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Transcriptional control of human p53-regulated genes.
Riley T, Sontag E, Chen P, Levine A. Riley T, et al. Nat Rev Mol Cell Biol. 2008 May;9(5):402-12. doi: 10.1038/nrm2395. Nat Rev Mol Cell Biol. 2008. PMID: 18431400 Review.
The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes.
Riley T, Yu X, Sontag E, Levine A. Riley T, et al. BMC Bioinformatics. 2009 Apr 20;10:111. doi: 10.1186/1471-2105-10-111. BMC Bioinformatics. 2009. PMID: 19379484 Free PMC article.
The regulation of the endosomal compartment by p53 the tumor suppressor gene.
Yu X, Riley T, Levine AJ. Yu X, et al. Among authors: riley t. FEBS J. 2009 Apr;276(8):2201-12. doi: 10.1111/j.1742-4658.2009.06949.x. Epub 2009 Mar 3. FEBS J. 2009. PMID: 19302216
Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.
Riley TR, Lazarovici A, Mann RS, Bussemaker HJ. Riley TR, et al. Elife. 2015 Dec 23;4:e06397. doi: 10.7554/eLife.06397. Elife. 2015. PMID: 26701911 Free PMC article.
Evaluation of methods for modeling transcription factor sequence specificity.
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Weirauch MT, et al. Among authors: riley tr. Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27. Nat Biotechnol. 2013. PMID: 23354101 Free PMC article.
SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.
Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ. Riley TR, et al. Methods Mol Biol. 2014;1196:255-78. doi: 10.1007/978-1-4939-1242-1_16. Methods Mol Biol. 2014. PMID: 25151169 Free PMC article.
Probing DNA shape and methylation state on a genomic scale with DNase I.
Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ. Lazarovici A, et al. Among authors: riley tr. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6376-81. doi: 10.1073/pnas.1216822110. Epub 2013 Apr 1. Proc Natl Acad Sci U S A. 2013. PMID: 23576721 Free PMC article.
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Slattery M, et al. Among authors: riley t. Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053. Cell. 2011. PMID: 22153072 Free PMC article.
TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements.
Tan AY, Riley TR, Coady T, Bussemaker HJ, Manley JL. Tan AY, et al. Among authors: riley tr. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6030-5. doi: 10.1073/pnas.1203028109. Epub 2012 Mar 29. Proc Natl Acad Sci U S A. 2012. PMID: 22460799 Free PMC article.
CXCL12/CXCR4-Mediated Procollagen Secretion Is Coupled To Cullin-RING Ubiquitin Ligase Activation.
Patalano S, Rodríguez-Nieves J, Colaneri C, Cotellessa J, Almanza D, Zhilin-Roth A, Riley T, Macoska J. Patalano S, et al. Among authors: riley t. Sci Rep. 2018 Feb 22;8(1):3499. doi: 10.1038/s41598-018-21506-7. Sci Rep. 2018. PMID: 29472636 Free PMC article.
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