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

Sent on Wednesday, 2014 February 05
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PubMed Results

Items 1 - 6 of 6

1.	Nature. 2014 Jan 23;505(7484):484. doi: 10.1038/505484a. Janet Rowley (1925-2013). Druker BJ. Author information: Knight Cancer Institute at Oregon Health & Science University, Portland, Oregon, and a Howard Hughes Medical Institute investigator. He shared the 2012 Japan Prize with Janet Rowley and Nicholas Lydon.
	PMID: 24451535 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Jan 23;505(7484):468-71. doi: 10.1038/505468a. Cloning comeback. Cyranoski D.
	PMID: 24451524 [PubMed - indexed for MEDLINE]
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3.	N Engl J Med. 2014 Jan 23;370(4):379-80. doi: 10.1056/NEJMcibr1314577. Immunotherapy for HIV Infection. Weiss RA.
	PMID: 24450898 [PubMed - indexed for MEDLINE]
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4.	Science. 2014 Jan 17;343(6168):262. doi: 10.1126/science.1249912. Retrospective. Frederick Sanger (1918-2013). Brenner S. Author information: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673.
	PMID: 24436413 [PubMed - indexed for MEDLINE]
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5.	Nature. 2014 Jan 23;505(7484):495-501. doi: 10.1038/nature12912. Epub 2014 Jan 5. Discovery and saturation analysis of cancer genes across 21 tumour types. Lawrence MS1, Stojanov P2, Mermel CH3, Robinson JT1, Garraway LA4, Golub TR5, Meyerson M4, Gabriel SB1, Lander ES6, Getz G7. Author information: 1Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. 21] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA. 31] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital, Cancer Center and Department of Pathology, 55 Fruit Street, Boston, Massachusetts 02114, USA. 41] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA. 51] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [4] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815, USA. 61] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [3] Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4]. 71] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Massachusetts General Hospital, Cancer Center and Department of Pathology, 55 Fruit Street, Boston, Massachusetts 02114, USA [3] Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA [4]. Abstract Although a few cancer genes are mutated in a high proportion of tumours of a given type (>20%), most are mutated at intermediate frequencies (2-20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600-5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.
	PMID: 24390350 [PubMed - indexed for MEDLINE]
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6.	Nature. 2014 Jan 23;505(7484):546-9. doi: 10.1038/nature12817. Epub 2013 Dec 18. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Dohm JC1, Minoche AE1, Holtgräwe D2, Capella-Gutiérrez S3, Zakrzewski F4, Tafer H5, Rupp O2, Sörensen TR2, Stracke R2, Reinhardt R6, Goesmann A2, Kraft T7, Schulz B8, Stadler PF5, Schmidt T4, Gabaldón T9, Lehrach H10, Weisshaar B2, Himmelbauer H11. Author information: 11] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [4]. 2Bielefeld University, CeBiTec and Department of Biology, Universitätsstraße 25, 33615 Bielefeld, Germany. 31] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain. 4TU Dresden, Department of Biology, Zellescher Weg 20b, 01217 Dresden, Germany. 5University of Leipzig, Department of Computer Science, Härtelstraße 16-18, 04107 Leipzig, Germany. 6Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Köln, Germany. 7Syngenta, Box 302, 26123 Landskrona, Sweden. 8KWS SAAT AG, Grimsehlstraße 31, 37574 Einbeck, Germany. 91] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain. 10Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany. 111] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain. Abstract Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.
	PMID: 24352233 [PubMed - indexed for MEDLINE]
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