Timothy R. Hughes

20 papers B 1Misc 2Journal 14Unranked 3
YearRankTypeTitle / Venue / Authors
2016 J jnl
Motif comparison based on similarity of binding affinity profiles.
Bioinform.
Samuel A. Lambert, Mihai Albu, Timothy R. Hughes, Hamed Shateri Najafabadi
2015 J jnl
Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.
Bioinform.
Hamed Shateri Najafabadi, Mihai Albu, Timothy R. Hughes
2013 J jnl
A compendium of RNA-binding motifs for decoding gene regulation.
Nat.
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
2012 J jnl
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.
Nucleic Acids Res.
Carl G. de Boer, Timothy R. Hughes
2011 J jnl
RBPDB: a database of RNA-binding specificities.
Nucleic Acids Res.
Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, Timothy R. Hughes
2010 J jnl
FuncBase : a resource for quantitative gene function annotation.
Bioinform.
John E. Beaver, Murat Tasan, Francis D. Gibbons, Weidong Tian, Timothy R. Hughes, Frederick P. Roth
2010 J jnl
Information propagation within the Genetic Network of Saccharomyces cerevisiae.
BMC Syst. Biol.
Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro
2010 J jnl
RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins.
PLoS Comput. Biol.
Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris
2009 J jnl
G+C content dominates intrinsic nucleosome occupancy.
BMC Bioinform.
Desiree Tillo, Timothy R. Hughes
2009 Misc conf
Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization.
Pacific Symposium on Biocomputing
Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris
2009 J jnl
Predicting the binding preference of transcription factors to individual DNA
Bioinform.
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
2008 — conf
A mixture model for the evolution of gene expression in non-homogeneous datasets.
NIPS
Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris
2007 J jnl
Considerations in the identification of functional RNA structural elements in genomic alignments.
BMC Bioinform.
Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes
2007 — conf
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.
ISMB/ECCB (Supplement of Bioinformatics)
Xiaoyu Chen, Timothy R. Hughes, Quaid Morris
2006 J jnl
GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data.
J. Comput. Biol.
Brendan J. Frey, Quaid Morris, Timothy R. Hughes
2005 B conf
Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model.
RECOMB
Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes
2005 Misc conf
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data.
Pacific Symposium on Biocomputing
Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes
2005 — conf
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data.
ISMB (Supplement of Bioinformatics)
Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey
2004 J jnl
MyMed: A database system for biomedical research on MEDLINE data.
IBM Syst. J.
Kimberly N. Lewis, Mark D. Robinson, Timothy R. Hughes, Christopher W. V. Hogue
2002 J jnl
FunSpec: a web-based cluster interpreter for yeast.
BMC Bioinform.
Mark D. Robinson, Jörg Grigull, Naveed Mohammad, Timothy R. Hughes