Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels
Identifieur interne : 001B43 ( Main/Curation ); précédent : 001B42; suivant : 001B44Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels
Auteurs : Xiaolei Wang ; Hiroyuki Kuwahara ; Xin GaoSource :
- BMC Systems Biology [ 1752-0509 ] ; 2014.
Descripteurs français
- KwdFr :
- ADN (), ADN (ultrastructure), Algorithmes, Analyse de séquence d'ADN (), Cartographie d'interactions entre protéines (), Données de séquences moléculaires, Facteurs de transcription (), Facteurs de transcription (ultrastructure), Liaison aux protéines, Machine à vecteur de support, Modèles chimiques, Modèles moléculaires, Simulation numérique, Sites de fixation, Séquence d'acides aminés, Séquence nucléotidique.
- MESH :
- ultrastructure : ADN, Facteurs de transcription.
- ADN, Algorithmes, Analyse de séquence d'ADN, Cartographie d'interactions entre protéines, Données de séquences moléculaires, Facteurs de transcription, Liaison aux protéines, Machine à vecteur de support, Modèles chimiques, Modèles moléculaires, Simulation numérique, Sites de fixation, Séquence d'acides aminés, Séquence nucléotidique.
English descriptors
- KwdEn :
- Algorithms, Amino Acid Sequence, Base Sequence, Binding Sites, Computer Simulation, DNA (chemistry), DNA (ultrastructure), Models, Chemical, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Interaction Mapping (methods), Sequence Analysis, DNA (methods), Support Vector Machine, Transcription Factors (chemistry), Transcription Factors (ultrastructure).
- MESH :
- chemical , chemistry : DNA, Transcription Factors.
- chemical , ultrastructure : DNA, Transcription Factors.
- methods : Protein Interaction Mapping, Sequence Analysis, DNA.
- Algorithms, Amino Acid Sequence, Base Sequence, Binding Sites, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Sequence Data, Protein Binding, Support Vector Machine.
Abstract
A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology.
Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in
We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify genetic parts to fine-tune gene expression rates is crucial to the design of biological systems, such a tool may play an important role in the success of synthetic biology going forward.
Url:
DOI: 10.1186/1752-0509-8-S5-S5
PubMed: 25605483
PubMed Central: 4305984
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<series><title level="j">BMC Systems Biology</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Amino Acid Sequence</term>
<term>Base Sequence</term>
<term>Binding Sites</term>
<term>Computer Simulation</term>
<term>DNA (chemistry)</term>
<term>DNA (ultrastructure)</term>
<term>Models, Chemical</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Protein Binding</term>
<term>Protein Interaction Mapping (methods)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Support Vector Machine</term>
<term>Transcription Factors (chemistry)</term>
<term>Transcription Factors (ultrastructure)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term>
<term>ADN (ultrastructure)</term>
<term>Algorithmes</term>
<term>Analyse de séquence d'ADN ()</term>
<term>Cartographie d'interactions entre protéines ()</term>
<term>Données de séquences moléculaires</term>
<term>Facteurs de transcription ()</term>
<term>Facteurs de transcription (ultrastructure)</term>
<term>Liaison aux protéines</term>
<term>Machine à vecteur de support</term>
<term>Modèles chimiques</term>
<term>Modèles moléculaires</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
<term>Séquence d'acides aminés</term>
<term>Séquence nucléotidique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="ultrastructure" xml:lang="en"><term>DNA</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Protein Interaction Mapping</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" qualifier="ultrastructure" xml:lang="fr"><term>ADN</term>
<term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Amino Acid Sequence</term>
<term>Base Sequence</term>
<term>Binding Sites</term>
<term>Computer Simulation</term>
<term>Models, Chemical</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Protein Binding</term>
<term>Support Vector Machine</term>
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<term>Algorithmes</term>
<term>Analyse de séquence d'ADN</term>
<term>Cartographie d'interactions entre protéines</term>
<term>Données de séquences moléculaires</term>
<term>Facteurs de transcription</term>
<term>Liaison aux protéines</term>
<term>Machine à vecteur de support</term>
<term>Modèles chimiques</term>
<term>Modèles moléculaires</term>
<term>Simulation numérique</term>
<term>Sites de fixation</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology.</p>
</sec>
<sec><title>Results</title>
<p>Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in <italic>Saccharomyces cerevisiae </italic>
using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in <italic>S. cerevisiae </italic>
demonstrated the generality of our method.</p>
</sec>
<sec><title>Conclusion</title>
<p>We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify genetic parts to fine-tune gene expression rates is crucial to the design of biological systems, such a tool may play an important role in the success of synthetic biology going forward.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Endy, D" uniqKey="Endy D">D Endy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Purnick, Pem" uniqKey="Purnick P">PEM Purnick</name>
</author>
<author><name sortKey="Weiss, R" uniqKey="Weiss R">R Weiss</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kuwahara, H" uniqKey="Kuwahara H">H Kuwahara</name>
</author>
<author><name sortKey="Fan, M" uniqKey="Fan M">M Fan</name>
</author>
<author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name>
</author>
<author><name sortKey="Gao, X" uniqKey="Gao X">X Gao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Alberts, B" uniqKey="Alberts B">B Alberts</name>
</author>
<author><name sortKey="Johnson, A" uniqKey="Johnson A">A Johnson</name>
</author>
<author><name sortKey="Lewis, J" uniqKey="Lewis J">J Lewis</name>
</author>
<author><name sortKey="Raff, M" uniqKey="Raff M">M Raff</name>
</author>
<author><name sortKey="Roberts, K" uniqKey="Roberts K">K Roberts</name>
</author>
<author><name sortKey="Walter, P" uniqKey="Walter P">P Walter</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gottardo, R" uniqKey="Gottardo R">R Gottardo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Maerkl, Sj" uniqKey="Maerkl S">SJ Maerkl</name>
</author>
<author><name sortKey="Quake, Sr" uniqKey="Quake S">SR Quake</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fordyce, Pm" uniqKey="Fordyce P">PM Fordyce</name>
</author>
<author><name sortKey="Gerber, D" uniqKey="Gerber D">D Gerber</name>
</author>
<author><name sortKey="Tran, D" uniqKey="Tran D">D Tran</name>
</author>
<author><name sortKey="Zheng, J" uniqKey="Zheng J">J Zheng</name>
</author>
<author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Derisi, Jl" uniqKey="Derisi J">JL DeRisi</name>
</author>
<author><name sortKey="Quake, Sr" uniqKey="Quake S">SR Quake</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nutiu, R" uniqKey="Nutiu R">R Nutiu</name>
</author>
<author><name sortKey="Friedman, Rc" uniqKey="Friedman R">RC Friedman</name>
</author>
<author><name sortKey="Luo, S" uniqKey="Luo S">S Luo</name>
</author>
<author><name sortKey="Khrebtukova, I" uniqKey="Khrebtukova I">I Khrebtukova</name>
</author>
<author><name sortKey="Silva, D" uniqKey="Silva D">D Silva</name>
</author>
<author><name sortKey="Li, R" uniqKey="Li R">R Li</name>
</author>
<author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name>
</author>
<author><name sortKey="Schroth, Gp" uniqKey="Schroth G">GP Schroth</name>
</author>
<author><name sortKey="Burge, Cb" uniqKey="Burge C">CB Burge</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Alleyne, Tm" uniqKey="Alleyne T">TM Alleyne</name>
</author>
<author><name sortKey="Pe A Castillo, L" uniqKey="Pe A Castillo L">L Peña-Castillo</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
<author><name sortKey="Morris, Qd" uniqKey="Morris Q">QD Morris</name>
</author>
<author><name sortKey="Hughes, Tr" uniqKey="Hughes T">TR Hughes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weirauch, Mt" uniqKey="Weirauch M">MT Weirauch</name>
</author>
<author><name sortKey="Cote, A" uniqKey="Cote A">A Cote</name>
</author>
<author><name sortKey="Norel, R" uniqKey="Norel R">R Norel</name>
</author>
<author><name sortKey="Annala, M" uniqKey="Annala M">M Annala</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Riley, Tr" uniqKey="Riley T">TR Riley</name>
</author>
<author><name sortKey="Saez Rodriguez, J" uniqKey="Saez Rodriguez J">J Saez-Rodriguez</name>
</author>
<author><name sortKey="Cokelaer, T" uniqKey="Cokelaer T">T Cokelaer</name>
</author>
<author><name sortKey="Vedenko, A" uniqKey="Vedenko A">A Vedenko</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
<author><name sortKey="Dreamc" uniqKey="Dreamc">DREAMC</name>
</author>
<author><name sortKey="Bussemaker, Hj" uniqKey="Bussemaker H">HJ Bussemaker</name>
</author>
<author><name sortKey="Morris, Qd" uniqKey="Morris Q">QD Morris</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
<author><name sortKey="Stolovitzky, G" uniqKey="Stolovitzky G">G Stolovitzky</name>
</author>
<author><name sortKey="Hughes, Tr" uniqKey="Hughes T">TR Hughes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berg, Og" uniqKey="Berg O">OG Berg</name>
</author>
<author><name sortKey="Von Hippel, Ph" uniqKey="Von Hippel P">PH von Hippel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Benos, Pv" uniqKey="Benos P">PV Benos</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
<author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
<author><name sortKey="Johnson, Plf" uniqKey="Johnson P">PLF Johnson</name>
</author>
<author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</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="Foat, Bc" uniqKey="Foat B">BC Foat</name>
</author>
<author><name sortKey="Morozov, Av" uniqKey="Morozov A">AV Morozov</name>
</author>
<author><name sortKey="Bussemaker, Hj" uniqKey="Bussemaker H">HJ Bussemaker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
<author><name sortKey="Hughes, Tr" uniqKey="Hughes T">TR Hughes</name>
</author>
<author><name sortKey="Morris, Q" uniqKey="Morris Q">Q Morris</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Agius, P" uniqKey="Agius P">P Agius</name>
</author>
<author><name sortKey="Arvey, A" uniqKey="Arvey A">A Arvey</name>
</author>
<author><name sortKey="Chang, W" uniqKey="Chang W">W Chang</name>
</author>
<author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name>
</author>
<author><name sortKey="Leslie, C" uniqKey="Leslie C">C Leslie</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lee, D" uniqKey="Lee D">D Lee</name>
</author>
<author><name sortKey="Karchin, R" uniqKey="Karchin R">R Karchin</name>
</author>
<author><name sortKey="Beer, Ma" uniqKey="Beer M">MA Beer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Annala, M" uniqKey="Annala M">M Annala</name>
</author>
<author><name sortKey="Laurila, K" uniqKey="Laurila K">K Laurila</name>
</author>
<author><name sortKey="L Hdesm Ki, H" uniqKey="L Hdesm Ki H">H Lähdesmäki</name>
</author>
<author><name sortKey="Nykter, M" uniqKey="Nykter M">M Nykter</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vapnik, V" uniqKey="Vapnik V">V Vapnik</name>
</author>
<author><name sortKey="Chervonenkis, A" uniqKey="Chervonenkis A">A Chervonenkis</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jebara, T" uniqKey="Jebara T">T Jebara</name>
</author>
<author><name sortKey="Kondor, R" uniqKey="Kondor R">R Kondor</name>
</author>
<author><name sortKey="Howard, A" uniqKey="Howard A">A Howard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xie, B" uniqKey="Xie B">B Xie</name>
</author>
<author><name sortKey="Jankovic, Br" uniqKey="Jankovic B">BR Jankovic</name>
</author>
<author><name sortKey="Bajic, Vb" uniqKey="Bajic V">VB Bajic</name>
</author>
<author><name sortKey="Song, L" uniqKey="Song L">L Song</name>
</author>
<author><name sortKey="Gao, X" uniqKey="Gao X">X Gao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Leslie, C" uniqKey="Leslie C">C Leslie</name>
</author>
<author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name>
</author>
<author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="R Tsch, G" uniqKey="R Tsch G">G Rätsch</name>
</author>
<author><name sortKey="Sonnenburg, S" uniqKey="Sonnenburg S">S Sonnenburg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Leslie, Cs" uniqKey="Leslie C">CS Leslie</name>
</author>
<author><name sortKey="Eskin, E" uniqKey="Eskin E">E Eskin</name>
</author>
<author><name sortKey="Cohen, A" uniqKey="Cohen A">A Cohen</name>
</author>
<author><name sortKey="Weston, J" uniqKey="Weston J">J Weston</name>
</author>
<author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="R Tsch, G" uniqKey="R Tsch G">G Rätsch</name>
</author>
<author><name sortKey="Sonnenburg, S" uniqKey="Sonnenburg S">S Sonnenburg</name>
</author>
<author><name sortKey="Sch Lkopf, B" uniqKey="Sch Lkopf B">B Schälkopf</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mohapatra, A" uniqKey="Mohapatra A">A Mohapatra</name>
</author>
<author><name sortKey="Mishra, Pm" uniqKey="Mishra P">PM Mishra</name>
</author>
<author><name sortKey="Padhy, S" uniqKey="Padhy S">S Padhy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sonnenburg, S" uniqKey="Sonnenburg S">S Sonnenburg</name>
</author>
<author><name sortKey="Zien, A" uniqKey="Zien A">A Zien</name>
</author>
<author><name sortKey="Philips, P" uniqKey="Philips P">P Philips</name>
</author>
<author><name sortKey="R Tsch, G" uniqKey="R Tsch G">G Rätsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Natarajan, K" uniqKey="Natarajan K">K Natarajan</name>
</author>
<author><name sortKey="Meyer, Mr" uniqKey="Meyer M">MR Meyer</name>
</author>
<author><name sortKey="Jackson, Bm" uniqKey="Jackson B">BM Jackson</name>
</author>
<author><name sortKey="Slade, D" uniqKey="Slade D">D Slade</name>
</author>
<author><name sortKey="Roberts, C" uniqKey="Roberts C">C Roberts</name>
</author>
<author><name sortKey="Hinnebusch, Ag" uniqKey="Hinnebusch A">AG Hinnebusch</name>
</author>
<author><name sortKey="Marton, Mj" uniqKey="Marton M">MJ Marton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hope, Ia" uniqKey="Hope I">IA Hope</name>
</author>
<author><name sortKey="Struhl, K" uniqKey="Struhl K">K Struhl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hill, De" uniqKey="Hill D">DE Hill</name>
</author>
<author><name sortKey="Hope, Ia" uniqKey="Hope I">IA Hope</name>
</author>
<author><name sortKey="Macke, Jp" uniqKey="Macke J">JP Macke</name>
</author>
<author><name sortKey="Struhl, K" uniqKey="Struhl K">K Struhl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sellers, Jw" uniqKey="Sellers J">JW Sellers</name>
</author>
<author><name sortKey="Vincent, Ac" uniqKey="Vincent A">AC Vincent</name>
</author>
<author><name sortKey="Struhl, K" uniqKey="Struhl K">K Struhl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hinnebusch, Ag" uniqKey="Hinnebusch A">AG Hinnebusch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhu, C" uniqKey="Zhu C">C Zhu</name>
</author>
<author><name sortKey="Byers, Kjrp" uniqKey="Byers K">KJRP Byers</name>
</author>
<author><name sortKey="Mccord, Rp" uniqKey="Mccord R">RP McCord</name>
</author>
<author><name sortKey="Shi, Z" uniqKey="Shi Z">Z Shi</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Newburger, De" uniqKey="Newburger D">DE Newburger</name>
</author>
<author><name sortKey="Saulrieta, K" uniqKey="Saulrieta K">K Saulrieta</name>
</author>
<author><name sortKey="Smith, Z" uniqKey="Smith Z">Z Smith</name>
</author>
<author><name sortKey="Shah, Mv" uniqKey="Shah M">MV Shah</name>
</author>
<author><name sortKey="Radhakrishnan, M" uniqKey="Radhakrishnan M">M Radhakrishnan</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Hu, Y" uniqKey="Hu Y">Y Hu</name>
</author>
<author><name sortKey="De Masi, F" uniqKey="De Masi F">F De Masi</name>
</author>
<author><name sortKey="Pacek, M" uniqKey="Pacek M">M Pacek</name>
</author>
<author><name sortKey="Rolfs, A" uniqKey="Rolfs A">A Rolfs</name>
</author>
<author><name sortKey="Murthy, T" uniqKey="Murthy T">T Murthy</name>
</author>
<author><name sortKey="Labaer, J" uniqKey="Labaer J">J Labaer</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sonnenburg, S" uniqKey="Sonnenburg S">S Sonnenburg</name>
</author>
<author><name sortKey="Zien, A" uniqKey="Zien A">A Zien</name>
</author>
<author><name sortKey="R Tsch, G" uniqKey="R Tsch G">G Rätsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sonnenburg, S" uniqKey="Sonnenburg S">S Sonnenburg</name>
</author>
<author><name sortKey="Schweikert, G" uniqKey="Schweikert G">G Schweikert</name>
</author>
<author><name sortKey="Philips, P" uniqKey="Philips P">P Philips</name>
</author>
<author><name sortKey="Behr, J" uniqKey="Behr J">J Behr</name>
</author>
<author><name sortKey="R Tsch, G" uniqKey="R Tsch G">G Rätsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schweikert, G" uniqKey="Schweikert G">G Schweikert</name>
</author>
<author><name sortKey="Zien, A" uniqKey="Zien A">A Zien</name>
</author>
<author><name sortKey="Zeller, G" uniqKey="Zeller G">G Zeller</name>
</author>
<author><name sortKey="Behr, J" uniqKey="Behr J">J Behr</name>
</author>
<author><name sortKey="Dieterich, C" uniqKey="Dieterich C">C Dieterich</name>
</author>
<author><name sortKey="Ong, Cs" uniqKey="Ong C">CS Ong</name>
</author>
<author><name sortKey="Philips, P" uniqKey="Philips P">P Philips</name>
</author>
<author><name sortKey="De Bona, F" uniqKey="De Bona F">F De Bona</name>
</author>
<author><name sortKey="Hartmann, L" uniqKey="Hartmann L">L Hartmann</name>
</author>
<author><name sortKey="Bohlen, A" uniqKey="Bohlen A">A Bohlen</name>
</author>
<author><name sortKey="Kruger, N" uniqKey="Kruger N">N Krüger</name>
</author>
<author><name sortKey="Sonnenburg, S" uniqKey="Sonnenburg S">S Sonnenburg</name>
</author>
<author><name sortKey="R Tsch, G" uniqKey="R Tsch G">G Rätsch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Saeys, Y" uniqKey="Saeys Y">Y Saeys</name>
</author>
<author><name sortKey="Abeel, T" uniqKey="Abeel T">T Abeel</name>
</author>
<author><name sortKey="Degroeve, S" uniqKey="Degroeve S">S Degroeve</name>
</author>
<author><name sortKey="Van, Y De Peer" uniqKey="Van Y">Y de Peer Van</name>
</author>
</analytic>
</biblStruct>
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