Timothy R. Hughes

Publication Activity (10 Years)

Years Active: 2002-2016
Publications (10 Years): 2

Top Topics

Component Analysis

Gene Regulation

Transcription Factors

Top Venues

Nucleic Acids Res.

Publications

Samuel A. Lambert, Mihai Albu, Timothy R. Hughes, Hamed Shateri Najafabadi
Motif comparison based on similarity of binding affinity profiles. Bioinform. 32 (22) (2016)
Hamed Shateri Najafabadi, Mihai Albu, Timothy R. Hughes
Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinform. 31 (17) (2015)
Debashish Ray, Hilal Kazan, Kate B. Cook, Matthew T. Weirauch, Hamed S. Najafabadi, Xiao Li, Serge Gueroussov, Mihai Albu, Hong Zheng, Ally Yang, Hong Na, Manuel Irimia, Leah H. Matzat, Ryan K. Dale, Sarah A. Smith, Christopher A. Yarosh, Seth M. Kelly, Behnam Nabet, Desirea Mecenas, Weimin Li, Rakesh S. Laishram, Mei Qiao, Howard D. Lipshitz, Fabio Piano, Anita H. Corbett, Russ P. Carstens, Brendan J. Frey, Richard A. Anderson, Kristen W. Lynch, Luiz O. F. Penalva, Elissa P. Lei, Andrew G. Fraser, Benjamin J. Blencowe, Quaid Morris, Timothy R. Hughes
A compendium of RNA-binding motifs for decoding gene regulation. Nat. 499 (7457) (2013)
Carl G. de Boer, Timothy R. Hughes
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res. 40 (Database-Issue) (2012)
Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, Timothy R. Hughes
RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 39 (Database-Issue) (2011)
Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro
Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst. Biol. 4 (2010)
John E. Beaver, Murat Tasan, Francis D. Gibbons, Weidong Tian, Timothy R. Hughes, Frederick P. Roth
FuncBase : a resource for quantitative gene function annotation. Bioinform. 26 (14) (2010)
Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris
RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. PLoS Comput. Biol. 6 (7) (2010)
Desiree Tillo, Timothy R. Hughes
G+C content dominates intrinsic nucleosome occupancy. BMC Bioinform. 10 (2009)
Trevis M. Alleyne, Lourdes Peña Castillo, Gwenael Badis, Shaheynoor Talukder, Michael F. Berger, Andrew R. Gehrke, Anthony A. Philippakis, Martha L. Bulyk, Quaid Morris, Timothy R. Hughes
-mers. Bioinform. 25 (8) (2009)
Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris
Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. Pacific Symposium on Biocomputing (2009)
Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris
A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS (2008)
Xiaoyu Chen, Timothy R. Hughes, Quaid Morris
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes
Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinform. 8 (2007)
Brendan J. Frey, Quaid Morris, Timothy R. Hughes
GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. J. Comput. Biol. 13 (2) (2006)
Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. Pacific Symposium on Biocomputing (2005)
Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes
Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. RECOMB (2005)
Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. ISMB (Supplement of Bioinformatics) (2005)
Kimberly N. Lewis, Mark D. Robinson, Timothy R. Hughes, Christopher W. V. Hogue
MyMed: A database system for biomedical research on MEDLINE data. IBM Syst. J. 43 (4) (2004)
Mark D. Robinson, Jörg Grigull, Naveed Mohammad, Timothy R. Hughes
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinform. 3 (2002)