T
Todd Riley
Researcher at University of Massachusetts Boston
Publications - 13
Citations - 3187
Todd Riley is an academic researcher from University of Massachusetts Boston. The author has contributed to research in topics: Regulation of gene expression & Gene. The author has an hindex of 10, co-authored 13 publications receiving 2925 citations. Previous affiliations of Todd Riley include Institute for Advanced Study & Columbia University.
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Journal ArticleDOI
Transcriptional control of human p53-regulated genes
TL;DR: The most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation is presented.
Journal ArticleDOI
Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins
Matthew Slattery,Todd Riley,Peng Liu,Peng Liu,Namiko Abe,Pilar Gomez-Alcala,Iris Dror,Tianyin Zhou,Remo Rohs,Barry Honig,Barry Honig,Harmen J. Bussemaker,Richard S. Mann +12 more
TL;DR: An experimental and computational platform that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex is developed, and it is shown that Drosophila Hox proteins obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax.
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Evaluation of methods for modeling transcription factor sequence specificity
Matthew T. Weirauch,Atina G. Cote,Raquel Norel,Matti Annala,Yue Zhao,Todd Riley,Julio Saez-Rodriguez,Thomas Cokelaer,Anastasia Vedenko,Shaheynoor Talukder,Harmen J. Bussemaker,Quaid Morris,Martha L. Bulyk,Gustavo Stolovitzky,Timothy P. Hughes +14 more
TL;DR: The results indicate that simple models based on mononucleotide position weight matrices trained by the best methods perform similarly to more complex models for most TFs examined, but fall short in specific cases.
Journal ArticleDOI
Probing DNA shape and methylation state on a genomic scale with DNase I
Allan Lazarovici,Tianyin Zhou,Anthony Shafer,Ana Carolina Dantas Machado,Todd Riley,Richard Sandstrom,Peter J. Sabo,Yan Lu,Remo Rohs,John A. Stamatoyannopoulos,Harmen J. Bussemaker +10 more
TL;DR: Analysis of millions of DNA backbone hydrolysis events on naked genomic DNA shows that the intrinsic rate of cleavage by DNase I closely tracks the width of the minor groove, and suggests a general mechanism by which CpG methylation can modulate protein–DNA interaction strength via the remodeling of DNA shape.
Journal ArticleDOI
TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements
TL;DR: The results indicate that TLS regulates expression of specific target genes, likely via recognition of specific single-stranded DNA sequences located within their promoter regions, and that purified TLS indeed binds these sequences with specificity in vitro.