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  • 1
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    The Norway spruce genome sequence and conifer genome evolution (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-05-24
    Description: Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the 〉100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (〉10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nystedt, Bjorn -- Street, Nathaniel R -- Wetterbom, Anna -- Zuccolo, Andrea -- Lin, Yao-Cheng -- Scofield, Douglas G -- Vezzi, Francesco -- Delhomme, Nicolas -- Giacomello, Stefania -- Alexeyenko, Andrey -- Vicedomini, Riccardo -- Sahlin, Kristoffer -- Sherwood, Ellen -- Elfstrand, Malin -- Gramzow, Lydia -- Holmberg, Kristina -- Hallman, Jimmie -- Keech, Olivier -- Klasson, Lisa -- Koriabine, Maxim -- Kucukoglu, Melis -- Kaller, Max -- Luthman, Johannes -- Lysholm, Fredrik -- Niittyla, Totte -- Olson, Ake -- Rilakovic, Nemanja -- Ritland, Carol -- Rossello, Josep A -- Sena, Juliana -- Svensson, Thomas -- Talavera-Lopez, Carlos -- Theissen, Gunter -- Tuominen, Hannele -- Vanneste, Kevin -- Wu, Zhi-Qiang -- Zhang, Bo -- Zerbe, Philipp -- Arvestad, Lars -- Bhalerao, Rishikesh -- Bohlmann, Joerg -- Bousquet, Jean -- Garcia Gil, Rosario -- Hvidsten, Torgeir R -- de Jong, Pieter -- MacKay, John -- Morgante, Michele -- Ritland, Kermit -- Sundberg, Bjorn -- Thompson, Stacey Lee -- Van de Peer, Yves -- Andersson, Bjorn -- Nilsson, Ove -- Ingvarsson, Par K -- Lundeberg, Joakim -- Jansson, Stefan -- England -- Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698360" target="_blank"〉PubMed〈/a〉
    Keywords: Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Silencing ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics ; Internet ; Introns/genetics ; Phenotype ; Picea/*genetics ; RNA, Untranslated/genetics ; Sequence Analysis, DNA ; Terminal Repeat Sequences/genetics ; Transcription, Genetic/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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  • 2
    Electronic Resource
    Electronic Resource
    Determination of metabolites by observing the change in reaction rate during the early course of a first order reaction, as applied to fructose-1-phosphate
    Amsterdam : Elsevier
    Analytical Biochemistry 63 (1975), S. 572-578 
    Details
    ISSN: 0003-2697
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0003-2697(75)90382-6
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  • 3
    Electronic Resource
    Electronic Resource
    Gastrin/CCK-like immunoreactivity in Hatschek's groove of Branchiostoma lanceolatum (Cephalochordata)
    Amsterdam : Elsevier
    General and Comparative Endocrinology 70 (1988), S. 436-441 
    Details
    ISSN: 0016-6480
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0016-6480(88)90119-0
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  • 4
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    Assembly scaffolding with PE-contaminated mate-pair libraries (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-25
    Description: Motivation : Scaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-end libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problems is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed before, in relation to integrated scaffolders, but solutions rely on the orientation being observable, e.g. by finding the junction adapter sequence in the reads. This is not always possible, making orientation and insert size of a read pair stochastic. To our knowledge, there is neither previous work on modeling PE-contamination, nor a study on the effect PE-contamination has on scaffolding quality. Results : We have addressed PE-contamination in an update to our scaffolder BESST. We formulate the problem as an integer linear program which is solved using an efficient heuristic. The new method shows significant improvement over both integrated and stand-alone scaffolders in our experiments. The impact of modeling PE-contamination is quantified by comparing with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in an increased number of misassemblies, more conservative scaffolding and inflated assembly sizes. Availability and implementation : The model is implemented in BESST. Source code and usage instructions are found at https://github.com/ksahlin/BESST . BESST can also be downloaded using PyPI. Contact: ksahlin@kth.se 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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  • 5
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    Improved gap size estimation for scaffolding algorithms (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-25
    Description: Motivation: One of the important steps of genome assembly is scaffolding, in which contigs are linked using information from read-pairs. Scaffolding provides estimates about the order, relative orientation and distance between contigs. We have found that contig distance estimates are generally strongly biased and based on false assumptions. Since erroneous distance estimates can mislead in subsequent analysis, it is important to provide unbiased estimation of contig distance. Results: In this article, we show that state-of-the-art programs for scaffolding are using an incorrect model of gap size estimation. We discuss why current maximum likelihood estimators are biased and describe what different cases of bias we are facing. Furthermore, we provide a model for the distribution of reads that span a gap and derive the maximum likelihood equation for the gap length. We motivate why this estimate is sound and show empirically that it outperforms gap estimators in popular scaffolding programs. Our results have consequences both for scaffolding software, structural variation detection and for library insert-size estimation as is commonly performed by read aligners. Availability: A reference implementation is provided at https://github.com/SciLifeLab/gapest Supplementary information: Supplementary data are availible at Bioinformatics online. Contact: ksahlin@csc.kth.se
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Determination of metabolites by observing the change in reaction rate during the early course of a first order reaction, as applied to fructose-1-phosphate (1975)
    Elsevier
    Details
    Publication Date: 1975-02-01
    Print ISSN: 0003-2697
    Electronic ISSN: 1096-0309
    Topics: Biology , Chemistry and Pharmacology
    Published by Elsevier
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