Publications
Riley, T. R., M. Slattery, R. S. Mann, H. J. Bussemaker. "Building accurate sequence-to-affinity models from high-throughput protein-DNA binding data using FeatureREDUCE." Manuscript in preparation.
Gomez-Alcala, P.*, T. R. Riley*, I. Mann, T. R. Hughes, H. J. Bussemaker. "Deciphering the specificity differences within the bHLH transcription factor family." Manuscript in preparation.
Riley, T. R., J. Vanicek, G. Atwal, M. Krasnitz, E. Sontag, A. J. Levine. "PURE: a motif finding algorithm that discovers regulatory sequence Patterns Using Relative Entropy." Manuscript in preparation.
Lazarovici, A., T. Zhou*, A. Shafer*, A. C. D. Machado*, T. R. Riley, R. Sandstrom, P. J. Sabo, Y. Lu, R. Rohs, J. A. Stamatoyannopoulos, H. J. Bussemaker. "Probing DNA shape and methylation state on a genomic scale with DNase I." Proc Natl Acad Sci USA In Press.
Weirauch, M., A. Cote1, R. Norel, M. Annala, Y. Zhao, T. R. Riley, J. Saez-Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, DREAM5 consortium, H. J. Bussemaker, Q. D. Morris, M. L. Bulyk, G. Stolovitzky, T. R. Hughes. "Evaluation of methods for modeling transcription factor sequence specificity." Nature Biotech 31(2): 126-134. PDF
Tan, A. Y., T. R. Riley, T. Coady, H. J. Bussemaker, J. L. Manley. (2012). "TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements." Proc Natl Acad Sci USA 109(16): 6030-6035. PMCID: PMC3341064 PDF
Slattery, M.*, T. Riley*, P. Liu*, N. Abe, P. Gomez-Alcala, I. Dror, T. Zhou, R. Rohs, B. Honig, H. J. Bussemaker, R. S. Mann. (2011). "Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins." Cell 147(6): 1270-1282. PMCID: PMC3319069 PDF
Riley, T., X. Yu, E. Sontag, A. J. Levine. (2009). "The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes." BMC Bioinformatics 10: 111. PMCID: PMC2685388 PDF
Yu, X., T. Riley, A. J. Levine. (2009). "The regulation of the endosomal compartment by p53 the tumor suppressor gene." FEBS J 276(8): 2201-2212. PMCID: PMC19302216 PDF
Riley, T., E. Sontag, P. Chen, A. J. Levine. (2008). "Transcriptional control of human p53-regulated genes." Nat Rev Mol Cell Biol 9(5): 402-412. PMCID: PMC18431400 PDF
* Authors contributed equally