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Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML. Berger MF, et al. Among authors: philippakis aa. Nat Biotechnol. 2006 Nov;24(11):1429-35. doi: 10.1038/nbt1246. Epub 2006 Sep 24. Nat Biotechnol. 2006. PMID: 16998473 Free PMC article.
High-resolution DNA-binding specificity analysis of yeast transcription factors.
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, Labaer J, Bulyk ML. Zhu C, et al. Among authors: philippakis aa. Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21. Genome Res. 2009. PMID: 19158363 Free PMC article.
Predicting the binding preference of transcription factors to individual DNA k-mers.
Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR. Alleyne TM, et al. Among authors: philippakis aa. Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16. Bioinformatics. 2009. PMID: 19088121 Free PMC article.
Design of compact, universal DNA microarrays for protein binding microarray experiments.
Philippakis AA, Qureshi AM, Berger MF, Bulyk ML. Philippakis AA, et al. J Comput Biol. 2008 Sep;15(7):655-65. doi: 10.1089/cmb.2007.0114. J Comput Biol. 2008. PMID: 18651798 Free PMC article.
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.
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, Hughes TR. Berger MF, et al. Among authors: philippakis aa. Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024. Cell. 2008. PMID: 18585359 Free PMC article.
Systematic identification of mammalian regulatory motifs' target genes and functions.
Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML. Warner JB, et al. Among authors: philippakis aa. Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2. Nat Methods. 2008. PMID: 18311145 Free PMC article.
Inferring condition-specific transcription factor function from DNA binding and gene expression data.
McCord RP, Berger MF, Philippakis AA, Bulyk ML. McCord RP, et al. Among authors: philippakis aa. Mol Syst Biol. 2007;3:100. doi: 10.1038/msb4100140. Epub 2007 Apr 17. Mol Syst Biol. 2007. PMID: 17437025 Free PMC article.
Modulefinder: a tool for computational discovery of cis regulatory modules.
Philippakis AA, He FS, Bulyk ML. Philippakis AA, et al. Pac Symp Biocomput. 2005:519-30. Pac Symp Biocomput. 2005. PMID: 15759656 Free PMC article.
Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.
Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, Michelson AM, Bulyk ML. Philippakis AA, et al. PLoS Comput Biol. 2006 May;2(5):e53. doi: 10.1371/journal.pcbi.0020053. Epub 2006 May 26. PLoS Comput Biol. 2006. PMID: 16733548 Free PMC article.
A framework for variation discovery and genotyping using next-generation DNA sequencing data.
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. DePristo MA, et al. Among authors: philippakis aa. Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10. Nat Genet. 2011. PMID: 21478889 Free PMC article.
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