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            <Year>2000</Year>
            <Month>03</Month>
            <Day>01</Day>
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        <DateCompleted>
            <Year>2000</Year>
            <Month>03</Month>
            <Day>01</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2006</Year>
            <Month>11</Month>
            <Day>15</Day>
        </DateRevised>
        <Article PubModel="Print">
            <Journal>
                <ISSN IssnType="Print">0923-2508</ISSN>
                <JournalIssue CitedMedium="Print">
                    <Volume>150</Volume>
                    <Issue>9-10</Issue>
                    <PubDate>
                        <MedlineDate>1999 Nov-Dec</MedlineDate>
                    </PubDate>
                </JournalIssue>
                <Title>Research in microbiology</Title>
                <ISOAbbreviation>Res. Microbiol.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>DNA uptake signal sequences in naturally transformable bacteria.</ArticleTitle>
            <Pagination>
                <MedlinePgn>603-16</MedlinePgn>
            </Pagination>
            <Abstract>
                <AbstractText>The naturally transformable bacterium Haemophilus influenzae Rd contains 1471 copies of the DNA uptake signal sequence (USS) 5'-AAGTGCGGT in its genome. Neisseria meningitidis contains 1891 copies of the USS sequence 5'-GCCGTCTGAA. The USSs are often found in the base paired stem of transcription terminators.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Smith</LastName>
                    <ForeName>H O</ForeName>
                    <Initials>HO</Initials>
                    <Affiliation>The Institute for Genomic Research, Rockville, MD 20850, USA. SmithHO@celera.com</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Gwinn</LastName>
                    <ForeName>M L</ForeName>
                    <Initials>ML</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Salzberg</LastName>
                    <ForeName>S L</ForeName>
                    <Initials>SL</Initials>
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            <Language>eng</Language>
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                <PublicationType>Journal Article</PublicationType>
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            <MedlineTA>Res Microbiol</MedlineTA>
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                <DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Chi-Square Distribution</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Consensus Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">DNA, Bacterial</DescriptorName>
                <QualifierName MajorTopicYN="Y">genetics</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
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            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Genome, Bacterial</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Gram-Negative Bacteria</DescriptorName>
                <QualifierName MajorTopicYN="Y">genetics</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Molecular Sequence Data</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Nucleotide Mapping</DescriptorName>
                <QualifierName MajorTopicYN="N">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Alignment</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Transcription, Genetic</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Transformation, Bacterial</DescriptorName>
                <QualifierName MajorTopicYN="Y">genetics</QualifierName>
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        <NumberOfReferences>39</NumberOfReferences>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">16056220</PMID>
        <DateCreated>
            <Year>2005</Year>
            <Month>09</Month>
            <Day>15</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2005</Year>
            <Month>09</Month>
            <Day>29</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2013</Year>
            <Month>09</Month>
            <Day>08</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1476-4687</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>437</Volume>
                    <Issue>7057</Issue>
                    <PubDate>
                        <Year>2005</Year>
                        <Month>Sep</Month>
                        <Day>15</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Nature</Title>
                <ISOAbbreviation>Nature</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Genome sequencing in microfabricated high-density picolitre reactors.</ArticleTitle>
            <Pagination>
                <MedlinePgn>376-80</MedlinePgn>
            </Pagination>
            <Abstract>
                <AbstractText>The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Margulies</LastName>
                    <ForeName>Marcel</ForeName>
                    <Initials>M</Initials>
                    <Affiliation>454 Life Sciences Corp., 20 Commercial Street, Branford, Connecticut 06405, USA.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Egholm</LastName>
                    <ForeName>Michael</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Altman</LastName>
                    <ForeName>William E</ForeName>
                    <Initials>WE</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Attiya</LastName>
                    <ForeName>Said</ForeName>
                    <Initials>S</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Bader</LastName>
                    <ForeName>Joel S</ForeName>
                    <Initials>JS</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Bemben</LastName>
                    <ForeName>Lisa A</ForeName>
                    <Initials>LA</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Berka</LastName>
                    <ForeName>Jan</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Braverman</LastName>
                    <ForeName>Michael S</ForeName>
                    <Initials>MS</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Chen</LastName>
                    <ForeName>Yi-Ju</ForeName>
                    <Initials>YJ</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Chen</LastName>
                    <ForeName>Zhoutao</ForeName>
                    <Initials>Z</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Dewell</LastName>
                    <ForeName>Scott B</ForeName>
                    <Initials>SB</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Du</LastName>
                    <ForeName>Lei</ForeName>
                    <Initials>L</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Fierro</LastName>
                    <ForeName>Joseph M</ForeName>
                    <Initials>JM</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Gomes</LastName>
                    <ForeName>Xavier V</ForeName>
                    <Initials>XV</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Godwin</LastName>
                    <ForeName>Brian C</ForeName>
                    <Initials>BC</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>He</LastName>
                    <ForeName>Wen</ForeName>
                    <Initials>W</Initials>
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                    <LastName>Helgesen</LastName>
                    <ForeName>Scott</ForeName>
                    <Initials>S</Initials>
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                <Author ValidYN="Y">
                    <LastName>Ho</LastName>
                    <ForeName>Chun Heen</ForeName>
                    <Initials>CH</Initials>
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                    <LastName>Ho</LastName>
                    <ForeName>Chun He</ForeName>
                    <Initials>CH</Initials>
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                    <LastName>Irzyk</LastName>
                    <ForeName>Gerard P</ForeName>
                    <Initials>GP</Initials>
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                <Author ValidYN="Y">
                    <LastName>Jando</LastName>
                    <ForeName>Szilveszter C</ForeName>
                    <Initials>SC</Initials>
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                <Author ValidYN="Y">
                    <LastName>Alenquer</LastName>
                    <ForeName>Maria L I</ForeName>
                    <Initials>ML</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Jarvie</LastName>
                    <ForeName>Thomas P</ForeName>
                    <Initials>TP</Initials>
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                <Author ValidYN="Y">
                    <LastName>Jirage</LastName>
                    <ForeName>Kshama B</ForeName>
                    <Initials>KB</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Kim</LastName>
                    <ForeName>Jong-Bum</ForeName>
                    <Initials>JB</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Knight</LastName>
                    <ForeName>James R</ForeName>
                    <Initials>JR</Initials>
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                <Author ValidYN="Y">
                    <LastName>Lanza</LastName>
                    <ForeName>Janna R</ForeName>
                    <Initials>JR</Initials>
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                <Author ValidYN="Y">
                    <LastName>Leamon</LastName>
                    <ForeName>John H</ForeName>
                    <Initials>JH</Initials>
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                    <LastName>Lefkowitz</LastName>
                    <ForeName>Steven M</ForeName>
                    <Initials>SM</Initials>
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                    <LastName>Lei</LastName>
                    <ForeName>Ming</ForeName>
                    <Initials>M</Initials>
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                    <LastName>Li</LastName>
                    <ForeName>Jing</ForeName>
                    <Initials>J</Initials>
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                <Author ValidYN="Y">
                    <LastName>Lohman</LastName>
                    <ForeName>Kenton L</ForeName>
                    <Initials>KL</Initials>
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                <Author ValidYN="Y">
                    <LastName>Lu</LastName>
                    <ForeName>Hong</ForeName>
                    <Initials>H</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Makhijani</LastName>
                    <ForeName>Vinod B</ForeName>
                    <Initials>VB</Initials>
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                <Author ValidYN="Y">
                    <LastName>McDade</LastName>
                    <ForeName>Keith E</ForeName>
                    <Initials>KE</Initials>
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                <Author ValidYN="Y">
                    <LastName>McKenna</LastName>
                    <ForeName>Michael P</ForeName>
                    <Initials>MP</Initials>
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                <Author ValidYN="Y">
                    <LastName>Myers</LastName>
                    <ForeName>Eugene W</ForeName>
                    <Initials>EW</Initials>
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                <Author ValidYN="Y">
                    <LastName>Nickerson</LastName>
                    <ForeName>Elizabeth</ForeName>
                    <Initials>E</Initials>
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                <Author ValidYN="Y">
                    <LastName>Nobile</LastName>
                    <ForeName>John R</ForeName>
                    <Initials>JR</Initials>
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                <Author ValidYN="Y">
                    <LastName>Plant</LastName>
                    <ForeName>Ramona</ForeName>
                    <Initials>R</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Puc</LastName>
                    <ForeName>Bernard P</ForeName>
                    <Initials>BP</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Ronan</LastName>
                    <ForeName>Michael T</ForeName>
                    <Initials>MT</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Roth</LastName>
                    <ForeName>George T</ForeName>
                    <Initials>GT</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Sarkis</LastName>
                    <ForeName>Gary J</ForeName>
                    <Initials>GJ</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Simons</LastName>
                    <ForeName>Jan Fredrik</ForeName>
                    <Initials>JF</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Simpson</LastName>
                    <ForeName>John W</ForeName>
                    <Initials>JW</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Srinivasan</LastName>
                    <ForeName>Maithreyan</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Tartaro</LastName>
                    <ForeName>Karrie R</ForeName>
                    <Initials>KR</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Tomasz</LastName>
                    <ForeName>Alexander</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Vogt</LastName>
                    <ForeName>Kari A</ForeName>
                    <Initials>KA</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Volkmer</LastName>
                    <ForeName>Greg A</ForeName>
                    <Initials>GA</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wang</LastName>
                    <ForeName>Shally H</ForeName>
                    <Initials>SH</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wang</LastName>
                    <ForeName>Yong</ForeName>
                    <Initials>Y</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Weiner</LastName>
                    <ForeName>Michael P</ForeName>
                    <Initials>MP</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Yu</LastName>
                    <ForeName>Pengguang</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Begley</LastName>
                    <ForeName>Richard F</ForeName>
                    <Initials>RF</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Rothberg</LastName>
                    <ForeName>Jonathan M</ForeName>
                    <Initials>JM</Initials>
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            </AuthorList>
            <Language>eng</Language>
            <GrantList CompleteYN="Y">
                <Grant>
                    <GrantID>P01 HG003022-020002</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01 HG003562-02</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
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                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, N.I.H., Extramural</PublicationType>
                <PublicationType>Research Support, U.S. Gov't, P.H.S.</PublicationType>
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            <ArticleDate DateType="Electronic">
                <Year>2005</Year>
                <Month>07</Month>
                <Day>31</Day>
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            <Country>England</Country>
            <MedlineTA>Nature</MedlineTA>
            <NlmUniqueID>0410462</NlmUniqueID>
            <ISSNLinking>0028-0836</ISSNLinking>
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            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Emulsions</NameOfSubstance>
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        </CommentsCorrectionsList>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Electrophoresis, Capillary</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Emulsions</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Fiber Optic Technology</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Genome, Bacterial</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Genomics</DescriptorName>
                <QualifierName MajorTopicYN="N">economics</QualifierName>
                <QualifierName MajorTopicYN="Y">instrumentation</QualifierName>
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            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Microchemistry</DescriptorName>
                <QualifierName MajorTopicYN="N">economics</QualifierName>
                <QualifierName MajorTopicYN="Y">instrumentation</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Mycoplasma genitalium</DescriptorName>
                <QualifierName MajorTopicYN="Y">genetics</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName>
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            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Reproducibility of Results</DescriptorName>
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            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sensitivity and Specificity</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
                <QualifierName MajorTopicYN="N">economics</QualifierName>
                <QualifierName MajorTopicYN="Y">instrumentation</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Time Factors</DescriptorName>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">18660515</PMID>
        <DateCreated>
            <Year>2008</Year>
            <Month>09</Month>
            <Day>10</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2008</Year>
            <Month>10</Month>
            <Day>06</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2013</Year>
            <Month>08</Month>
            <Day>30</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1362-4962</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>36</Volume>
                    <Issue>16</Issue>
                    <PubDate>
                        <Year>2008</Year>
                        <Month>Sep</Month>
                    </PubDate>
                </JournalIssue>
                <Title>Nucleic acids research</Title>
                <ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.</ArticleTitle>
            <Pagination>
                <MedlinePgn>e105</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkn425</ELocationID>
            <Abstract>
                <AbstractText>Novel sequencing technologies permit the rapid production of large sequence data sets. These technologies are likely to revolutionize genetics and biomedical research, but a thorough characterization of the ultra-short read output is necessary. We generated and analyzed two Illumina 1G ultra-short read data sets, i.e. 2.8 million 27mer reads from a Beta vulgaris genomic clone and 12.3 million 36mers from the Helicobacter acinonychis genome. We found that error rates range from 0.3% at the beginning of reads to 3.8% at the end of reads. Wrong base calls are frequently preceded by base G. Base substitution error frequencies vary by 10- to 11-fold, with A &gt; C transversion being among the most frequent and C &gt; G transversions among the least frequent substitution errors. Insertions and deletions of single bases occur at very low rates. When simulating re-sequencing we found a 20-fold sequencing coverage to be sufficient to compensate errors by correct reads. The read coverage of the sequenced regions is biased; the highest read density was found in intervals with elevated GC content. High Solexa quality scores are over-optimistic and low scores underestimate the data quality. Our results show different types of biases and ways to detect them. Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Dohm</LastName>
                    <ForeName>Juliane C</ForeName>
                    <Initials>JC</Initials>
                    <Affiliation>Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Lottaz</LastName>
                    <ForeName>Claudio</ForeName>
                    <Initials>C</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Borodina</LastName>
                    <ForeName>Tatiana</ForeName>
                    <Initials>T</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Himmelbauer</LastName>
                    <ForeName>Heinz</ForeName>
                    <Initials>H</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Evaluation Studies</PublicationType>
                <PublicationType>Journal Article</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2008</Year>
                <Month>07</Month>
                <Day>26</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>England</Country>
            <MedlineTA>Nucleic Acids Res</MedlineTA>
            <NlmUniqueID>0411011</NlmUniqueID>
            <ISSNLinking>0305-1048</ISSNLinking>
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            <Chemical>
                <RegistryNumber>9007-49-2</RegistryNumber>
                <NameOfSubstance>DNA</NameOfSubstance>
            </Chemical>
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        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Base Composition</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Beta vulgaris</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">DNA</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Helicobacter</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
                <QualifierName MajorTopicYN="Y">standards</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Deletion</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Software</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
        <OtherID Source="NLM">PMC2532726</OtherID>
    </MedlineCitation>
    <PubmedData>
        <History>
            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2008</Year>
                <Month>7</Month>
                <Day>26</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="pubmed">
                <Year>2008</Year>
                <Month>7</Month>
                <Day>29</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
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            <PubMedPubDate PubStatus="medline">
                <Year>2008</Year>
                <Month>10</Month>
                <Day>7</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
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            <PubMedPubDate PubStatus="entrez">
                <Year>2008</Year>
                <Month>7</Month>
                <Day>29</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
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        </History>
        <PublicationStatus>ppublish</PublicationStatus>
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            <ArticleId IdType="pii">gkn425</ArticleId>
            <ArticleId IdType="doi">10.1093/nar/gkn425</ArticleId>
            <ArticleId IdType="pubmed">18660515</ArticleId>
            <ArticleId IdType="pmc">PMC2532726</ArticleId>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">18809713</PMID>
        <DateCreated>
            <Year>2008</Year>
            <Month>09</Month>
            <Day>30</Day>
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        <DateCompleted>
            <Year>2008</Year>
            <Month>10</Month>
            <Day>14</Day>
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        <DateRevised>
            <Year>2013</Year>
            <Month>08</Month>
            <Day>29</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1540-9538</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>205</Volume>
                    <Issue>10</Issue>
                    <PubDate>
                        <Year>2008</Year>
                        <Month>Sep</Month>
                        <Day>29</Day>
                    </PubDate>
                </JournalIssue>
                <Title>The Journal of experimental medicine</Title>
                <ISOAbbreviation>J. Exp. Med.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Dissecting T cell lineage relationships by cellular barcoding.</ArticleTitle>
            <Pagination>
                <MedlinePgn>2309-18</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1084/jem.20072462</ELocationID>
            <Abstract>
                <AbstractText>T cells, as well as other cell types, are composed of phenotypically and functionally distinct subsets. However, for many of these populations it is unclear whether they develop from common or separate progenitors. To address such issues, we developed a novel approach, termed cellular barcoding, that allows the dissection of lineage relationships. We demonstrate that the labeling of cells with unique identifiers coupled to a microarray-based detection system can be used to analyze family relationships between the progeny of such cells. To exemplify the potential of this technique, we studied migration patterns of families of antigen-specific CD8(+) T cells in vivo. We demonstrate that progeny of individual T cells rapidly seed independent lymph nodes and that antigen-specific CD8(+) T cells present at different effector sites are largely derived from a common pool of precursors. These data show how locally primed T cells disperse and provide a technology for kinship analysis with wider utility.</AbstractText>
            </Abstract>
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                <Author ValidYN="Y">
                    <LastName>Schepers</LastName>
                    <ForeName>Koen</ForeName>
                    <Initials>K</Initials>
                    <Affiliation>Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.</Affiliation>
                </Author>
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                    <LastName>Swart</LastName>
                    <ForeName>Erwin</ForeName>
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            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
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            <ArticleDate DateType="Electronic">
                <Year>2008</Year>
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            <Country>United States</Country>
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                <QualifierName MajorTopicYN="Y">methods</QualifierName>
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                <DescriptorName MajorTopicYN="N">Neoplasms</DescriptorName>
                <QualifierName MajorTopicYN="N">immunology</QualifierName>
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                <DescriptorName MajorTopicYN="N">T-Lymphocyte Subsets</DescriptorName>
                <QualifierName MajorTopicYN="Y">cytology</QualifierName>
                <QualifierName MajorTopicYN="N">immunology</QualifierName>
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                <DescriptorName MajorTopicYN="N">T-Lymphocytes</DescriptorName>
                <QualifierName MajorTopicYN="Y">cytology</QualifierName>
                <QualifierName MajorTopicYN="N">immunology</QualifierName>
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        </MeshHeadingList>
        <OtherID Source="NLM">PMC2556794</OtherID>
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                <Month>9</Month>
                <Day>22</Day>
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            <PubMedPubDate PubStatus="pubmed">
                <Year>2008</Year>
                <Month>9</Month>
                <Day>24</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2008</Year>
                <Month>10</Month>
                <Day>15</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
                <Year>2008</Year>
                <Month>9</Month>
                <Day>24</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">jem.20072462</ArticleId>
            <ArticleId IdType="doi">10.1084/jem.20072462</ArticleId>
            <ArticleId IdType="pubmed">18809713</ArticleId>
            <ArticleId IdType="pmc">PMC2556794</ArticleId>
        </ArticleIdList>
    </PubmedData>
</PubmedArticle>


<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">19023044</PMID>
        <DateCreated>
            <Year>2009</Year>
            <Month>01</Month>
            <Day>02</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2009</Year>
            <Month>01</Month>
            <Day>21</Day>
        </DateCompleted>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1095-9203</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>323</Volume>
                    <Issue>5910</Issue>
                    <PubDate>
                        <Year>2009</Year>
                        <Month>Jan</Month>
                        <Day>2</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Science (New York, N.Y.)</Title>
                <ISOAbbreviation>Science</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Real-time DNA sequencing from single polymerase molecules.</ArticleTitle>
            <Pagination>
                <MedlinePgn>133-8</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1126/science.1162986</ELocationID>
            <Abstract>
                <AbstractText>We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs). We detected the temporal order of their enzymatic incorporation into a growing DNA strand with zero-mode waveguide nanostructure arrays, which provide optical observation volume confinement and enable parallel, simultaneous detection of thousands of single-molecule sequencing reactions. Conjugation of fluorophores to the terminal phosphate moiety of the dNTPs allows continuous observation of DNA synthesis over thousands of bases without steric hindrance. The data report directly on polymerase dynamics, revealing distinct polymerization states and pause sites corresponding to DNA secondary structure. Sequence data were aligned with the known reference sequence to assay biophysical parameters of polymerization for each template position. Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Eid</LastName>
                    <ForeName>John</ForeName>
                    <Initials>J</Initials>
                    <Affiliation>Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Fehr</LastName>
                    <ForeName>Adrian</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Gray</LastName>
                    <ForeName>Jeremy</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Luong</LastName>
                    <ForeName>Khai</ForeName>
                    <Initials>K</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Lyle</LastName>
                    <ForeName>John</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Otto</LastName>
                    <ForeName>Geoff</ForeName>
                    <Initials>G</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Peluso</LastName>
                    <ForeName>Paul</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Rank</LastName>
                    <ForeName>David</ForeName>
                    <Initials>D</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Baybayan</LastName>
                    <ForeName>Primo</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Bettman</LastName>
                    <ForeName>Brad</ForeName>
                    <Initials>B</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Bibillo</LastName>
                    <ForeName>Arkadiusz</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Bjornson</LastName>
                    <ForeName>Keith</ForeName>
                    <Initials>K</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Chaudhuri</LastName>
                    <ForeName>Bidhan</ForeName>
                    <Initials>B</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Christians</LastName>
                    <ForeName>Frederick</ForeName>
                    <Initials>F</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Cicero</LastName>
                    <ForeName>Ronald</ForeName>
                    <Initials>R</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Clark</LastName>
                    <ForeName>Sonya</ForeName>
                    <Initials>S</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Dalal</LastName>
                    <ForeName>Ravindra</ForeName>
                    <Initials>R</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Dewinter</LastName>
                    <ForeName>Alex</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Dixon</LastName>
                    <ForeName>John</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Foquet</LastName>
                    <ForeName>Mathieu</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Gaertner</LastName>
                    <ForeName>Alfred</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Hardenbol</LastName>
                    <ForeName>Paul</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Heiner</LastName>
                    <ForeName>Cheryl</ForeName>
                    <Initials>C</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Hester</LastName>
                    <ForeName>Kevin</ForeName>
                    <Initials>K</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Holden</LastName>
                    <ForeName>David</ForeName>
                    <Initials>D</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Kearns</LastName>
                    <ForeName>Gregory</ForeName>
                    <Initials>G</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Kong</LastName>
                    <ForeName>Xiangxu</ForeName>
                    <Initials>X</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Kuse</LastName>
                    <ForeName>Ronald</ForeName>
                    <Initials>R</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Lacroix</LastName>
                    <ForeName>Yves</ForeName>
                    <Initials>Y</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Lin</LastName>
                    <ForeName>Steven</ForeName>
                    <Initials>S</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Lundquist</LastName>
                    <ForeName>Paul</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Ma</LastName>
                    <ForeName>Congcong</ForeName>
                    <Initials>C</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Marks</LastName>
                    <ForeName>Patrick</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Maxham</LastName>
                    <ForeName>Mark</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Murphy</LastName>
                    <ForeName>Devon</ForeName>
                    <Initials>D</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Park</LastName>
                    <ForeName>Insil</ForeName>
                    <Initials>I</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Pham</LastName>
                    <ForeName>Thang</ForeName>
                    <Initials>T</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Phillips</LastName>
                    <ForeName>Michael</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Roy</LastName>
                    <ForeName>Joy</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Sebra</LastName>
                    <ForeName>Robert</ForeName>
                    <Initials>R</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Shen</LastName>
                    <ForeName>Gene</ForeName>
                    <Initials>G</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Sorenson</LastName>
                    <ForeName>Jon</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Tomaney</LastName>
                    <ForeName>Austin</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Travers</LastName>
                    <ForeName>Kevin</ForeName>
                    <Initials>K</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Trulson</LastName>
                    <ForeName>Mark</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Vieceli</LastName>
                    <ForeName>John</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wegener</LastName>
                    <ForeName>Jeffrey</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wu</LastName>
                    <ForeName>Dawn</ForeName>
                    <Initials>D</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Yang</LastName>
                    <ForeName>Alicia</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Zaccarin</LastName>
                    <ForeName>Denis</ForeName>
                    <Initials>D</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Zhao</LastName>
                    <ForeName>Peter</ForeName>
                    <Initials>P</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Zhong</LastName>
                    <ForeName>Frank</ForeName>
                    <Initials>F</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Korlach</LastName>
                    <ForeName>Jonas</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Turner</LastName>
                    <ForeName>Stephen</ForeName>
                    <Initials>S</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <GrantList CompleteYN="Y">
                <Grant>
                    <GrantID>R01HG003710</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
            </GrantList>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, N.I.H., Extramural</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2008</Year>
                <Month>11</Month>
                <Day>20</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>United States</Country>
            <MedlineTA>Science</MedlineTA>
            <NlmUniqueID>0404511</NlmUniqueID>
            <ISSNLinking>0036-8075</ISSNLinking>
        </MedlineJournalInfo>
        <ChemicalList>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>DNA, Circular</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>DNA, Single-Stranded</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Deoxyribonucleotides</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Enzymes, Immobilized</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Fluorescent Dyes</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>9007-49-2</RegistryNumber>
                <NameOfSubstance>DNA</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>EC 2.7.7.7</RegistryNumber>
                <NameOfSubstance>DNA-Directed DNA Polymerase</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Consensus Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">DNA</DescriptorName>
                <QualifierName MajorTopicYN="N">biosynthesis</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">DNA, Circular</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">DNA, Single-Stranded</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">DNA-Directed DNA Polymerase</DescriptorName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Deoxyribonucleotides</DescriptorName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Enzymes, Immobilized</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Fluorescent Dyes</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Kinetics</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Nanostructures</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
                <QualifierName MajorTopicYN="Y">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Spectrometry, Fluorescence</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
    <PubmedData>
        <History>
            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2008</Year>
                <Month>11</Month>
                <Day>20</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="pubmed">
                <Year>2008</Year>
                <Month>11</Month>
                <Day>22</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2009</Year>
                <Month>1</Month>
                <Day>22</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
                <Year>2008</Year>
                <Month>11</Month>
                <Day>22</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">1162986</ArticleId>
            <ArticleId IdType="doi">10.1126/science.1162986</ArticleId>
            <ArticleId IdType="pubmed">19023044</ArticleId>
        </ArticleIdList>
    </PubmedData>
</PubmedArticle>


<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">19561594</PMID>
        <DateCreated>
            <Year>2009</Year>
            <Month>07</Month>
            <Day>09</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2009</Year>
            <Month>09</Month>
            <Day>28</Day>
        </DateCompleted>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1546-1696</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>27</Volume>
                    <Issue>7</Issue>
                    <PubDate>
                        <Year>2009</Year>
                        <Month>Jul</Month>
                    </PubDate>
                </JournalIssue>
                <Title>Nature biotechnology</Title>
                <ISOAbbreviation>Nat. Biotechnol.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.</ArticleTitle>
            <Pagination>
                <MedlinePgn>667-70</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1038/nbt.1550</ELocationID>
            <Abstract>
                <AbstractText>Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined. Current techniques for determining RNA targets, including in vitro selection and RNA co-immunoprecipitation, require significant time and labor investment. Here we introduce RNAcompete, a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. We tested RNAcompete by analyzing nine diverse RBPs (HuR, Vts1, FUSIP1, PTB, U1A, SF2/ASF, SLM2, RBM4 and YB1). RNAcompete identified expected and previously unknown RNA binding preferences. Using in vitro and in vivo binding data, we demonstrate that preferences for individual 7-mers identified by RNAcompete are a more accurate representation of binding activity than are conventional motif models. We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Ray</LastName>
                    <ForeName>Debashish</ForeName>
                    <Initials>D</Initials>
                    <Affiliation>Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Kazan</LastName>
                    <ForeName>Hilal</ForeName>
                    <Initials>H</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Chan</LastName>
                    <ForeName>Esther T</ForeName>
                    <Initials>ET</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Peña Castillo</LastName>
                    <ForeName>Lourdes</ForeName>
                    <Initials>L</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Chaudhry</LastName>
                    <ForeName>Sidharth</ForeName>
                    <Initials>S</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Talukder</LastName>
                    <ForeName>Shaheynoor</ForeName>
                    <Initials>S</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Blencowe</LastName>
                    <ForeName>Benjamin J</ForeName>
                    <Initials>BJ</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Morris</LastName>
                    <ForeName>Quaid</ForeName>
                    <Initials>Q</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Hughes</LastName>
                    <ForeName>Timothy R</ForeName>
                    <Initials>TR</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <DataBankList CompleteYN="Y">
                <DataBank>
                    <DataBankName>GEO</DataBankName>
                    <AccessionNumberList>
                        <AccessionNumber>GSE15769</AccessionNumber>
                    </AccessionNumberList>
                </DataBank>
            </DataBankList>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2009</Year>
                <Month>06</Month>
                <Day>28</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>United States</Country>
            <MedlineTA>Nat Biotechnol</MedlineTA>
            <NlmUniqueID>9604648</NlmUniqueID>
            <ISSNLinking>1087-0156</ISSNLinking>
        </MedlineJournalInfo>
        <ChemicalList>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>RNA-Binding Proteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>63231-63-0</RegistryNumber>
                <NameOfSubstance>RNA</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Animals</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Binding Sites</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Genome</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Molecular Sequence Data</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName>
                <QualifierName MajorTopicYN="Y">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">RNA</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">RNA-Binding Proteins</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">ROC Curve</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Substrate Specificity</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
    <PubmedData>
        <History>
            <PubMedPubDate PubStatus="received">
                <Year>2009</Year>
                <Month>4</Month>
                <Day>13</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="accepted">
                <Year>2009</Year>
                <Month>6</Month>
                <Day>08</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2009</Year>
                <Month>6</Month>
                <Day>28</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
                <Year>2009</Year>
                <Month>6</Month>
                <Day>30</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="pubmed">
                <Year>2009</Year>
                <Month>6</Month>
                <Day>30</Day>
                <Hour>9</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2009</Year>
                <Month>9</Month>
                <Day>29</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">nbt.1550</ArticleId>
            <ArticleId IdType="doi">10.1038/nbt.1550</ArticleId>
            <ArticleId IdType="pubmed">19561594</ArticleId>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">21148542</PMID>
        <DateCreated>
            <Year>2011</Year>
            <Month>02</Month>
            <Day>10</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2011</Year>
            <Month>04</Month>
            <Day>19</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2013</Year>
            <Month>10</Month>
            <Day>21</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1367-4811</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>27</Volume>
                    <Issue>4</Issue>
                    <PubDate>
                        <Year>2011</Year>
                        <Month>Feb</Month>
                        <Day>15</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Bioinformatics (Oxford, England)</Title>
                <ISOAbbreviation>Bioinformatics</ISOAbbreviation>
            </Journal>
            <ArticleTitle>SlideSort: all pairs similarity search for short reads.</ArticleTitle>
            <Pagination>
                <MedlinePgn>464-70</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btq677</ELocationID>
            <Abstract>
                <AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses.</AbstractText>
                <AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, we designed and implemented an exact algorithm SlideSort that finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. In comparison to backtracking methods such as BWA, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing short reads for further processing.</AbstractText>
                <AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">Executable binary files and C++ libraries are available at http://www.cbrc.jp/~shimizu/slidesort/ for Linux and Windows.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Shimizu</LastName>
                    <ForeName>Kana</ForeName>
                    <Initials>K</Initials>
                    <Affiliation>Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Tsuda</LastName>
                    <ForeName>Koji</ForeName>
                    <Initials>K</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2010</Year>
                <Month>12</Month>
                <Day>09</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>England</Country>
            <MedlineTA>Bioinformatics</MedlineTA>
            <NlmUniqueID>9808944</NlmUniqueID>
            <ISSNLinking>1367-4803</ISSNLinking>
        </MedlineJournalInfo>
        <CitationSubset>IM</CitationSubset>
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            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Algorithms</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Computational Biology</DescriptorName>
                <QualifierName MajorTopicYN="N">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
                <QualifierName MajorTopicYN="Y">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Software</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
        <OtherID Source="NLM">PMC3035798</OtherID>
    </MedlineCitation>
    <PubmedData>
        <History>
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                <Year>2010</Year>
                <Month>12</Month>
                <Day>9</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
                <Year>2010</Year>
                <Month>12</Month>
                <Day>15</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="pubmed">
                <Year>2010</Year>
                <Month>12</Month>
                <Day>15</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2011</Year>
                <Month>4</Month>
                <Day>20</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">btq677</ArticleId>
            <ArticleId IdType="doi">10.1093/bioinformatics/btq677</ArticleId>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">21576222</PMID>
        <DateCreated>
            <Year>2011</Year>
            <Month>07</Month>
            <Day>25</Day>
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            <Year>2011</Year>
            <Month>10</Month>
            <Day>03</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2013</Year>
            <Month>10</Month>
            <Day>17</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1362-4962</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>39</Volume>
                    <Issue>13</Issue>
                    <PubDate>
                        <Year>2011</Year>
                        <Month>Jul</Month>
                    </PubDate>
                </JournalIssue>
                <Title>Nucleic acids research</Title>
                <ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Sequence-specific error profile of Illumina sequencers.</ArticleTitle>
            <Pagination>
                <MedlinePgn>e90</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkr344</ELocationID>
            <Abstract>
                <AbstractText>We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Nakamura</LastName>
                    <ForeName>Kensuke</ForeName>
                    <Initials>K</Initials>
                    <Affiliation>Graduate School of Information Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Oshima</LastName>
                    <ForeName>Taku</ForeName>
                    <Initials>T</Initials>
                </Author>
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                    <LastName>Morimoto</LastName>
                    <ForeName>Takuya</ForeName>
                    <Initials>T</Initials>
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                    <LastName>Ikeda</LastName>
                    <ForeName>Shun</ForeName>
                    <Initials>S</Initials>
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                <Author ValidYN="Y">
                    <LastName>Yoshikawa</LastName>
                    <ForeName>Hirofumi</ForeName>
                    <Initials>H</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Shiwa</LastName>
                    <ForeName>Yuh</ForeName>
                    <Initials>Y</Initials>
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                <Author ValidYN="Y">
                    <LastName>Ishikawa</LastName>
                    <ForeName>Shu</ForeName>
                    <Initials>S</Initials>
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                    <LastName>Linak</LastName>
                    <ForeName>Margaret C</ForeName>
                    <Initials>MC</Initials>
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                    <LastName>Hirai</LastName>
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                    <Initials>A</Initials>
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                    <LastName>Takahashi</LastName>
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                    <LastName>Kanaya</LastName>
                    <ForeName>Shigehiko</ForeName>
                    <Initials>S</Initials>
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            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2011</Year>
                <Month>05</Month>
                <Day>16</Day>
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            <Country>England</Country>
            <MedlineTA>Nucleic Acids Res</MedlineTA>
            <NlmUniqueID>0411011</NlmUniqueID>
            <ISSNLinking>0305-1048</ISSNLinking>
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                <DescriptorName MajorTopicYN="N">Bacillus subtilis</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
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                <DescriptorName MajorTopicYN="N">Base Pair Mismatch</DescriptorName>
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                <DescriptorName MajorTopicYN="Y">Sequence Analysis, RNA</DescriptorName>
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        <OtherID Source="NLM">PMC3141275</OtherID>
    </MedlineCitation>
    <PubmedData>
        <History>
            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2011</Year>
                <Month>5</Month>
                <Day>16</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
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                <Year>2011</Year>
                <Month>5</Month>
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                <Hour>6</Hour>
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                <Year>2011</Year>
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                <Hour>6</Hour>
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        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">gkr344</ArticleId>
            <ArticleId IdType="doi">10.1093/nar/gkr344</ArticleId>
            <ArticleId IdType="pubmed">21576222</ArticleId>
            <ArticleId IdType="pmc">PMC3141275</ArticleId>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">21810899</PMID>
        <DateCreated>
            <Year>2011</Year>
            <Month>09</Month>
            <Day>07</Day>
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            <Year>2013</Year>
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        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1367-4811</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>27</Volume>
                    <Issue>18</Issue>
                    <PubDate>
                        <Year>2011</Year>
                        <Month>Sep</Month>
                        <Day>15</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Bioinformatics (Oxford, England)</Title>
                <ISOAbbreviation>Bioinformatics</ISOAbbreviation>
            </Journal>
            <ArticleTitle>SEED: efficient clustering of next-generation sequences.</ArticleTitle>
            <Pagination>
                <MedlinePgn>2502-9</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btr447</ELocationID>
            <Abstract>
                <AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Similarity clustering of next-generation sequences (NGS) is an important computational problem to study the population sizes of DNA/RNA molecules and to reduce the redundancies in NGS data. Currently, most sequence clustering algorithms are limited by their speed and scalability, and thus cannot handle data with tens of millions of reads.</AbstractText>
                <AbstractText Label="RESULTS" NlmCategory="RESULTS">Here, we introduce SEED-an efficient algorithm for clustering very large NGS sets. It joins sequences into clusters that can differ by up to three mismatches and three overhanging residues from their virtual center. It is based on a modified spaced seed method, called block spaced seeds. Its clustering component operates on the hash tables by first identifying virtual center sequences and then finding all their neighboring sequences that meet the similarity parameters. SEED can cluster 100 million short read sequences in &lt;4 h with a linear time and memory performance. When using SEED as a preprocessing tool on genome/transcriptome assembly data, it was able to reduce the time and memory requirements of the Velvet/Oasis assembler for the datasets used in this study by 60-85% and 21-41%, respectively. In addition, the assemblies contained longer contigs than non-preprocessed data as indicated by 12-27% larger N50 values. Compared with other clustering tools, SEED showed the best performance in generating clusters of NGS data similar to true cluster results with a 2- to 10-fold better time performance. While most of SEED's utilities fall into the preprocessing area of NGS data, our tests also demonstrate its efficiency as stand-alone tool for discovering clusters of small RNA sequences in NGS data from unsequenced organisms.</AbstractText>
                <AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">The SEED software can be downloaded for free from this site: http://manuals.bioinformatics.ucr.edu/home/seed.</AbstractText>
                <AbstractText Label="CONTACT" NlmCategory="BACKGROUND">thomas.girke@ucr.edu</AbstractText>
                <AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Bao</LastName>
                    <ForeName>Ergude</ForeName>
                    <Initials>E</Initials>
                    <Affiliation>Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Jiang</LastName>
                    <ForeName>Tao</ForeName>
                    <Initials>T</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Kaloshian</LastName>
                    <ForeName>Isgouhi</ForeName>
                    <Initials>I</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Girke</LastName>
                    <ForeName>Thomas</ForeName>
                    <Initials>T</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2011</Year>
                <Month>08</Month>
                <Day>02</Day>
            </ArticleDate>
        </Article>
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            <Country>England</Country>
            <MedlineTA>Bioinformatics</MedlineTA>
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            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>MicroRNAs</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
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        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Algorithms</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Cluster Analysis</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Genome</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">MicroRNAs</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis</DescriptorName>
                <QualifierName MajorTopicYN="Y">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Software</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Transcriptome</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
        <OtherID Source="NLM">PMC3167058</OtherID>
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            <ArticleId IdType="doi">10.1093/bioinformatics/btr447</ArticleId>
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    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">22942077</PMID>
        <DateCreated>
            <Year>2012</Year>
            <Month>10</Month>
            <Day>22</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2013</Year>
            <Month>06</Month>
            <Day>20</Day>
        </DateCompleted>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1367-4811</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>28</Volume>
                    <Issue>21</Issue>
                    <PubDate>
                        <Year>2012</Year>
                        <Month>Nov</Month>
                        <Day>1</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Bioinformatics (Oxford, England)</Title>
                <ISOAbbreviation>Bioinformatics</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.</ArticleTitle>
            <Pagination>
                <MedlinePgn>2732-7</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/bts482</ELocationID>
            <Abstract>
                <AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">The innovation of restriction-site associated DNA sequencing (RAD-seq) method takes full advantage of next-generation sequencing technology. By clustering paired-end short reads into groups with their own unique tags, RAD-seq assembly problem is divided into subproblems. Fast and accurately clustering and assembling millions of RAD-seq reads with sequencing errors, different levels of heterozygosity and repetitive sequences is a challenging question.</AbstractText>
                <AbstractText Label="RESULTS" NlmCategory="RESULTS">Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. And along a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, we show that Rainbow is more competent than the other tools in dealing with RAD-seq data.</AbstractText>
                <AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">Source code in C, Rainbow is freely available at http://sourceforge.net/projects/bio-rainbow/files/</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Chong</LastName>
                    <ForeName>Zechen</ForeName>
                    <Initials>Z</Initials>
                    <Affiliation>Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Ruan</LastName>
                    <ForeName>Jue</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wu</LastName>
                    <ForeName>Chung-I</ForeName>
                    <Initials>CI</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Comparative Study</PublicationType>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2012</Year>
                <Month>09</Month>
                <Day>01</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>England</Country>
            <MedlineTA>Bioinformatics</MedlineTA>
            <NlmUniqueID>9808944</NlmUniqueID>
            <ISSNLinking>1367-4803</ISSNLinking>
        </MedlineJournalInfo>
        <CitationSubset>IM</CitationSubset>
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                <DescriptorName MajorTopicYN="N">Abstracting and Indexing as Topic</DescriptorName>
                <QualifierName MajorTopicYN="N">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Algorithms</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Cluster Analysis</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Evolution, Molecular</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Genetics, Population</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Haplotypes</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Humans</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Models, Genetic</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
                <QualifierName MajorTopicYN="Y">instrumentation</QualifierName>
                <QualifierName MajorTopicYN="N">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Software</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
    <PubmedData>
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                <Year>2012</Year>
                <Month>9</Month>
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                <Year>2012</Year>
                <Month>9</Month>
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                <Day>21</Day>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">23060610</PMID>
        <DateCreated>
            <Year>2012</Year>
            <Month>11</Month>
            <Day>29</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2013</Year>
            <Month>08</Month>
            <Day>05</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2013</Year>
            <Month>11</Month>
            <Day>14</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1367-4811</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>28</Volume>
                    <Issue>23</Issue>
                    <PubDate>
                        <Year>2012</Year>
                        <Month>Dec</Month>
                        <Day>1</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Bioinformatics (Oxford, England)</Title>
                <ISOAbbreviation>Bioinformatics</ISOAbbreviation>
            </Journal>
            <ArticleTitle>CD-HIT: accelerated for clustering the next-generation sequencing data.</ArticleTitle>
            <Pagination>
                <MedlinePgn>3150-2</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/bts565</ELocationID>
            <Abstract>
                <AbstractText Label="SUMMARY" NlmCategory="CONCLUSIONS">CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions.</AbstractText>
                <AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">http://cd-hit.org.</AbstractText>
                <AbstractText Label="CONTACT" NlmCategory="BACKGROUND">liwz@sdsc.edu</AbstractText>
                <AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Fu</LastName>
                    <ForeName>Limin</ForeName>
                    <Initials>L</Initials>
                    <Affiliation>Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Niu</LastName>
                    <ForeName>Beifang</ForeName>
                    <Initials>B</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Zhu</LastName>
                    <ForeName>Zhengwei</ForeName>
                    <Initials>Z</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wu</LastName>
                    <ForeName>Sitao</ForeName>
                    <Initials>S</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Li</LastName>
                    <ForeName>Weizhong</ForeName>
                    <Initials>W</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <GrantList CompleteYN="Y">
                <Grant>
                    <GrantID>R01 HG005978</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01 RR025030</GrantID>
                    <Acronym>RR</Acronym>
                    <Agency>NCRR NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01HG005978</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01RR025030</GrantID>
                    <Acronym>RR</Acronym>
                    <Agency>NCRR NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
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            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, N.I.H., Extramural</PublicationType>
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            <ArticleDate DateType="Electronic">
                <Year>2012</Year>
                <Month>10</Month>
                <Day>11</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>England</Country>
            <MedlineTA>Bioinformatics</MedlineTA>
            <NlmUniqueID>9808944</NlmUniqueID>
            <ISSNLinking>1367-4803</ISSNLinking>
        </MedlineJournalInfo>
        <CitationSubset>IM</CitationSubset>
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                <PMID Version="1">18402669</PMID>
            </CommentsCorrections>
        </CommentsCorrectionsList>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Algorithms</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Cluster Analysis</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Computational Biology</DescriptorName>
                <QualifierName MajorTopicYN="Y">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, Protein</DescriptorName>
                <QualifierName MajorTopicYN="Y">methods</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Software</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
        <OtherID Source="NLM">PMC3516142</OtherID>
    </MedlineCitation>
    <PubmedData>
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            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2012</Year>
                <Month>10</Month>
                <Day>11</Day>
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                <Year>2012</Year>
                <Month>10</Month>
                <Day>13</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
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            <PubMedPubDate PubStatus="pubmed">
                <Year>2012</Year>
                <Month>10</Month>
                <Day>13</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2013</Year>
                <Month>8</Month>
                <Day>6</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
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        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">bts565</ArticleId>
            <ArticleId IdType="doi">10.1093/bioinformatics/bts565</ArticleId>
            <ArticleId IdType="pubmed">23060610</ArticleId>
            <ArticleId IdType="pmc">PMC3516142</ArticleId>
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<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">23253355</PMID>
        <DateCreated>
            <Year>2013</Year>
            <Month>02</Month>
            <Day>13</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2013</Year>
            <Month>07</Month>
            <Day>23</Day>
        </DateCompleted>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1879-033X</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>23</Volume>
                    <Issue>1</Issue>
                    <PubDate>
                        <Year>2013</Year>
                        <Month>Feb</Month>
                    </PubDate>
                </JournalIssue>
                <Title>Current opinion in structural biology</Title>
                <ISOAbbreviation>Curr. Opin. Struct. Biol.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>RRM-RNA recognition: NMR or crystallography…and new findings.</ArticleTitle>
            <Pagination>
                <MedlinePgn>100-8</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1016/j.sbi.2012.11.006</ELocationID>
            <ELocationID EIdType="pii" ValidYN="Y">S0959-440X(12)00190-X</ELocationID>
            <Abstract>
                <AbstractText>To characterize protein-RNA recognition at the molecular level, structural biology has turned out to be an indispensable approach. Detailed and direct insights into the mechanism of RNA binding and specificity have emerged from protein-RNA structures, especially from the most abundant RNA recognition motif (RRM). Although this protein domain has a very conserved α-β fold, it can recognize a large number of different RNA sequences and shapes and can be involved in a multitude of biological processes. Here, we report on recent single and multiple RRM-RNA structures and point out those features that provide novel insights into the mechanism of RNA recognition by RRMs. We further outline inherent problems to both NMR spectroscopy and X-ray crystallography methods and review recent strategies that emphasize the need to use both methodologies for more rapid and accurate structure determinations.</AbstractText>
                <CopyrightInformation>Copyright © 2012 Elsevier Ltd. All rights reserved.</CopyrightInformation>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Daubner</LastName>
                    <ForeName>Gerrit M</ForeName>
                    <Initials>GM</Initials>
                    <Affiliation>Institute of Molecular Biology and Biophysics, ETH Zürich, Switzerland.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Cléry</LastName>
                    <ForeName>Antoine</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Allain</LastName>
                    <ForeName>Frédéric H-T</ForeName>
                    <Initials>FH</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
                <PublicationType>Review</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2012</Year>
                <Month>12</Month>
                <Day>14</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>England</Country>
            <MedlineTA>Curr Opin Struct Biol</MedlineTA>
            <NlmUniqueID>9107784</NlmUniqueID>
            <ISSNLinking>0959-440X</ISSNLinking>
        </MedlineJournalInfo>
        <ChemicalList>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Nuclear Proteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>RNA-Binding Proteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Ribonucleoproteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>splicing factor U2AF</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>63231-63-0</RegistryNumber>
                <NameOfSubstance>RNA</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Binding Sites</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Crystallography, X-Ray</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Humans</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Hydrogen Bonding</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Magnetic Resonance Spectroscopy</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Nuclear Proteins</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Protein Binding</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Protein Conformation</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Protein Interaction Domains and Motifs</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">RNA</DescriptorName>
                <QualifierName MajorTopicYN="Y">chemistry</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">RNA-Binding Proteins</DescriptorName>
                <QualifierName MajorTopicYN="Y">chemistry</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Ribonucleoproteins</DescriptorName>
                <QualifierName MajorTopicYN="N">chemistry</QualifierName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
    <PubmedData>
        <History>
            <PubMedPubDate PubStatus="received">
                <Year>2012</Year>
                <Month>9</Month>
                <Day>27</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="revised">
                <Year>2012</Year>
                <Month>11</Month>
                <Day>2</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="accepted">
                <Year>2012</Year>
                <Month>11</Month>
                <Day>20</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2012</Year>
                <Month>12</Month>
                <Day>14</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
                <Year>2012</Year>
                <Month>12</Month>
                <Day>21</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="pubmed">
                <Year>2012</Year>
                <Month>12</Month>
                <Day>21</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2013</Year>
                <Month>7</Month>
                <Day>24</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
        </History>
        <PublicationStatus>ppublish</PublicationStatus>
        <ArticleIdList>
            <ArticleId IdType="pii">S0959-440X(12)00190-X</ArticleId>
            <ArticleId IdType="doi">10.1016/j.sbi.2012.11.006</ArticleId>
            <ArticleId IdType="pubmed">23253355</ArticleId>
        </ArticleIdList>
    </PubmedData>
</PubmedArticle>


<PubmedArticle>
    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">23562324</PMID>
        <DateCreated>
            <Year>2013</Year>
            <Month>04</Month>
            <Day>29</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2013</Year>
            <Month>07</Month>
            <Day>02</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2014</Year>
            <Month>05</Month>
            <Day>07</Day>
        </DateRevised>
        <Article PubModel="Print-Electronic">
            <Journal>
                <ISSN IssnType="Electronic">1097-4164</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>50</Volume>
                    <Issue>2</Issue>
                    <PubDate>
                        <Year>2013</Year>
                        <Month>Apr</Month>
                        <Day>25</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Molecular cell</Title>
                <ISOAbbreviation>Mol. Cell</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.</ArticleTitle>
            <Pagination>
                <MedlinePgn>223-35</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1016/j.molcel.2013.03.001</ELocationID>
            <ELocationID EIdType="pii" ValidYN="Y">S1097-2765(13)00204-9</ELocationID>
            <Abstract>
                <AbstractText>SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins, SRSF1 (SF2/ASF) and SRSF2 (SC35), using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes.</AbstractText>
                <CopyrightInformation>Copyright © 2013 Elsevier Inc. All rights reserved.</CopyrightInformation>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Pandit</LastName>
                    <ForeName>Shatakshi</ForeName>
                    <Initials>S</Initials>
                    <Affiliation>Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Zhou</LastName>
                    <ForeName>Yu</ForeName>
                    <Initials>Y</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Shiue</LastName>
                    <ForeName>Lily</ForeName>
                    <Initials>L</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Coutinho-Mansfield</LastName>
                    <ForeName>Gabriela</ForeName>
                    <Initials>G</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Li</LastName>
                    <ForeName>Hairi</ForeName>
                    <Initials>H</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Qiu</LastName>
                    <ForeName>Jinsong</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Huang</LastName>
                    <ForeName>Jie</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Yeo</LastName>
                    <ForeName>Gene W</ForeName>
                    <Initials>GW</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Ares</LastName>
                    <ForeName>Manuel</ForeName>
                    <Initials>M</Initials>
                    <Suffix>Jr</Suffix>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Fu</LastName>
                    <ForeName>Xiang-Dong</ForeName>
                    <Initials>XD</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <DataBankList CompleteYN="Y">
                <DataBank>
                    <DataBankName>GEO</DataBankName>
                    <AccessionNumberList>
                        <AccessionNumber>GSE44583</AccessionNumber>
                        <AccessionNumber>GSE44591</AccessionNumber>
                    </AccessionNumberList>
                </DataBank>
            </DataBankList>
            <GrantList CompleteYN="Y">
                <Grant>
                    <GrantID>GM049369</GrantID>
                    <Acronym>GM</Acronym>
                    <Agency>NIGMS NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>GM084317</GrantID>
                    <Acronym>GM</Acronym>
                    <Agency>NIGMS NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>HG004659</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01 GM049369</GrantID>
                    <Acronym>GM</Acronym>
                    <Agency>NIGMS NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01 GM052872</GrantID>
                    <Acronym>GM</Acronym>
                    <Agency>NIGMS NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01 HG004659</GrantID>
                    <Acronym>HG</Acronym>
                    <Agency>NHGRI NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
                <Grant>
                    <GrantID>R01 NS075449</GrantID>
                    <Acronym>NS</Acronym>
                    <Agency>NINDS NIH HHS</Agency>
                    <Country>United States</Country>
                </Grant>
            </GrantList>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, N.I.H., Extramural</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
            </PublicationTypeList>
            <ArticleDate DateType="Electronic">
                <Year>2013</Year>
                <Month>04</Month>
                <Day>04</Day>
            </ArticleDate>
        </Article>
        <MedlineJournalInfo>
            <Country>United States</Country>
            <MedlineTA>Mol Cell</MedlineTA>
            <NlmUniqueID>9802571</NlmUniqueID>
            <ISSNLinking>1097-2765</ISSNLinking>
        </MedlineJournalInfo>
        <ChemicalList>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Nuclear Proteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>RNA-Binding Proteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Ribonucleoproteins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Sfrs2 protein, mouse</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>170974-22-8</RegistryNumber>
                <NameOfSubstance>serine-arginine-rich splicing proteins</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
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        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Alternative Splicing</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Animals</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Binding Sites</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Cells, Cultured</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Consensus Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Exons</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Fibroblasts</DescriptorName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Gene Knockout Techniques</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Genome</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Introns</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Mice</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Mice, Knockout</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Nuclear Proteins</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Protein Binding</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">RNA Splicing</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">RNA-Binding Proteins</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Ribonucleoproteins</DescriptorName>
                <QualifierName MajorTopicYN="N">genetics</QualifierName>
                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Transcriptome</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
        <OtherID Source="NLM">NIHMS455011</OtherID>
        <OtherID Source="NLM">PMC3640356</OtherID>
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                <Year>2012</Year>
                <Month>10</Month>
                <Day>10</Day>
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            <PubMedPubDate PubStatus="revised">
                <Year>2013</Year>
                <Month>1</Month>
                <Day>2</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="accepted">
                <Year>2013</Year>
                <Month>2</Month>
                <Day>25</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="aheadofprint">
                <Year>2013</Year>
                <Month>4</Month>
                <Day>4</Day>
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                <Year>2013</Year>
                <Month>4</Month>
                <Day>9</Day>
                <Hour>6</Hour>
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                <Day>9</Day>
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                <Year>2013</Year>
                <Month>7</Month>
                <Day>3</Day>
                <Hour>6</Hour>
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            <ArticleId IdType="pii">S1097-2765(13)00204-9</ArticleId>
            <ArticleId IdType="doi">10.1016/j.molcel.2013.03.001</ArticleId>
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    <MedlineCitation Owner="NLM" Status="MEDLINE">
        <PMID Version="1">23953119</PMID>
        <DateCreated>
            <Year>2013</Year>
            <Month>08</Month>
            <Day>19</Day>
        </DateCreated>
        <DateCompleted>
            <Year>2013</Year>
            <Month>11</Month>
            <Day>12</Day>
        </DateCompleted>
        <Article PubModel="Print">
            <Journal>
                <ISSN IssnType="Electronic">1097-4172</ISSN>
                <JournalIssue CitedMedium="Internet">
                    <Volume>154</Volume>
                    <Issue>4</Issue>
                    <PubDate>
                        <Year>2013</Year>
                        <Month>Aug</Month>
                        <Day>15</Day>
                    </PubDate>
                </JournalIssue>
                <Title>Cell</Title>
                <ISOAbbreviation>Cell</ISOAbbreviation>
            </Journal>
            <ArticleTitle>Chromatin position effects assayed by thousands of reporters integrated in parallel.</ArticleTitle>
            <Pagination>
                <MedlinePgn>914-27</MedlinePgn>
            </Pagination>
            <ELocationID EIdType="doi" ValidYN="Y">10.1016/j.cell.2013.07.018</ELocationID>
            <ELocationID EIdType="pii" ValidYN="Y">S0092-8674(13)00889-1</ELocationID>
            <Abstract>
                <AbstractText>Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ∼1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over ∼20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.</AbstractText>
                <CopyrightInformation>Copyright © 2013 Elsevier Inc. All rights reserved.</CopyrightInformation>
            </Abstract>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Akhtar</LastName>
                    <ForeName>Waseem</ForeName>
                    <Initials>W</Initials>
                    <Affiliation>Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.</Affiliation>
                </Author>
                <Author ValidYN="Y">
                    <LastName>de Jong</LastName>
                    <ForeName>Johann</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Pindyurin</LastName>
                    <ForeName>Alexey V</ForeName>
                    <Initials>AV</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Pagie</LastName>
                    <ForeName>Ludo</ForeName>
                    <Initials>L</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Meuleman</LastName>
                    <ForeName>Wouter</ForeName>
                    <Initials>W</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>de Ridder</LastName>
                    <ForeName>Jeroen</ForeName>
                    <Initials>J</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Berns</LastName>
                    <ForeName>Anton</ForeName>
                    <Initials>A</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wessels</LastName>
                    <ForeName>Lodewyk F A</ForeName>
                    <Initials>LF</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>van Lohuizen</LastName>
                    <ForeName>Maarten</ForeName>
                    <Initials>M</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>van Steensel</LastName>
                    <ForeName>Bas</ForeName>
                    <Initials>B</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
                <PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
            </PublicationTypeList>
        </Article>
        <MedlineJournalInfo>
            <Country>United States</Country>
            <MedlineTA>Cell</MedlineTA>
            <NlmUniqueID>0413066</NlmUniqueID>
            <ISSNLinking>0092-8674</ISSNLinking>
        </MedlineJournalInfo>
        <ChemicalList>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Chromatin</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
        <CommentsCorrectionsList>
            <CommentsCorrections RefType="CommentIn">
                <RefSource>Nat Methods. 2013 Oct;10(10):937</RefSource>
                <PMID Version="1">24161983</PMID>
            </CommentsCorrections>
        </CommentsCorrectionsList>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Animals</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Chromatin</DescriptorName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Chromosomal Position Effects</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Embryonic Stem Cells</DescriptorName>
                <QualifierName MajorTopicYN="N">metabolism</QualifierName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Genes, Reporter</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Genetic Techniques</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Mice</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
    <PubmedData>
        <History>
            <PubMedPubDate PubStatus="received">
                <Year>2013</Year>
                <Month>2</Month>
                <Day>19</Day>
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            <PubMedPubDate PubStatus="revised">
                <Year>2013</Year>
                <Month>5</Month>
                <Day>31</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="accepted">
                <Year>2013</Year>
                <Month>7</Month>
                <Day>12</Day>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="entrez">
                <Year>2013</Year>
                <Month>8</Month>
                <Day>20</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
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                <Year>2013</Year>
                <Month>8</Month>
                <Day>21</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="medline">
                <Year>2013</Year>
                <Month>11</Month>
                <Day>13</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
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        <PublicationStatus>ppublish</PublicationStatus>
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            <ArticleId IdType="doi">10.1016/j.cell.2013.07.018</ArticleId>
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        <PMID Version="1">5420325</PMID>
        <DateCreated>
            <Year>1970</Year>
            <Month>07</Month>
            <Day>29</Day>
        </DateCreated>
        <DateCompleted>
            <Year>1970</Year>
            <Month>07</Month>
            <Day>29</Day>
        </DateCompleted>
        <DateRevised>
            <Year>2000</Year>
            <Month>12</Month>
            <Day>18</Day>
        </DateRevised>
        <Article PubModel="Print">
            <Journal>
                <ISSN IssnType="Print">0022-2836</ISSN>
                <JournalIssue CitedMedium="Print">
                    <Volume>48</Volume>
                    <Issue>3</Issue>
                    <PubDate>
                        <Year>1970</Year>
                        <Month>Mar</Month>
                    </PubDate>
                </JournalIssue>
                <Title>Journal of molecular biology</Title>
                <ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation>
            </Journal>
            <ArticleTitle>A general method applicable to the search for similarities in the amino acid sequence of two proteins.</ArticleTitle>
            <Pagination>
                <MedlinePgn>443-53</MedlinePgn>
            </Pagination>
            <AuthorList CompleteYN="Y">
                <Author ValidYN="Y">
                    <LastName>Needleman</LastName>
                    <ForeName>S B</ForeName>
                    <Initials>SB</Initials>
                </Author>
                <Author ValidYN="Y">
                    <LastName>Wunsch</LastName>
                    <ForeName>C D</ForeName>
                    <Initials>CD</Initials>
                </Author>
            </AuthorList>
            <Language>eng</Language>
            <PublicationTypeList>
                <PublicationType>Journal Article</PublicationType>
            </PublicationTypeList>
        </Article>
        <MedlineJournalInfo>
            <Country>ENGLAND</Country>
            <MedlineTA>J Mol Biol</MedlineTA>
            <NlmUniqueID>2985088R</NlmUniqueID>
            <ISSNLinking>0022-2836</ISSNLinking>
        </MedlineJournalInfo>
        <ChemicalList>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Hemoglobins</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>0</RegistryNumber>
                <NameOfSubstance>Myoglobin</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>EC 3.1.-</RegistryNumber>
                <NameOfSubstance>Ribonucleases</NameOfSubstance>
            </Chemical>
            <Chemical>
                <RegistryNumber>EC 3.2.1.17</RegistryNumber>
                <NameOfSubstance>Muramidase</NameOfSubstance>
            </Chemical>
        </ChemicalList>
        <CitationSubset>IM</CitationSubset>
        <MeshHeadingList>
            <MeshHeading>
                <DescriptorName MajorTopicYN="Y">Amino Acid Sequence</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Computers</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Hemoglobins</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Methods</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Muramidase</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Myoglobin</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Probability</DescriptorName>
            </MeshHeading>
            <MeshHeading>
                <DescriptorName MajorTopicYN="N">Ribonucleases</DescriptorName>
            </MeshHeading>
        </MeshHeadingList>
    </MedlineCitation>
    <PubmedData>
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                <Year>1970</Year>
                <Month>3</Month>
                <Day>1</Day>
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                <Year>1970</Year>
                <Month>3</Month>
                <Day>1</Day>
                <Hour>0</Hour>
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                <Day>1</Day>
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            <ArticleId IdType="pii">0022-2836(70)90057-4</ArticleId>
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