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  • 1
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    A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-25
    Description: Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073058/" 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/PMC3073058/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Dongying -- Hugenholtz, Philip -- Mavromatis, Konstantinos -- Pukall, Rudiger -- Dalin, Eileen -- Ivanova, Natalia N -- Kunin, Victor -- Goodwin, Lynne -- Wu, Martin -- Tindall, Brian J -- Hooper, Sean D -- Pati, Amrita -- Lykidis, Athanasios -- Spring, Stefan -- Anderson, Iain J -- D'haeseleer, Patrik -- Zemla, Adam -- Singer, Mitchell -- Lapidus, Alla -- Nolan, Matt -- Copeland, Alex -- Han, Cliff -- Chen, Feng -- Cheng, Jan-Fang -- Lucas, Susan -- Kerfeld, Cheryl -- Lang, Elke -- Gronow, Sabine -- Chain, Patrick -- Bruce, David -- Rubin, Edward M -- Kyrpides, Nikos C -- Klenk, Hans-Peter -- Eisen, Jonathan A -- R01 GM054592-09/GM/NIGMS NIH HHS/ -- R01 GM067012-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DOE Joint Genome Institute, Walnut Creek, California 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033048" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry ; Amino Acid Sequence ; Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Bacterial Proteins/chemistry ; Biodiversity ; Databases, Genetic ; Genes, rRNA/genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment
    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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  • 2
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    The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-18
    Description: Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520129/" 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/PMC3520129/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Loftus, Brendan J -- Fung, Eula -- Roncaglia, Paola -- Rowley, Don -- Amedeo, Paolo -- Bruno, Dan -- Vamathevan, Jessica -- Miranda, Molly -- Anderson, Iain J -- Fraser, James A -- Allen, Jonathan E -- Bosdet, Ian E -- Brent, Michael R -- Chiu, Readman -- Doering, Tamara L -- Donlin, Maureen J -- D'Souza, Cletus A -- Fox, Deborah S -- Grinberg, Viktoriya -- Fu, Jianmin -- Fukushima, Marilyn -- Haas, Brian J -- Huang, James C -- Janbon, Guilhem -- Jones, Steven J M -- Koo, Hean L -- Krzywinski, Martin I -- Kwon-Chung, June K -- Lengeler, Klaus B -- Maiti, Rama -- Marra, Marco A -- Marra, Robert E -- Mathewson, Carrie A -- Mitchell, Thomas G -- Pertea, Mihaela -- Riggs, Florenta R -- Salzberg, Steven L -- Schein, Jacqueline E -- Shvartsbeyn, Alla -- Shin, Heesun -- Shumway, Martin -- Specht, Charles A -- Suh, Bernard B -- Tenney, Aaron -- Utterback, Terry R -- Wickes, Brian L -- Wortman, Jennifer R -- Wye, Natasja H -- Kronstad, James W -- Lodge, Jennifer K -- Heitman, Joseph -- Davis, Ronald W -- Fraser, Claire M -- Hyman, Richard W -- AI47087/AI/NIAID NIH HHS/ -- AI48594/AI/NIAID NIH HHS/ -- R01 AI050184/AI/NIAID NIH HHS/ -- R01 AI050184-05/AI/NIAID NIH HHS/ -- R01 HL088905/HL/NHLBI NIH HHS/ -- R01 HL088905-04A2/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1321-4. Epub 2005 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bjloftus@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15653466" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Cell Wall/metabolism ; Chromosomes, Fungal/genetics ; Computational Biology ; Cryptococcus neoformans/*genetics/pathogenicity/physiology ; DNA Transposable Elements ; Fungal Proteins/metabolism ; Gene Library ; Genes, Fungal ; *Genome, Fungal ; Humans ; Introns ; Molecular Sequence Data ; Phenotype ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Polysaccharides/metabolism ; RNA, Antisense ; Sequence Analysis, DNA ; Transcription, Genetic ; Virulence ; Virulence Factors/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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    Insights into the phylogeny and coding potential of microbial dark matter (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-16
    Description: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rinke, Christian -- Schwientek, Patrick -- Sczyrba, Alexander -- Ivanova, Natalia N -- Anderson, Iain J -- Cheng, Jan-Fang -- Darling, Aaron -- Malfatti, Stephanie -- Swan, Brandon K -- Gies, Esther A -- Dodsworth, Jeremy A -- Hedlund, Brian P -- Tsiamis, George -- Sievert, Stefan M -- Liu, Wen-Tso -- Eisen, Jonathan A -- Hallam, Steven J -- Kyrpides, Nikos C -- Stepanauskas, Ramunas -- Rubin, Edward M -- Hugenholtz, Philip -- Woyke, Tanja -- England -- Nature. 2013 Jul 25;499(7459):431-7. doi: 10.1038/nature12352. Epub 2013 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DOE Joint Genome Institute, Walnut Creek, California 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23851394" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/*classification/*genetics/isolation & purification/metabolism ; Bacteria/*classification/*genetics/isolation & purification/metabolism ; Ecosystem ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Metagenome/genetics ; *Metagenomics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Single-Cell Analysis
    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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    Diastems in the Pecan Gap Chalk of Travis County, Texas (1950)
    Society for Sedimentary Geology
    Details
    Publication Date: 1950-01-01
    Print ISSN: 1527-1404
    Electronic ISSN: 1938-3681
    Topics: Geosciences
    Published by Society for Sedimentary Geology
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  • 5
    Electronic Resource
    Electronic Resource
    Parallel factorization of banded linear matrices using a systolic array processor (1996)
    Springer
    Advances in computational mathematics 5 (1996), S. 1-14 
    Details
    ISSN: 1572-9044
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract A parallel algorithm for calculating theQR factorization of a banded system of linear equations using a systolic array processor is presented and an application to spline fitting is given. The major advantage of the method is that the size of the processor array is fixed by the size of the bandwidth of the system to be solved. This allows the factorization of large systems using small systolic arrays. The cost of the method, in terms of storage and time, is optimal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02124732
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Tensor-product spline interpolation to data on or near a family of lines (1993)
    Springer
    Numerical algorithms 5 (1993), S. 193-204 
    Details
    ISSN: 1572-9265
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract Algorithms exist for least-squares tensor-product splineapproximation to data (a) on a rectangular mesh, (b) on a family of parallel lines and (c) that is generally scattered. In contrast,direct algorithms for tensor-product splineinterpolation are available only for data type (a). The structure of the data in cases (a) and (b) is such that the corresponding algorithms are particularly efficient. This paper extends the range of solvable spline interpolation problems by describing how tensor product spline interpolants can be constructed efficiently and directly for data type (b). Moreover, for a limited class of data of type (c), viz. when the data liesclose to a family of parallel lines, it is shown that iterative application of our approach for data type (b) can be used to provide an interpolant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02210502
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  • 7
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    Needle-like structures discovered on positively charged lightning branches (2019)
    Springer Nature
    In: Nature
    Details
    Publication Date: 2019
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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