A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
Identifieur interne : 000918 ( Ncbi/Merge ); précédent : 000917; suivant : 000919A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
Auteurs : Xiaotu Ma ; Ashwinikumar Kulkarni ; Zhihua Zhang ; Zhenyu Xuan ; Robert Serfling [États-Unis] ; Michael Q. Zhang [République populaire de Chine]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2011.
Descripteurs français
- KwdFr :
- Algorithmes, Analyse de regroupements, Analyse de séquence d'ADN, Animaux, Cellules souches embryonnaires (métabolisme), Drosophila melanogaster (génétique), Facteurs de transcription (métabolisme), Immunoprécipitation de la chromatine, Logiciel, Motifs nucléotidiques, Protéines de répression, Réseaux de régulation génique, Simulation numérique, Sites de fixation, Souris, Séquençage nucléotidique à haut débit, Séquençage par oligonucléotides en batterie, Éléments de régulation transcriptionnelle.
- MESH :
- génétique : Drosophila melanogaster.
- métabolisme : Cellules souches embryonnaires, Facteurs de transcription.
- Algorithmes, Analyse de regroupements, Analyse de séquence d'ADN, Animaux, Immunoprécipitation de la chromatine, Logiciel, Motifs nucléotidiques, Protéines de répression, Réseaux de régulation génique, Simulation numérique, Sites de fixation, Souris, Séquençage nucléotidique à haut débit, Séquençage par oligonucléotides en batterie, Éléments de régulation transcriptionnelle.
English descriptors
- KwdEn :
- Algorithms, Animals, Binding Sites, CCCTC-Binding Factor, Chromatin Immunoprecipitation, Cluster Analysis, Computer Simulation, Drosophila melanogaster (genetics), Embryonic Stem Cells (metabolism), Gene Regulatory Networks, High-Throughput Nucleotide Sequencing, Mice, Nucleotide Motifs, Oligonucleotide Array Sequence Analysis, Regulatory Elements, Transcriptional, Repressor Proteins, Sequence Analysis, DNA, Software, Transcription Factors (metabolism).
- MESH :
- chemical , metabolism : Transcription Factors.
- chemical : CCCTC-Binding Factor, Repressor Proteins.
- genetics : Drosophila melanogaster.
- metabolism : Embryonic Stem Cells.
- Algorithms, Animals, Binding Sites, Chromatin Immunoprecipitation, Cluster Analysis, Computer Simulation, Gene Regulatory Networks, High-Throughput Nucleotide Sequencing, Mice, Nucleotide Motifs, Oligonucleotide Array Sequence Analysis, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Software.
Abstract
Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new
Url:
DOI: 10.1093/nar/gkr1135
PubMed: 22228832
PubMed Central: 3326300
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000F49
- to stream Pmc, to step Curation: 000F49
- to stream Pmc, to step Checkpoint: 001335
- to stream PubMed, to step Corpus: 001E18
- to stream PubMed, to step Curation: 001E18
- to stream PubMed, to step Checkpoint: 001D11
Links to Exploration step
PMC:3326300Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information</title>
<author><name sortKey="Ma, Xiaotu" sort="Ma, Xiaotu" uniqKey="Ma X" first="Xiaotu" last="Ma">Xiaotu Ma</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Kulkarni, Ashwinikumar" sort="Kulkarni, Ashwinikumar" uniqKey="Kulkarni A" first="Ashwinikumar" last="Kulkarni">Ashwinikumar Kulkarni</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Zhang, Zhihua" sort="Zhang, Zhihua" uniqKey="Zhang Z" first="Zhihua" last="Zhang">Zhihua Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Xuan, Zhenyu" sort="Xuan, Zhenyu" uniqKey="Xuan Z" first="Zhenyu" last="Xuan">Zhenyu Xuan</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Serfling, Robert" sort="Serfling, Robert" uniqKey="Serfling R" first="Robert" last="Serfling">Robert Serfling</name>
<affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr1135-AFF1">Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhang, Michael Q" sort="Zhang, Michael Q" uniqKey="Zhang M" first="Michael Q." last="Zhang">Michael Q. Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="gkr1135-AFF1">Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22228832</idno>
<idno type="pmc">3326300</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326300</idno>
<idno type="RBID">PMC:3326300</idno>
<idno type="doi">10.1093/nar/gkr1135</idno>
<date when="2011">2011</date>
<idno type="wicri:Area/Pmc/Corpus">000F49</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F49</idno>
<idno type="wicri:Area/Pmc/Curation">000F49</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F49</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001335</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001335</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:22228832</idno>
<idno type="wicri:Area/PubMed/Corpus">001E18</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E18</idno>
<idno type="wicri:Area/PubMed/Curation">001E18</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E18</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001D11</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001D11</idno>
<idno type="wicri:Area/Ncbi/Merge">000918</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information</title>
<author><name sortKey="Ma, Xiaotu" sort="Ma, Xiaotu" uniqKey="Ma X" first="Xiaotu" last="Ma">Xiaotu Ma</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Kulkarni, Ashwinikumar" sort="Kulkarni, Ashwinikumar" uniqKey="Kulkarni A" first="Ashwinikumar" last="Kulkarni">Ashwinikumar Kulkarni</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Zhang, Zhihua" sort="Zhang, Zhihua" uniqKey="Zhang Z" first="Zhihua" last="Zhang">Zhihua Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Xuan, Zhenyu" sort="Xuan, Zhenyu" uniqKey="Xuan Z" first="Zhenyu" last="Xuan">Zhenyu Xuan</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Serfling, Robert" sort="Serfling, Robert" uniqKey="Serfling R" first="Robert" last="Serfling">Robert Serfling</name>
<affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr1135-AFF1">Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhang, Michael Q" sort="Zhang, Michael Q" uniqKey="Zhang M" first="Michael Q." last="Zhang">Michael Q. Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="gkr1135-AFF1">Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Binding Sites</term>
<term>CCCTC-Binding Factor</term>
<term>Chromatin Immunoprecipitation</term>
<term>Cluster Analysis</term>
<term>Computer Simulation</term>
<term>Drosophila melanogaster (genetics)</term>
<term>Embryonic Stem Cells (metabolism)</term>
<term>Gene Regulatory Networks</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Mice</term>
<term>Nucleotide Motifs</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Regulatory Elements, Transcriptional</term>
<term>Repressor Proteins</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Cellules souches embryonnaires (métabolisme)</term>
<term>Drosophila melanogaster (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Logiciel</term>
<term>Motifs nucléotidiques</term>
<term>Protéines de répression</term>
<term>Réseaux de régulation génique</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Séquençage par oligonucléotides en batterie</term>
<term>Éléments de régulation transcriptionnelle</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>CCCTC-Binding Factor</term>
<term>Repressor Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Drosophila melanogaster</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Drosophila melanogaster</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Embryonic Stem Cells</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cellules souches embryonnaires</term>
<term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Binding Sites</term>
<term>Chromatin Immunoprecipitation</term>
<term>Cluster Analysis</term>
<term>Computer Simulation</term>
<term>Gene Regulatory Networks</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Mice</term>
<term>Nucleotide Motifs</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Regulatory Elements, Transcriptional</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Logiciel</term>
<term>Motifs nucléotidiques</term>
<term>Protéines de répression</term>
<term>Réseaux de régulation génique</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Séquençage par oligonucléotides en batterie</term>
<term>Éléments de régulation transcriptionnelle</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new <italic>k-</italic>
mer occurrence model to reflect the fact that functional DNA <italic>k</italic>
-mers often cluster around ChIP peak summits. With this model, we introduced a new measure to discover functional <italic>k-</italic>
mers. Using simulation, we demonstrated that our method is more robust against noises in ChIP data than available methods. A novel word clustering method is also implemented to group similar <italic>k</italic>
-mers into position weight matrices (PWMs). Our method was applied to a diverse set of ChIP experiments to demonstrate its high sensitivity and specificity. Importantly, our method is much faster than several other methods for large sample sizes. Thus, we have developed an efficient and effective motif discovery method for ChIP experiments.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name>
</author>
<author><name sortKey="Li, N" uniqKey="Li N">N Li</name>
</author>
<author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
<author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name>
</author>
<author><name sortKey="De Moor, B" uniqKey="De Moor B">B De Moor</name>
</author>
<author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name>
</author>
<author><name sortKey="Favorov, Av" uniqKey="Favorov A">AV Favorov</name>
</author>
<author><name sortKey="Frith, Mc" uniqKey="Frith M">MC Frith</name>
</author>
<author><name sortKey="Fu, Y" uniqKey="Fu Y">Y Fu</name>
</author>
<author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vaquerizas, Jm" uniqKey="Vaquerizas J">JM Vaquerizas</name>
</author>
<author><name sortKey="Kummerfeld, Sk" uniqKey="Kummerfeld S">SK Kummerfeld</name>
</author>
<author><name sortKey="Teichmann, Sa" uniqKey="Teichmann S">SA Teichmann</name>
</author>
<author><name sortKey="Luscombe, Nm" uniqKey="Luscombe N">NM Luscombe</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Portales Casamar, E" uniqKey="Portales Casamar E">E Portales-Casamar</name>
</author>
<author><name sortKey="Thongjuea, S" uniqKey="Thongjuea S">S Thongjuea</name>
</author>
<author><name sortKey="Kwon, At" uniqKey="Kwon A">AT Kwon</name>
</author>
<author><name sortKey="Arenillas, D" uniqKey="Arenillas D">D Arenillas</name>
</author>
<author><name sortKey="Zhao, X" uniqKey="Zhao X">X Zhao</name>
</author>
<author><name sortKey="Valen, E" uniqKey="Valen E">E Valen</name>
</author>
<author><name sortKey="Yusuf, D" uniqKey="Yusuf D">D Yusuf</name>
</author>
<author><name sortKey="Lenhard, B" uniqKey="Lenhard B">B Lenhard</name>
</author>
<author><name sortKey="Wasserman, Ww" uniqKey="Wasserman W">WW Wasserman</name>
</author>
<author><name sortKey="Sandelin, A" uniqKey="Sandelin A">A Sandelin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gerstein, Mb" uniqKey="Gerstein M">MB Gerstein</name>
</author>
<author><name sortKey="Lu, Zj" uniqKey="Lu Z">ZJ Lu</name>
</author>
<author><name sortKey="Van Nostrand, El" uniqKey="Van Nostrand E">EL Van Nostrand</name>
</author>
<author><name sortKey="Cheng, C" uniqKey="Cheng C">C Cheng</name>
</author>
<author><name sortKey="Arshinoff, Bi" uniqKey="Arshinoff B">BI Arshinoff</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
<author><name sortKey="Yip, Ky" uniqKey="Yip K">KY Yip</name>
</author>
<author><name sortKey="Robilotto, R" uniqKey="Robilotto R">R Robilotto</name>
</author>
<author><name sortKey="Rechtsteiner, A" uniqKey="Rechtsteiner A">A Rechtsteiner</name>
</author>
<author><name sortKey="Ikegami, K" uniqKey="Ikegami K">K Ikegami</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roy, S" uniqKey="Roy S">S Roy</name>
</author>
<author><name sortKey="Ernst, J" uniqKey="Ernst J">J Ernst</name>
</author>
<author><name sortKey="Kharchenko, Pv" uniqKey="Kharchenko P">PV Kharchenko</name>
</author>
<author><name sortKey="Kheradpour, P" uniqKey="Kheradpour P">P Kheradpour</name>
</author>
<author><name sortKey="Negre, N" uniqKey="Negre N">N Negre</name>
</author>
<author><name sortKey="Eaton, Ml" uniqKey="Eaton M">ML Eaton</name>
</author>
<author><name sortKey="Landolin, Jm" uniqKey="Landolin J">JM Landolin</name>
</author>
<author><name sortKey="Bristow, Ca" uniqKey="Bristow C">CA Bristow</name>
</author>
<author><name sortKey="Ma, L" uniqKey="Ma L">L Ma</name>
</author>
<author><name sortKey="Lin, Mf" uniqKey="Lin M">MF Lin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jothi, R" uniqKey="Jothi R">R Jothi</name>
</author>
<author><name sortKey="Cuddapah, S" uniqKey="Cuddapah S">S Cuddapah</name>
</author>
<author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name>
</author>
<author><name sortKey="Cui, K" uniqKey="Cui K">K Cui</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
<author><name sortKey="Elkan, C" uniqKey="Elkan C">C Elkan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Buhler, J" uniqKey="Buhler J">J Buhler</name>
</author>
<author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name>
</author>
<author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ettwiller, L" uniqKey="Ettwiller L">L Ettwiller</name>
</author>
<author><name sortKey="Paten, B" uniqKey="Paten B">B Paten</name>
</author>
<author><name sortKey="Ramialison, M" uniqKey="Ramialison M">M Ramialison</name>
</author>
<author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name>
</author>
<author><name sortKey="Wittbrodt, J" uniqKey="Wittbrodt J">J Wittbrodt</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fratkin, E" uniqKey="Fratkin E">E Fratkin</name>
</author>
<author><name sortKey="Naughton, Bt" uniqKey="Naughton B">BT Naughton</name>
</author>
<author><name sortKey="Brutlag, Dl" uniqKey="Brutlag D">DL Brutlag</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lawrence, Ce" uniqKey="Lawrence C">CE Lawrence</name>
</author>
<author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name>
</author>
<author><name sortKey="Boguski, Ms" uniqKey="Boguski M">MS Boguski</name>
</author>
<author><name sortKey="Liu, Js" uniqKey="Liu J">JS Liu</name>
</author>
<author><name sortKey="Neuwald, Af" uniqKey="Neuwald A">AF Neuwald</name>
</author>
<author><name sortKey="Wootton, Jc" uniqKey="Wootton J">JC Wootton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Liu, Xs" uniqKey="Liu X">XS Liu</name>
</author>
<author><name sortKey="Brutlag, Dl" uniqKey="Brutlag D">DL Brutlag</name>
</author>
<author><name sortKey="Liu, Js" uniqKey="Liu J">JS Liu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marsan, L" uniqKey="Marsan L">L Marsan</name>
</author>
<author><name sortKey="Sagot, Mf" uniqKey="Sagot M">MF Sagot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pavesi, G" uniqKey="Pavesi G">G Pavesi</name>
</author>
<author><name sortKey="Mereghetti, P" uniqKey="Mereghetti P">P Mereghetti</name>
</author>
<author><name sortKey="Mauri, G" uniqKey="Mauri G">G Mauri</name>
</author>
<author><name sortKey="Pesole, G" uniqKey="Pesole G">G Pesole</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roth, Fp" uniqKey="Roth F">FP Roth</name>
</author>
<author><name sortKey="Hughes, Jd" uniqKey="Hughes J">JD Hughes</name>
</author>
<author><name sortKey="Estep, Pw" uniqKey="Estep P">PW Estep</name>
</author>
<author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vardhanabhuti, S" uniqKey="Vardhanabhuti S">S Vardhanabhuti</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Hannenhalli, S" uniqKey="Hannenhalli S">S Hannenhalli</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Linhart, C" uniqKey="Linhart C">C Linhart</name>
</author>
<author><name sortKey="Halperin, Y" uniqKey="Halperin Y">Y Halperin</name>
</author>
<author><name sortKey="Shamir, R" uniqKey="Shamir R">R Shamir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kim, Nk" uniqKey="Kim N">NK Kim</name>
</author>
<author><name sortKey="Tharakaraman, K" uniqKey="Tharakaraman K">K Tharakaraman</name>
</author>
<author><name sortKey="Marino Ramirez, L" uniqKey="Marino Ramirez L">L Marino-Ramirez</name>
</author>
<author><name sortKey="Spouge, Jl" uniqKey="Spouge J">JL Spouge</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Narang, V" uniqKey="Narang V">V Narang</name>
</author>
<author><name sortKey="Mittal, A" uniqKey="Mittal A">A Mittal</name>
</author>
<author><name sortKey="Sung, Wk" uniqKey="Sung W">WK Sung</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Keilwagen, J" uniqKey="Keilwagen J">J Keilwagen</name>
</author>
<author><name sortKey="Grau, J" uniqKey="Grau J">J Grau</name>
</author>
<author><name sortKey="Paponov, Ia" uniqKey="Paponov I">IA Paponov</name>
</author>
<author><name sortKey="Posch, S" uniqKey="Posch S">S Posch</name>
</author>
<author><name sortKey="Strickert, M" uniqKey="Strickert M">M Strickert</name>
</author>
<author><name sortKey="Grosse, I" uniqKey="Grosse I">I Grosse</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hu, M" uniqKey="Hu M">M Hu</name>
</author>
<author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name>
</author>
<author><name sortKey="Taylor, Jm" uniqKey="Taylor J">JM Taylor</name>
</author>
<author><name sortKey="Chinnaiyan, Am" uniqKey="Chinnaiyan A">AM Chinnaiyan</name>
</author>
<author><name sortKey="Qin, Zs" uniqKey="Qin Z">ZS Qin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kulakovskiy, Iv" uniqKey="Kulakovskiy I">IV Kulakovskiy</name>
</author>
<author><name sortKey="Boeva, Va" uniqKey="Boeva V">VA Boeva</name>
</author>
<author><name sortKey="Favorov, Av" uniqKey="Favorov A">AV Favorov</name>
</author>
<author><name sortKey="Makeev, Vj" uniqKey="Makeev V">VJ Makeev</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schmid, Cd" uniqKey="Schmid C">CD Schmid</name>
</author>
<author><name sortKey="Bucher, P" uniqKey="Bucher P">P Bucher</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ji, H" uniqKey="Ji H">H Ji</name>
</author>
<author><name sortKey="Jiang, H" uniqKey="Jiang H">H Jiang</name>
</author>
<author><name sortKey="Ma, W" uniqKey="Ma W">W Ma</name>
</author>
<author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Wong, Wh" uniqKey="Wong W">WH Wong</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Corbo, Jc" uniqKey="Corbo J">JC Corbo</name>
</author>
<author><name sortKey="Lawrence, Ka" uniqKey="Lawrence K">KA Lawrence</name>
</author>
<author><name sortKey="Karlstetter, M" uniqKey="Karlstetter M">M Karlstetter</name>
</author>
<author><name sortKey="Myers, Ca" uniqKey="Myers C">CA Myers</name>
</author>
<author><name sortKey="Abdelaziz, M" uniqKey="Abdelaziz M">M Abdelaziz</name>
</author>
<author><name sortKey="Dirkes, W" uniqKey="Dirkes W">W Dirkes</name>
</author>
<author><name sortKey="Weigelt, K" uniqKey="Weigelt K">K Weigelt</name>
</author>
<author><name sortKey="Seifert, M" uniqKey="Seifert M">M Seifert</name>
</author>
<author><name sortKey="Benes, V" uniqKey="Benes V">V Benes</name>
</author>
<author><name sortKey="Fritsche, Lg" uniqKey="Fritsche L">LG Fritsche</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robertson, G" uniqKey="Robertson G">G Robertson</name>
</author>
<author><name sortKey="Hirst, M" uniqKey="Hirst M">M Hirst</name>
</author>
<author><name sortKey="Bainbridge, M" uniqKey="Bainbridge M">M Bainbridge</name>
</author>
<author><name sortKey="Bilenky, M" uniqKey="Bilenky M">M Bilenky</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Zeng, T" uniqKey="Zeng T">T Zeng</name>
</author>
<author><name sortKey="Euskirchen, G" uniqKey="Euskirchen G">G Euskirchen</name>
</author>
<author><name sortKey="Bernier, B" uniqKey="Bernier B">B Bernier</name>
</author>
<author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name>
</author>
<author><name sortKey="Delaney, A" uniqKey="Delaney A">A Delaney</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name>
</author>
<author><name sortKey="Cuddapah, S" uniqKey="Cuddapah S">S Cuddapah</name>
</author>
<author><name sortKey="Cui, K" uniqKey="Cui K">K Cui</name>
</author>
<author><name sortKey="Roh, Ty" uniqKey="Roh T">TY Roh</name>
</author>
<author><name sortKey="Schones, De" uniqKey="Schones D">DE Schones</name>
</author>
<author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name>
</author>
<author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name>
</author>
<author><name sortKey="Chepelev, I" uniqKey="Chepelev I">I Chepelev</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wederell, Ed" uniqKey="Wederell E">ED Wederell</name>
</author>
<author><name sortKey="Bilenky, M" uniqKey="Bilenky M">M Bilenky</name>
</author>
<author><name sortKey="Cullum, R" uniqKey="Cullum R">R Cullum</name>
</author>
<author><name sortKey="Thiessen, N" uniqKey="Thiessen N">N Thiessen</name>
</author>
<author><name sortKey="Dagpinar, M" uniqKey="Dagpinar M">M Dagpinar</name>
</author>
<author><name sortKey="Delaney, A" uniqKey="Delaney A">A Delaney</name>
</author>
<author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Zeng, T" uniqKey="Zeng T">T Zeng</name>
</author>
<author><name sortKey="Bernier, B" uniqKey="Bernier B">B Bernier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kim, Th" uniqKey="Kim T">TH Kim</name>
</author>
<author><name sortKey="Abdullaev, Zk" uniqKey="Abdullaev Z">ZK Abdullaev</name>
</author>
<author><name sortKey="Smith, Ad" uniqKey="Smith A">AD Smith</name>
</author>
<author><name sortKey="Ching, Ka" uniqKey="Ching K">KA Ching</name>
</author>
<author><name sortKey="Loukinov, Di" uniqKey="Loukinov D">DI Loukinov</name>
</author>
<author><name sortKey="Green, Rd" uniqKey="Green R">RD Green</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
<author><name sortKey="Lobanenkov, Vv" uniqKey="Lobanenkov V">VV Lobanenkov</name>
</author>
<author><name sortKey="Ren, B" uniqKey="Ren B">B Ren</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bradley, Rk" uniqKey="Bradley R">RK Bradley</name>
</author>
<author><name sortKey="Li, Xy" uniqKey="Li X">XY Li</name>
</author>
<author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name>
</author>
<author><name sortKey="Davidson, S" uniqKey="Davidson S">S Davidson</name>
</author>
<author><name sortKey="Pachter, L" uniqKey="Pachter L">L Pachter</name>
</author>
<author><name sortKey="Chu, Hc" uniqKey="Chu H">HC Chu</name>
</author>
<author><name sortKey="Tonkin, La" uniqKey="Tonkin L">LA Tonkin</name>
</author>
<author><name sortKey="Biggin, Md" uniqKey="Biggin M">MD Biggin</name>
</author>
<author><name sortKey="Eisen, Mb" uniqKey="Eisen M">MB Eisen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
<author><name sortKey="Xu, H" uniqKey="Xu H">H Xu</name>
</author>
<author><name sortKey="Yuan, P" uniqKey="Yuan P">P Yuan</name>
</author>
<author><name sortKey="Fang, F" uniqKey="Fang F">F Fang</name>
</author>
<author><name sortKey="Huss, M" uniqKey="Huss M">M Huss</name>
</author>
<author><name sortKey="Vega, Vb" uniqKey="Vega V">VB Vega</name>
</author>
<author><name sortKey="Wong, E" uniqKey="Wong E">E Wong</name>
</author>
<author><name sortKey="Orlov, Yl" uniqKey="Orlov Y">YL Orlov</name>
</author>
<author><name sortKey="Zhang, W" uniqKey="Zhang W">W Zhang</name>
</author>
<author><name sortKey="Jiang, J" uniqKey="Jiang J">J Jiang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
<author><name sortKey="Meyer, Ca" uniqKey="Meyer C">CA Meyer</name>
</author>
<author><name sortKey="Eeckhoute, J" uniqKey="Eeckhoute J">J Eeckhoute</name>
</author>
<author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Bernstein, Be" uniqKey="Bernstein B">BE Bernstein</name>
</author>
<author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C Nusbaum</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Brown, M" uniqKey="Brown M">M Brown</name>
</author>
<author><name sortKey="Li, W" uniqKey="Li W">W Li</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wilbanks, Eg" uniqKey="Wilbanks E">EG Wilbanks</name>
</author>
<author><name sortKey="Facciotti, Mt" uniqKey="Facciotti M">MT Facciotti</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dean, N" uniqKey="Dean N">N Dean</name>
</author>
<author><name sortKey="Raftery, Ae" uniqKey="Raftery A">AE Raftery</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schones, De" uniqKey="Schones D">DE Schones</name>
</author>
<author><name sortKey="Sumazin, P" uniqKey="Sumazin P">P Sumazin</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mahony, S" uniqKey="Mahony S">S Mahony</name>
</author>
<author><name sortKey="Auron, Pe" uniqKey="Auron P">PE Auron</name>
</author>
<author><name sortKey="Benos, Pv" uniqKey="Benos P">PV Benos</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Smith, Ad" uniqKey="Smith A">AD Smith</name>
</author>
<author><name sortKey="Sumazin, P" uniqKey="Sumazin P">P Sumazin</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sinha, S" uniqKey="Sinha S">S Sinha</name>
</author>
<author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sumazin, P" uniqKey="Sumazin P">P Sumazin</name>
</author>
<author><name sortKey="Chen, G" uniqKey="Chen G">G Chen</name>
</author>
<author><name sortKey="Hata, N" uniqKey="Hata N">N Hata</name>
</author>
<author><name sortKey="Smith, Ad" uniqKey="Smith A">AD Smith</name>
</author>
<author><name sortKey="Zhang, T" uniqKey="Zhang T">T Zhang</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Valouev, A" uniqKey="Valouev A">A Valouev</name>
</author>
<author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Sundquist, A" uniqKey="Sundquist A">A Sundquist</name>
</author>
<author><name sortKey="Medina, C" uniqKey="Medina C">C Medina</name>
</author>
<author><name sortKey="Anton, E" uniqKey="Anton E">E Anton</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Sidow, A" uniqKey="Sidow A">A Sidow</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cao, Ar" uniqKey="Cao A">AR Cao</name>
</author>
<author><name sortKey="Rabinovich, R" uniqKey="Rabinovich R">R Rabinovich</name>
</author>
<author><name sortKey="Xu, M" uniqKey="Xu M">M Xu</name>
</author>
<author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name>
</author>
<author><name sortKey="Jin, Vx" uniqKey="Jin V">VX Jin</name>
</author>
<author><name sortKey="Farnham, Pj" uniqKey="Farnham P">PJ Farnham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tuteja, G" uniqKey="Tuteja G">G Tuteja</name>
</author>
<author><name sortKey="White, P" uniqKey="White P">P White</name>
</author>
<author><name sortKey="Schug, J" uniqKey="Schug J">J Schug</name>
</author>
<author><name sortKey="Kaestner, Kh" uniqKey="Kaestner K">KH Kaestner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Liang, Hl" uniqKey="Liang H">HL Liang</name>
</author>
<author><name sortKey="Nien, Cy" uniqKey="Nien C">CY Nien</name>
</author>
<author><name sortKey="Liu, Hy" uniqKey="Liu H">HY Liu</name>
</author>
<author><name sortKey="Metzstein, Mm" uniqKey="Metzstein M">MM Metzstein</name>
</author>
<author><name sortKey="Kirov, N" uniqKey="Kirov N">N Kirov</name>
</author>
<author><name sortKey="Rushlow, C" uniqKey="Rushlow C">C Rushlow</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wei, Gh" uniqKey="Wei G">GH Wei</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T Kivioja</name>
</author>
<author><name sortKey="Palin, K" uniqKey="Palin K">K Palin</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Bonke, M" uniqKey="Bonke M">M Bonke</name>
</author>
<author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Varjosalo, M" uniqKey="Varjosalo M">M Varjosalo</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Qureshi, Am" uniqKey="Qureshi A">AM Qureshi</name>
</author>
<author><name sortKey="He, Fs" uniqKey="He F">FS He</name>
</author>
<author><name sortKey="Estep, Pw" uniqKey="Estep P">PW Estep</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Whitington, T" uniqKey="Whitington T">T Whitington</name>
</author>
<author><name sortKey="Frith, Mc" uniqKey="Frith M">MC Frith</name>
</author>
<author><name sortKey="Johnson, J" uniqKey="Johnson J">J Johnson</name>
</author>
<author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<double pmid="22228832"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information</title>
<author><name sortKey="Ma, Xiaotu" sort="Ma, Xiaotu" uniqKey="Ma X" first="Xiaotu" last="Ma">Xiaotu Ma</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Kulkarni, Ashwinikumar" sort="Kulkarni, Ashwinikumar" uniqKey="Kulkarni A" first="Ashwinikumar" last="Kulkarni">Ashwinikumar Kulkarni</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Zhang, Zhihua" sort="Zhang, Zhihua" uniqKey="Zhang Z" first="Zhihua" last="Zhang">Zhihua Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Xuan, Zhenyu" sort="Xuan, Zhenyu" uniqKey="Xuan Z" first="Zhenyu" last="Xuan">Zhenyu Xuan</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Serfling, Robert" sort="Serfling, Robert" uniqKey="Serfling R" first="Robert" last="Serfling">Robert Serfling</name>
<affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr1135-AFF1">Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhang, Michael Q" sort="Zhang, Michael Q" uniqKey="Zhang M" first="Michael Q." last="Zhang">Michael Q. Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="gkr1135-AFF1">Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22228832</idno>
<idno type="pmc">3326300</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326300</idno>
<idno type="RBID">PMC:3326300</idno>
<idno type="doi">10.1093/nar/gkr1135</idno>
<date when="2011">2011</date>
<idno type="wicri:Area/Pmc/Corpus">000F49</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F49</idno>
<idno type="wicri:Area/Pmc/Curation">000F49</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F49</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001335</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001335</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information</title>
<author><name sortKey="Ma, Xiaotu" sort="Ma, Xiaotu" uniqKey="Ma X" first="Xiaotu" last="Ma">Xiaotu Ma</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Kulkarni, Ashwinikumar" sort="Kulkarni, Ashwinikumar" uniqKey="Kulkarni A" first="Ashwinikumar" last="Kulkarni">Ashwinikumar Kulkarni</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Zhang, Zhihua" sort="Zhang, Zhihua" uniqKey="Zhang Z" first="Zhihua" last="Zhang">Zhihua Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Xuan, Zhenyu" sort="Xuan, Zhenyu" uniqKey="Xuan Z" first="Zhenyu" last="Xuan">Zhenyu Xuan</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Serfling, Robert" sort="Serfling, Robert" uniqKey="Serfling R" first="Robert" last="Serfling">Robert Serfling</name>
<affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr1135-AFF1">Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Mathematics, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Zhang, Michael Q" sort="Zhang, Michael Q" uniqKey="Zhang M" first="Michael Q." last="Zhang">Michael Q. Zhang</name>
<affiliation><nlm:aff id="gkr1135-AFF1">Department of Molecular and Cell Biology, Center for Systems Biology,</nlm:aff>
<wicri:noCountry code="subfield">Center for Systems Biology</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="gkr1135-AFF1">Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new <italic>k-</italic>
mer occurrence model to reflect the fact that functional DNA <italic>k</italic>
-mers often cluster around ChIP peak summits. With this model, we introduced a new measure to discover functional <italic>k-</italic>
mers. Using simulation, we demonstrated that our method is more robust against noises in ChIP data than available methods. A novel word clustering method is also implemented to group similar <italic>k</italic>
-mers into position weight matrices (PWMs). Our method was applied to a diverse set of ChIP experiments to demonstrate its high sensitivity and specificity. Importantly, our method is much faster than several other methods for large sample sizes. Thus, we have developed an efficient and effective motif discovery method for ChIP experiments.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name>
</author>
<author><name sortKey="Li, N" uniqKey="Li N">N Li</name>
</author>
<author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
<author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name>
</author>
<author><name sortKey="De Moor, B" uniqKey="De Moor B">B De Moor</name>
</author>
<author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name>
</author>
<author><name sortKey="Favorov, Av" uniqKey="Favorov A">AV Favorov</name>
</author>
<author><name sortKey="Frith, Mc" uniqKey="Frith M">MC Frith</name>
</author>
<author><name sortKey="Fu, Y" uniqKey="Fu Y">Y Fu</name>
</author>
<author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vaquerizas, Jm" uniqKey="Vaquerizas J">JM Vaquerizas</name>
</author>
<author><name sortKey="Kummerfeld, Sk" uniqKey="Kummerfeld S">SK Kummerfeld</name>
</author>
<author><name sortKey="Teichmann, Sa" uniqKey="Teichmann S">SA Teichmann</name>
</author>
<author><name sortKey="Luscombe, Nm" uniqKey="Luscombe N">NM Luscombe</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Portales Casamar, E" uniqKey="Portales Casamar E">E Portales-Casamar</name>
</author>
<author><name sortKey="Thongjuea, S" uniqKey="Thongjuea S">S Thongjuea</name>
</author>
<author><name sortKey="Kwon, At" uniqKey="Kwon A">AT Kwon</name>
</author>
<author><name sortKey="Arenillas, D" uniqKey="Arenillas D">D Arenillas</name>
</author>
<author><name sortKey="Zhao, X" uniqKey="Zhao X">X Zhao</name>
</author>
<author><name sortKey="Valen, E" uniqKey="Valen E">E Valen</name>
</author>
<author><name sortKey="Yusuf, D" uniqKey="Yusuf D">D Yusuf</name>
</author>
<author><name sortKey="Lenhard, B" uniqKey="Lenhard B">B Lenhard</name>
</author>
<author><name sortKey="Wasserman, Ww" uniqKey="Wasserman W">WW Wasserman</name>
</author>
<author><name sortKey="Sandelin, A" uniqKey="Sandelin A">A Sandelin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gerstein, Mb" uniqKey="Gerstein M">MB Gerstein</name>
</author>
<author><name sortKey="Lu, Zj" uniqKey="Lu Z">ZJ Lu</name>
</author>
<author><name sortKey="Van Nostrand, El" uniqKey="Van Nostrand E">EL Van Nostrand</name>
</author>
<author><name sortKey="Cheng, C" uniqKey="Cheng C">C Cheng</name>
</author>
<author><name sortKey="Arshinoff, Bi" uniqKey="Arshinoff B">BI Arshinoff</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
<author><name sortKey="Yip, Ky" uniqKey="Yip K">KY Yip</name>
</author>
<author><name sortKey="Robilotto, R" uniqKey="Robilotto R">R Robilotto</name>
</author>
<author><name sortKey="Rechtsteiner, A" uniqKey="Rechtsteiner A">A Rechtsteiner</name>
</author>
<author><name sortKey="Ikegami, K" uniqKey="Ikegami K">K Ikegami</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roy, S" uniqKey="Roy S">S Roy</name>
</author>
<author><name sortKey="Ernst, J" uniqKey="Ernst J">J Ernst</name>
</author>
<author><name sortKey="Kharchenko, Pv" uniqKey="Kharchenko P">PV Kharchenko</name>
</author>
<author><name sortKey="Kheradpour, P" uniqKey="Kheradpour P">P Kheradpour</name>
</author>
<author><name sortKey="Negre, N" uniqKey="Negre N">N Negre</name>
</author>
<author><name sortKey="Eaton, Ml" uniqKey="Eaton M">ML Eaton</name>
</author>
<author><name sortKey="Landolin, Jm" uniqKey="Landolin J">JM Landolin</name>
</author>
<author><name sortKey="Bristow, Ca" uniqKey="Bristow C">CA Bristow</name>
</author>
<author><name sortKey="Ma, L" uniqKey="Ma L">L Ma</name>
</author>
<author><name sortKey="Lin, Mf" uniqKey="Lin M">MF Lin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jothi, R" uniqKey="Jothi R">R Jothi</name>
</author>
<author><name sortKey="Cuddapah, S" uniqKey="Cuddapah S">S Cuddapah</name>
</author>
<author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name>
</author>
<author><name sortKey="Cui, K" uniqKey="Cui K">K Cui</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
<author><name sortKey="Elkan, C" uniqKey="Elkan C">C Elkan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Buhler, J" uniqKey="Buhler J">J Buhler</name>
</author>
<author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name>
</author>
<author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ettwiller, L" uniqKey="Ettwiller L">L Ettwiller</name>
</author>
<author><name sortKey="Paten, B" uniqKey="Paten B">B Paten</name>
</author>
<author><name sortKey="Ramialison, M" uniqKey="Ramialison M">M Ramialison</name>
</author>
<author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name>
</author>
<author><name sortKey="Wittbrodt, J" uniqKey="Wittbrodt J">J Wittbrodt</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fratkin, E" uniqKey="Fratkin E">E Fratkin</name>
</author>
<author><name sortKey="Naughton, Bt" uniqKey="Naughton B">BT Naughton</name>
</author>
<author><name sortKey="Brutlag, Dl" uniqKey="Brutlag D">DL Brutlag</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lawrence, Ce" uniqKey="Lawrence C">CE Lawrence</name>
</author>
<author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name>
</author>
<author><name sortKey="Boguski, Ms" uniqKey="Boguski M">MS Boguski</name>
</author>
<author><name sortKey="Liu, Js" uniqKey="Liu J">JS Liu</name>
</author>
<author><name sortKey="Neuwald, Af" uniqKey="Neuwald A">AF Neuwald</name>
</author>
<author><name sortKey="Wootton, Jc" uniqKey="Wootton J">JC Wootton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Liu, Xs" uniqKey="Liu X">XS Liu</name>
</author>
<author><name sortKey="Brutlag, Dl" uniqKey="Brutlag D">DL Brutlag</name>
</author>
<author><name sortKey="Liu, Js" uniqKey="Liu J">JS Liu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marsan, L" uniqKey="Marsan L">L Marsan</name>
</author>
<author><name sortKey="Sagot, Mf" uniqKey="Sagot M">MF Sagot</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pavesi, G" uniqKey="Pavesi G">G Pavesi</name>
</author>
<author><name sortKey="Mereghetti, P" uniqKey="Mereghetti P">P Mereghetti</name>
</author>
<author><name sortKey="Mauri, G" uniqKey="Mauri G">G Mauri</name>
</author>
<author><name sortKey="Pesole, G" uniqKey="Pesole G">G Pesole</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roth, Fp" uniqKey="Roth F">FP Roth</name>
</author>
<author><name sortKey="Hughes, Jd" uniqKey="Hughes J">JD Hughes</name>
</author>
<author><name sortKey="Estep, Pw" uniqKey="Estep P">PW Estep</name>
</author>
<author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vardhanabhuti, S" uniqKey="Vardhanabhuti S">S Vardhanabhuti</name>
</author>
<author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name>
</author>
<author><name sortKey="Hannenhalli, S" uniqKey="Hannenhalli S">S Hannenhalli</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Linhart, C" uniqKey="Linhart C">C Linhart</name>
</author>
<author><name sortKey="Halperin, Y" uniqKey="Halperin Y">Y Halperin</name>
</author>
<author><name sortKey="Shamir, R" uniqKey="Shamir R">R Shamir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kim, Nk" uniqKey="Kim N">NK Kim</name>
</author>
<author><name sortKey="Tharakaraman, K" uniqKey="Tharakaraman K">K Tharakaraman</name>
</author>
<author><name sortKey="Marino Ramirez, L" uniqKey="Marino Ramirez L">L Marino-Ramirez</name>
</author>
<author><name sortKey="Spouge, Jl" uniqKey="Spouge J">JL Spouge</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Narang, V" uniqKey="Narang V">V Narang</name>
</author>
<author><name sortKey="Mittal, A" uniqKey="Mittal A">A Mittal</name>
</author>
<author><name sortKey="Sung, Wk" uniqKey="Sung W">WK Sung</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Keilwagen, J" uniqKey="Keilwagen J">J Keilwagen</name>
</author>
<author><name sortKey="Grau, J" uniqKey="Grau J">J Grau</name>
</author>
<author><name sortKey="Paponov, Ia" uniqKey="Paponov I">IA Paponov</name>
</author>
<author><name sortKey="Posch, S" uniqKey="Posch S">S Posch</name>
</author>
<author><name sortKey="Strickert, M" uniqKey="Strickert M">M Strickert</name>
</author>
<author><name sortKey="Grosse, I" uniqKey="Grosse I">I Grosse</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hu, M" uniqKey="Hu M">M Hu</name>
</author>
<author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name>
</author>
<author><name sortKey="Taylor, Jm" uniqKey="Taylor J">JM Taylor</name>
</author>
<author><name sortKey="Chinnaiyan, Am" uniqKey="Chinnaiyan A">AM Chinnaiyan</name>
</author>
<author><name sortKey="Qin, Zs" uniqKey="Qin Z">ZS Qin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kulakovskiy, Iv" uniqKey="Kulakovskiy I">IV Kulakovskiy</name>
</author>
<author><name sortKey="Boeva, Va" uniqKey="Boeva V">VA Boeva</name>
</author>
<author><name sortKey="Favorov, Av" uniqKey="Favorov A">AV Favorov</name>
</author>
<author><name sortKey="Makeev, Vj" uniqKey="Makeev V">VJ Makeev</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schmid, Cd" uniqKey="Schmid C">CD Schmid</name>
</author>
<author><name sortKey="Bucher, P" uniqKey="Bucher P">P Bucher</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ji, H" uniqKey="Ji H">H Ji</name>
</author>
<author><name sortKey="Jiang, H" uniqKey="Jiang H">H Jiang</name>
</author>
<author><name sortKey="Ma, W" uniqKey="Ma W">W Ma</name>
</author>
<author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Wong, Wh" uniqKey="Wong W">WH Wong</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Corbo, Jc" uniqKey="Corbo J">JC Corbo</name>
</author>
<author><name sortKey="Lawrence, Ka" uniqKey="Lawrence K">KA Lawrence</name>
</author>
<author><name sortKey="Karlstetter, M" uniqKey="Karlstetter M">M Karlstetter</name>
</author>
<author><name sortKey="Myers, Ca" uniqKey="Myers C">CA Myers</name>
</author>
<author><name sortKey="Abdelaziz, M" uniqKey="Abdelaziz M">M Abdelaziz</name>
</author>
<author><name sortKey="Dirkes, W" uniqKey="Dirkes W">W Dirkes</name>
</author>
<author><name sortKey="Weigelt, K" uniqKey="Weigelt K">K Weigelt</name>
</author>
<author><name sortKey="Seifert, M" uniqKey="Seifert M">M Seifert</name>
</author>
<author><name sortKey="Benes, V" uniqKey="Benes V">V Benes</name>
</author>
<author><name sortKey="Fritsche, Lg" uniqKey="Fritsche L">LG Fritsche</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robertson, G" uniqKey="Robertson G">G Robertson</name>
</author>
<author><name sortKey="Hirst, M" uniqKey="Hirst M">M Hirst</name>
</author>
<author><name sortKey="Bainbridge, M" uniqKey="Bainbridge M">M Bainbridge</name>
</author>
<author><name sortKey="Bilenky, M" uniqKey="Bilenky M">M Bilenky</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Zeng, T" uniqKey="Zeng T">T Zeng</name>
</author>
<author><name sortKey="Euskirchen, G" uniqKey="Euskirchen G">G Euskirchen</name>
</author>
<author><name sortKey="Bernier, B" uniqKey="Bernier B">B Bernier</name>
</author>
<author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name>
</author>
<author><name sortKey="Delaney, A" uniqKey="Delaney A">A Delaney</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name>
</author>
<author><name sortKey="Cuddapah, S" uniqKey="Cuddapah S">S Cuddapah</name>
</author>
<author><name sortKey="Cui, K" uniqKey="Cui K">K Cui</name>
</author>
<author><name sortKey="Roh, Ty" uniqKey="Roh T">TY Roh</name>
</author>
<author><name sortKey="Schones, De" uniqKey="Schones D">DE Schones</name>
</author>
<author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name>
</author>
<author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name>
</author>
<author><name sortKey="Chepelev, I" uniqKey="Chepelev I">I Chepelev</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wederell, Ed" uniqKey="Wederell E">ED Wederell</name>
</author>
<author><name sortKey="Bilenky, M" uniqKey="Bilenky M">M Bilenky</name>
</author>
<author><name sortKey="Cullum, R" uniqKey="Cullum R">R Cullum</name>
</author>
<author><name sortKey="Thiessen, N" uniqKey="Thiessen N">N Thiessen</name>
</author>
<author><name sortKey="Dagpinar, M" uniqKey="Dagpinar M">M Dagpinar</name>
</author>
<author><name sortKey="Delaney, A" uniqKey="Delaney A">A Delaney</name>
</author>
<author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Zeng, T" uniqKey="Zeng T">T Zeng</name>
</author>
<author><name sortKey="Bernier, B" uniqKey="Bernier B">B Bernier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kim, Th" uniqKey="Kim T">TH Kim</name>
</author>
<author><name sortKey="Abdullaev, Zk" uniqKey="Abdullaev Z">ZK Abdullaev</name>
</author>
<author><name sortKey="Smith, Ad" uniqKey="Smith A">AD Smith</name>
</author>
<author><name sortKey="Ching, Ka" uniqKey="Ching K">KA Ching</name>
</author>
<author><name sortKey="Loukinov, Di" uniqKey="Loukinov D">DI Loukinov</name>
</author>
<author><name sortKey="Green, Rd" uniqKey="Green R">RD Green</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
<author><name sortKey="Lobanenkov, Vv" uniqKey="Lobanenkov V">VV Lobanenkov</name>
</author>
<author><name sortKey="Ren, B" uniqKey="Ren B">B Ren</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bradley, Rk" uniqKey="Bradley R">RK Bradley</name>
</author>
<author><name sortKey="Li, Xy" uniqKey="Li X">XY Li</name>
</author>
<author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name>
</author>
<author><name sortKey="Davidson, S" uniqKey="Davidson S">S Davidson</name>
</author>
<author><name sortKey="Pachter, L" uniqKey="Pachter L">L Pachter</name>
</author>
<author><name sortKey="Chu, Hc" uniqKey="Chu H">HC Chu</name>
</author>
<author><name sortKey="Tonkin, La" uniqKey="Tonkin L">LA Tonkin</name>
</author>
<author><name sortKey="Biggin, Md" uniqKey="Biggin M">MD Biggin</name>
</author>
<author><name sortKey="Eisen, Mb" uniqKey="Eisen M">MB Eisen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
<author><name sortKey="Xu, H" uniqKey="Xu H">H Xu</name>
</author>
<author><name sortKey="Yuan, P" uniqKey="Yuan P">P Yuan</name>
</author>
<author><name sortKey="Fang, F" uniqKey="Fang F">F Fang</name>
</author>
<author><name sortKey="Huss, M" uniqKey="Huss M">M Huss</name>
</author>
<author><name sortKey="Vega, Vb" uniqKey="Vega V">VB Vega</name>
</author>
<author><name sortKey="Wong, E" uniqKey="Wong E">E Wong</name>
</author>
<author><name sortKey="Orlov, Yl" uniqKey="Orlov Y">YL Orlov</name>
</author>
<author><name sortKey="Zhang, W" uniqKey="Zhang W">W Zhang</name>
</author>
<author><name sortKey="Jiang, J" uniqKey="Jiang J">J Jiang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
<author><name sortKey="Meyer, Ca" uniqKey="Meyer C">CA Meyer</name>
</author>
<author><name sortKey="Eeckhoute, J" uniqKey="Eeckhoute J">J Eeckhoute</name>
</author>
<author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Bernstein, Be" uniqKey="Bernstein B">BE Bernstein</name>
</author>
<author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C Nusbaum</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Brown, M" uniqKey="Brown M">M Brown</name>
</author>
<author><name sortKey="Li, W" uniqKey="Li W">W Li</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wilbanks, Eg" uniqKey="Wilbanks E">EG Wilbanks</name>
</author>
<author><name sortKey="Facciotti, Mt" uniqKey="Facciotti M">MT Facciotti</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dean, N" uniqKey="Dean N">N Dean</name>
</author>
<author><name sortKey="Raftery, Ae" uniqKey="Raftery A">AE Raftery</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schones, De" uniqKey="Schones D">DE Schones</name>
</author>
<author><name sortKey="Sumazin, P" uniqKey="Sumazin P">P Sumazin</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mahony, S" uniqKey="Mahony S">S Mahony</name>
</author>
<author><name sortKey="Auron, Pe" uniqKey="Auron P">PE Auron</name>
</author>
<author><name sortKey="Benos, Pv" uniqKey="Benos P">PV Benos</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Smith, Ad" uniqKey="Smith A">AD Smith</name>
</author>
<author><name sortKey="Sumazin, P" uniqKey="Sumazin P">P Sumazin</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sinha, S" uniqKey="Sinha S">S Sinha</name>
</author>
<author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sumazin, P" uniqKey="Sumazin P">P Sumazin</name>
</author>
<author><name sortKey="Chen, G" uniqKey="Chen G">G Chen</name>
</author>
<author><name sortKey="Hata, N" uniqKey="Hata N">N Hata</name>
</author>
<author><name sortKey="Smith, Ad" uniqKey="Smith A">AD Smith</name>
</author>
<author><name sortKey="Zhang, T" uniqKey="Zhang T">T Zhang</name>
</author>
<author><name sortKey="Zhang, Mq" uniqKey="Zhang M">MQ Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Valouev, A" uniqKey="Valouev A">A Valouev</name>
</author>
<author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name>
</author>
<author><name sortKey="Sundquist, A" uniqKey="Sundquist A">A Sundquist</name>
</author>
<author><name sortKey="Medina, C" uniqKey="Medina C">C Medina</name>
</author>
<author><name sortKey="Anton, E" uniqKey="Anton E">E Anton</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name>
</author>
<author><name sortKey="Sidow, A" uniqKey="Sidow A">A Sidow</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cao, Ar" uniqKey="Cao A">AR Cao</name>
</author>
<author><name sortKey="Rabinovich, R" uniqKey="Rabinovich R">R Rabinovich</name>
</author>
<author><name sortKey="Xu, M" uniqKey="Xu M">M Xu</name>
</author>
<author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name>
</author>
<author><name sortKey="Jin, Vx" uniqKey="Jin V">VX Jin</name>
</author>
<author><name sortKey="Farnham, Pj" uniqKey="Farnham P">PJ Farnham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tuteja, G" uniqKey="Tuteja G">G Tuteja</name>
</author>
<author><name sortKey="White, P" uniqKey="White P">P White</name>
</author>
<author><name sortKey="Schug, J" uniqKey="Schug J">J Schug</name>
</author>
<author><name sortKey="Kaestner, Kh" uniqKey="Kaestner K">KH Kaestner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Liang, Hl" uniqKey="Liang H">HL Liang</name>
</author>
<author><name sortKey="Nien, Cy" uniqKey="Nien C">CY Nien</name>
</author>
<author><name sortKey="Liu, Hy" uniqKey="Liu H">HY Liu</name>
</author>
<author><name sortKey="Metzstein, Mm" uniqKey="Metzstein M">MM Metzstein</name>
</author>
<author><name sortKey="Kirov, N" uniqKey="Kirov N">N Kirov</name>
</author>
<author><name sortKey="Rushlow, C" uniqKey="Rushlow C">C Rushlow</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wei, Gh" uniqKey="Wei G">GH Wei</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T Kivioja</name>
</author>
<author><name sortKey="Palin, K" uniqKey="Palin K">K Palin</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Bonke, M" uniqKey="Bonke M">M Bonke</name>
</author>
<author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Varjosalo, M" uniqKey="Varjosalo M">M Varjosalo</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Qureshi, Am" uniqKey="Qureshi A">AM Qureshi</name>
</author>
<author><name sortKey="He, Fs" uniqKey="He F">FS He</name>
</author>
<author><name sortKey="Estep, Pw" uniqKey="Estep P">PW Estep</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Whitington, T" uniqKey="Whitington T">T Whitington</name>
</author>
<author><name sortKey="Frith, Mc" uniqKey="Frith M">MC Frith</name>
</author>
<author><name sortKey="Johnson, J" uniqKey="Johnson J">J Johnson</name>
</author>
<author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</pmc>
<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.</title>
<author><name sortKey="Ma, Xiaotu" sort="Ma, Xiaotu" uniqKey="Ma X" first="Xiaotu" last="Ma">Xiaotu Ma</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Kulkarni, Ashwinikumar" sort="Kulkarni, Ashwinikumar" uniqKey="Kulkarni A" first="Ashwinikumar" last="Kulkarni">Ashwinikumar Kulkarni</name>
</author>
<author><name sortKey="Zhang, Zhihua" sort="Zhang, Zhihua" uniqKey="Zhang Z" first="Zhihua" last="Zhang">Zhihua Zhang</name>
</author>
<author><name sortKey="Xuan, Zhenyu" sort="Xuan, Zhenyu" uniqKey="Xuan Z" first="Zhenyu" last="Xuan">Zhenyu Xuan</name>
</author>
<author><name sortKey="Serfling, Robert" sort="Serfling, Robert" uniqKey="Serfling R" first="Robert" last="Serfling">Robert Serfling</name>
</author>
<author><name sortKey="Zhang, Michael Q" sort="Zhang, Michael Q" uniqKey="Zhang M" first="Michael Q" last="Zhang">Michael Q. Zhang</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2012">2012</date>
<idno type="RBID">pubmed:22228832</idno>
<idno type="pmid">22228832</idno>
<idno type="doi">10.1093/nar/gkr1135</idno>
<idno type="wicri:Area/PubMed/Corpus">001E18</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E18</idno>
<idno type="wicri:Area/PubMed/Curation">001E18</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E18</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001D11</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001D11</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.</title>
<author><name sortKey="Ma, Xiaotu" sort="Ma, Xiaotu" uniqKey="Ma X" first="Xiaotu" last="Ma">Xiaotu Ma</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080</wicri:regionArea>
<placeName><region type="state">Texas</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Kulkarni, Ashwinikumar" sort="Kulkarni, Ashwinikumar" uniqKey="Kulkarni A" first="Ashwinikumar" last="Kulkarni">Ashwinikumar Kulkarni</name>
</author>
<author><name sortKey="Zhang, Zhihua" sort="Zhang, Zhihua" uniqKey="Zhang Z" first="Zhihua" last="Zhang">Zhihua Zhang</name>
</author>
<author><name sortKey="Xuan, Zhenyu" sort="Xuan, Zhenyu" uniqKey="Xuan Z" first="Zhenyu" last="Xuan">Zhenyu Xuan</name>
</author>
<author><name sortKey="Serfling, Robert" sort="Serfling, Robert" uniqKey="Serfling R" first="Robert" last="Serfling">Robert Serfling</name>
</author>
<author><name sortKey="Zhang, Michael Q" sort="Zhang, Michael Q" uniqKey="Zhang M" first="Michael Q" last="Zhang">Michael Q. Zhang</name>
</author>
</analytic>
<series><title level="j">Nucleic acids research</title>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2012" type="published">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Binding Sites</term>
<term>CCCTC-Binding Factor</term>
<term>Chromatin Immunoprecipitation</term>
<term>Cluster Analysis</term>
<term>Computer Simulation</term>
<term>Drosophila melanogaster (genetics)</term>
<term>Embryonic Stem Cells (metabolism)</term>
<term>Gene Regulatory Networks</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Mice</term>
<term>Nucleotide Motifs</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Regulatory Elements, Transcriptional</term>
<term>Repressor Proteins</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Cellules souches embryonnaires (métabolisme)</term>
<term>Drosophila melanogaster (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Logiciel</term>
<term>Motifs nucléotidiques</term>
<term>Protéines de répression</term>
<term>Réseaux de régulation génique</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Séquençage par oligonucléotides en batterie</term>
<term>Éléments de régulation transcriptionnelle</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>CCCTC-Binding Factor</term>
<term>Repressor Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Drosophila melanogaster</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Drosophila melanogaster</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Embryonic Stem Cells</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cellules souches embryonnaires</term>
<term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Binding Sites</term>
<term>Chromatin Immunoprecipitation</term>
<term>Cluster Analysis</term>
<term>Computer Simulation</term>
<term>Gene Regulatory Networks</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Mice</term>
<term>Nucleotide Motifs</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Regulatory Elements, Transcriptional</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de regroupements</term>
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Logiciel</term>
<term>Motifs nucléotidiques</term>
<term>Protéines de répression</term>
<term>Réseaux de régulation génique</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Séquençage par oligonucléotides en batterie</term>
<term>Éléments de régulation transcriptionnelle</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new k-mer occurrence model to reflect the fact that functional DNA k-mers often cluster around ChIP peak summits. With this model, we introduced a new measure to discover functional k-mers. Using simulation, we demonstrated that our method is more robust against noises in ChIP data than available methods. A novel word clustering method is also implemented to group similar k-mers into position weight matrices (PWMs). Our method was applied to a diverse set of ChIP experiments to demonstrate its high sensitivity and specificity. Importantly, our method is much faster than several other methods for large sample sizes. Thus, we have developed an efficient and effective motif discovery method for ChIP experiments.</div>
</front>
</TEI>
</pubmed>
</double>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000918 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000918 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Ncbi |étape= Merge |type= RBID |clé= PMC:3326300 |texte= A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:22228832" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |