Todd Riley
Affiliations: | The Institute for Advanced Study | Princeton University, Princeton, NJ |
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The Institute for Advanced Study, Princeton, New Jersey, USA
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Publications
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| Farahmand S, Riley T, Zarringhalam K. (2019) ModEx: A text mining system for extracting mode of regulation of Transcription Factor-gene regulatory interaction. Journal of Biomedical Informatics. 103353 |
| Patalano S, Rodríguez-Nieves J, Colaneri C, et al. (2018) CXCL12/CXCR4-Mediated Procollagen Secretion Is Coupled To Cullin-RING Ubiquitin Ligase Activation. Scientific Reports. 8: 3499 |
| Riley TR, Lazarovici A, Mann RS, et al. (2015) Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE. Elife. 4 |
| Riley TR, Slattery M, Abe N, et al. (2014) SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods in Molecular Biology (Clifton, N.J.). 1196: 255-78 |
| Lazarovici A, Zhou T, Shafer A, et al. (2013) Probing DNA shape and methylation state on a genomic scale with DNase I. Proceedings of the National Academy of Sciences of the United States of America. 110: 6376-81 |
| Weirauch MT, Cote A, Norel R, et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34 |
| Tan AY, Riley TR, Coady T, et al. (2012) TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements. Proceedings of the National Academy of Sciences of the United States of America. 109: 6030-5 |
| Slattery M, Riley T, Liu P, et al. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 147: 1270-82 |
| Riley T, Yu X, Sontag E, et al. (2009) The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes. Bmc Bioinformatics. 10: 111 |
| Riley T, Sontag E, Chen P, et al. (2008) Transcriptional control of human p53-regulated genes. Nature Reviews. Molecular Cell Biology. 9: 402-12 |