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  • 1
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    zCall: a rare variant caller for array-based genotyping: Genetics and population analysis (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-30
    Description: : zCall is a variant caller specifically designed for calling rare single-nucleotide polymorphisms from array-based technology. This caller is implemented as a post-processing step after a default calling algorithm has been applied. The algorithm uses the intensity profile of the common allele homozygote cluster to define the location of the other two genotype clusters. We demonstrate improved detection of rare alleles when applying zCall to samples that have both Illumina Infinium HumanExome BeadChip and exome sequencing data available. Availability: http://atguweb.mgh.harvard.edu/apps/zcall . Contact: bneale@broadinstitute.org 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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    Comparative genomics of the neglected human malaria parasite Plasmodium vivax (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-10
    Description: The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non-human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651158/" 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/PMC2651158/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carlton, Jane M -- Adams, John H -- Silva, Joana C -- Bidwell, Shelby L -- Lorenzi, Hernan -- Caler, Elisabet -- Crabtree, Jonathan -- Angiuoli, Samuel V -- Merino, Emilio F -- Amedeo, Paolo -- Cheng, Qin -- Coulson, Richard M R -- Crabb, Brendan S -- Del Portillo, Hernando A -- Essien, Kobby -- Feldblyum, Tamara V -- Fernandez-Becerra, Carmen -- Gilson, Paul R -- Gueye, Amy H -- Guo, Xiang -- Kang'a, Simon -- Kooij, Taco W A -- Korsinczky, Michael -- Meyer, Esmeralda V-S -- Nene, Vish -- Paulsen, Ian -- White, Owen -- Ralph, Stuart A -- Ren, Qinghu -- Sargeant, Tobias J -- Salzberg, Steven L -- Stoeckert, Christian J -- Sullivan, Steven A -- Yamamoto, Marcio M -- Hoffman, Stephen L -- Wortman, Jennifer R -- Gardner, Malcolm J -- Galinski, Mary R -- Barnwell, John W -- Fraser-Liggett, Claire M -- N01 AI030071/AI/NIAID NIH HHS/ -- R01 AI064478/AI/NIAID NIH HHS/ -- R01 AI064478-05/AI/NIAID NIH HHS/ -- R01 GM070793/GM/NIGMS NIH HHS/ -- R01 GM070793-01A2/GM/NIGMS NIH HHS/ -- R01 GM083873/GM/NIGMS NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-09/LM/NLM NIH HHS/ -- England -- Nature. 2008 Oct 9;455(7214):757-63. doi: 10.1038/nature07327.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Institute for Genomic Research/J. Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA. jane.carlton@nyumc.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18843361" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Artemisinins/metabolism/pharmacology ; Atovaquone/metabolism/pharmacology ; Cell Nucleus/genetics ; Chromosomes/genetics ; Conserved Sequence/genetics ; Erythrocytes/parasitology ; Evolution, Molecular ; Genome, Protozoan/*genetics ; *Genomics ; Haplorhini/parasitology ; Humans ; Isochores/genetics ; Ligands ; Malaria, Vivax/metabolism/*parasitology ; Multigene Family ; Plasmodium vivax/drug effects/*genetics/pathogenicity/physiology ; Sequence Analysis, DNA ; Species Specificity ; Synteny/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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  • 3
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    Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-08
    Description: Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seshadri, Rekha -- Adrian, Lorenz -- Fouts, Derrick E -- Eisen, Jonathan A -- Phillippy, Adam M -- Methe, Barbara A -- Ward, Naomi L -- Nelson, William C -- Deboy, Robert T -- Khouri, Hoda M -- Kolonay, James F -- Dodson, Robert J -- Daugherty, Sean C -- Brinkac, Lauren M -- Sullivan, Steven A -- Madupu, Ramana -- Nelson, Karen E -- Kang, Katherine H -- Impraim, Marjorie -- Tran, Kevin -- Robinson, Jeffrey M -- Forberger, Heather A -- Fraser, Claire M -- Zinder, Stephen H -- Heidelberg, John F -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):105-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. rekha@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637277" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/biosynthesis ; Biodegradation, Environmental ; Chloroflexi/*genetics/*metabolism ; Gene Duplication ; Genes, Bacterial ; *Genome, Bacterial ; Hydrogen/metabolism ; Molecular Sequence Data ; Nitrogenase/genetics/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Quinones/metabolism ; Sequence Analysis, DNA ; Tetrachloroethylene/*metabolism ; Transcription Factors/genetics/metabolism ; Water Pollutants, Chemical/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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  • 4
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    Genome of Geobacter sulfurreducens: metal reduction in subsurface environments (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-13
    Description: The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Methe, B A -- Nelson, K E -- Eisen, J A -- Paulsen, I T -- Nelson, W -- Heidelberg, J F -- Wu, D -- Wu, M -- Ward, N -- Beanan, M J -- Dodson, R J -- Madupu, R -- Brinkac, L M -- Daugherty, S C -- DeBoy, R T -- Durkin, A S -- Gwinn, M -- Kolonay, J F -- Sullivan, S A -- Haft, D H -- Selengut, J -- Davidsen, T M -- Zafar, N -- White, O -- Tran, B -- Romero, C -- Forberger, H A -- Weidman, J -- Khouri, H -- Feldblyum, T V -- Utterback, T R -- Van Aken, S E -- Lovley, D R -- Fraser, C M -- New York, N.Y. -- Science. 2003 Dec 12;302(5652):1967-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bmethe@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671304" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/metabolism ; Acetyl Coenzyme A/metabolism ; Aerobiosis ; Anaerobiosis ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Chemotaxis ; Chromosomes, Bacterial/genetics ; Cytochromes c/genetics/metabolism ; Electron Transport ; Energy Metabolism ; Genes, Bacterial ; Genes, Regulator ; *Genome, Bacterial ; Geobacter/*genetics/*metabolism/physiology ; Hydrogen/metabolism ; Metals/*metabolism ; Movement ; Open Reading Frames ; Oxidation-Reduction ; Phylogeny
    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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    Growth and maturation of a mid- to shallow-crustal intrusive complex, North Cascades, Washington (2016)
    Geological Society of America (GSA)
    In: Geosphere
    Details
    Publication Date: 2016-10-08
    Description: Studies of plutons indicate that they are the result of a complex interplay of magmatic processes occurring during magma generation, ascent, and emplacement. A critical tool for deciphering these processes is high-precision geochronology, which can help determine the timing and rates of magmatism in the crust. We conducted a field and U-Pb geochronological study of the Cretaceous Black Peak intrusive complex in the North Cascades of Washington State to investigate magmatism at a detailed scale and to refine estimates of plutonic construction rates. High-precision chemical abrasion–thermal ionization mass spectrometry (CA-TIMS) U-Pb geochronology was carried out on 31 samples from five mapped intrusive phases. Field relations in the Black Peak intrusive complex show intrusive contacts that vary from sharp to gradational. Whole-rock Sm/Nd, zircon oxygen isotopes, and zircon trace elements were obtained on subsets of representative samples. The U-Pb geochronology from the Black Peak intrusive complex documents batholith intrusion over 4.5 m.y. and suggests that magmatism was semicontinuous for a minimum of 3.5 m.y. Individual samples display age dispersion in single-zircon dates that ranges from ~10 5 yr to several 10 6 yr, with a general increase in the age range for younger samples. Whole-rock Nd and zircon 18 O for all Black Peak intrusive complex samples indicate that magmas were derived from mantle and crustal sources and that all magmas were isotopically homogenized prior to zircon saturation. Ti-in-zircon temperatures from zircon cores are generally above calculated zircon saturation temperatures, which suggests that most Black Peak intrusive complex magmas were zircon undersaturated in the melt source region. A range of thicknesses was considered, and a thickness of ~10 km for the Black Peak intrusive complex gives an average intrusion rate of ~1.1 x 10 –3 km 3 /yr, which is high enough to sustain a magma reservoir in the shallow crust. The field evidence and long overall duration of intrusion are incompatible with the entire Black Peak intrusive complex being molten at any one time, but the larger, more compositionally homogeneous domains in the Black Peak intrusive complex are likely the solidified remnants of mushy magma bodies with ~10 5 yr durations. These data suggest that the Black Peak intrusive complex may have remained "mushy" for long periods of time (10 5 yr) and may indicate that the spread in dates within individual samples is best interpreted as either antecrystic recycling and/or protracted autocrystic growth.
    Electronic ISSN: 1553-040X
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 6
    Electronic Resource
    Electronic Resource
    Nucleophilic reactions of anions with PF3 and OPF3 in the gas phase by ion cyclotron resonance spectroscopy (1978)
    s.l. : American Chemical Society
    Inorganic chemistry 17 (1978), S. 1589-1595 
    Details
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ic50184a039
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    Paper (German National Licenses)
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  • 7
    Electronic Resource
    Electronic Resource
    Nucleophilic reactions of anions with trimethyl phosphate in the gas phase by ion cyclotron resonance spectroscopy (1980)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 102 (1980), S. 935-938 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00523a007
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  • 8
    Electronic Resource
    Electronic Resource
    Exchange elasticity in copper(II) dinuclear cryptates (1980)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 102 (1980), S. 5935-5936 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00538a052
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  • 9
    Electronic Resource
    Electronic Resource
    Gas-phase reactions of anions with substituted silanes (1980)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 102 (1980), S. 5012-5015 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00535a031
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  • 10
    Electronic Resource
    Electronic Resource
    Gas-phase reactions of cyclic silanes (1981)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 103 (1981), S. 480-481 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00392a048
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