Papers authored by Philippakis AA

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Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo.
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Enriquez J, Boukhatmi H, Dubois L, Philippakis AA, Bulyk ML, Michelson AM, Crozatier M, and Vincent A
Development (Cambridge, England) 137(3):457-66, 2010 Feb - Who cited this? | PubMed ID: 20056681 | Fulltext
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Diversity and complexity in DNA recognition by transcription factors.
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Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, 
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Science (New York, N.Y.) 324(5935):1720-3, 2009 Jun 26 - Who cited this? | PubMed ID: 19443739 | Fulltext
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Predicting the binding preference of transcription factors to individual DNA k-mers.
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Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, and Hughes TR
Bioinformatics (Oxford, England) 25(8):1012-8, 2009 Apr 15 - Who cited this? | PubMed ID: 19088121 | Fulltext
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High-resolution DNA-binding specificity analysis of yeast transcription factors.
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Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, 
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Genome research 19(4):556-66, 2009 Apr - Who cited this? | PubMed ID: 19158363 | Fulltext
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Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments.
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Philippakis AA, Qureshi AM, Berger MF, and Bulyk ML
Journal of computational biology : a journal of computational molecular cell biology, 2008 Jul 23 - Who cited this? | PubMed ID: 18651798 | Fulltext
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Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.
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Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, 
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Cell 133(7):1266, 2008 Jun 27 - Who cited this? | PubMed ID: 18585359 | Fulltext
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Systematic identification of mammalian regulatory motifs' target genes and functions.
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Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, and Bulyk ML
Nature methods 5(4):347-53, 2008 Apr - Who cited this? | PubMed ID: 18311145 | Fulltext
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Inferring condition-specific transcription factor function from DNA binding and gene expression data.
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McCord RP, Berger MF, Philippakis AA, and Bulyk ML
Molecular systems biology 3:100, 2007 - Who cited this? | PubMed ID: 17437025 | Fulltext
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Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
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Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, and Bulyk ML
Nature biotechnology 24(11):1429-35, 2006 Nov - Who cited this? | PubMed ID: 16998473 | Fulltext
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Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.
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Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, Michelson AM, and Bulyk ML
PLoS computational biology 2(5):e53, 2006 May - Who cited this? | PubMed ID: 16733548 | Fulltext
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Modulefinder: a tool for computational discovery of cis regulatory modules.
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Philippakis AA, He FS, and Bulyk ML
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:519-30, 2005 - Who cited this? | PubMed ID: 15759656 | Fulltext
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