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ORCIDTimothy R. Hughes
- > Home > Persons > Timothy R. Hughes
Publications
- 2016
[j14]Samuel A. Lambert
, Mihai Albu, Timothy R. Hughes, Hamed Shateri Najafabadi:
Motif comparison based on similarity of binding affinity profiles. Bioinform. 32(22): 3504-3506 (2016)- 2015
- [j13]Hamed Shateri Najafabadi, Mihai Albu, Timothy R. Hughes:
Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinform. 31(17): 2879-2881 (2015) - 2013
- [j12]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): 172-177 (2013) - 2011
- [j10]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): 301-308 (2011) - 2010
- [j9]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): 1806-1807 (2010) - [j7]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) - 2009
- [j6]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:
Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinform. 25(8): 1012-1018 (2009) - [c6]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: 545-548 - 2008
- [c5]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: 1297-1304 - 2007
- [j4]Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes:
Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinform. 8 (2007) - [c4]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: 72-79 - 2006
- [j3]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): 200-214 (2006) - 2005
- [c3]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: 222-231 - [c2]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 - [c1]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: 66-82 - 2004
- [j2]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): 756- (2004) - 2002
- [j1]Mark D. Robinson, Jörg Grigull, Naveed Mohammad, Timothy R. Hughes:
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinform. 3: 35 (2002)
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