rodriguez H10, Townsend RR7, Ellis MJ7, Carr SA11, Tabb DL2, Coffey RJ12, Slebos RJ13, Liebler DC4; NCI CPTAC. Collaborators: Carr SA, Gillette MA, Klauser KR, Kuhn E, Mani DR, Mertins P, Ketchum KA, Paulovich AG, Whiteaker JR, Edwards NJ, McGarvey PB, Madhavan S, Wang P, Chan D, Pandey A, Shih IeM, Zhang H, Zhang Z, Zhu H, Whiteley GA, Skates SJ, White FM, Levine DA, Boja ES, Kinsinger CR, Hiltke T, Mesri M, Rivers RC, Rodriguez H, Shaw KM, Stein SE, Fenyo D, Liu T, McDermott JE, Payne SH, Rodland KD, Smith RD, Rudnick P, Snyder M, Zhao Y, Chen X, Ransohoff DF, Hoofnagle AN, Liebler DC, Sanders ME, Shi Z, Slebos RJ, Tabb DL, Zhang B, Zimmerman LJ, Wang Y, Davies SR, Ding L, Ellis MJ, Townsend RR. Author information: 11] Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA [2] Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA. 2Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA. 31] Advanced Computing Center for Research and Education, Vanderbilt University, Nashville, Tennessee 37232, USA [2] Department of Electrical Engineering and Computer Science, Vanderbilt University, Tennessee 37232, USA. 41] Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232, USA. 5Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232, USA. 6 Directorate of Fundamental and Computational Sciences, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. 7Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA. 8Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M2-B500, Seattle, Washington 98109, USA. 9Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, New York 10029, USA. 10Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892, USA. 11Broad Institute of MIT and Harvard, Cambridge, Maryland 02142, USA. 12Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA. 131] Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232, USA. Abstract Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tumours. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA 'microsatellite instability/CpG island methylation phenotype' transcriptomic subtype, but had distinct mutation, methylation and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates, including HNF4A (hepatocyte nuclear factor 4, alpha), TOMM34 (translocase of outer mitochondrial membrane 34) and SRC (SRC proto-oncogene, non-receptor tyrosine kinase). Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology.
	PMID: 25043054 [PubMed - indexed for MEDLINE]
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