Timothy R. Hughes

According to our database, Timothy R. Hughes authored at least 20 papers between 2002 and 2016.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2016

Motif comparison based on similarity of binding affinity profiles.

Samuel A. Lambert, Mihai Albu, Timothy R. Hughes, Hamed Shateri Najafabadi

Bioinform., 2016

2015

Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.

Hamed Shateri Najafabadi, Mihai Albu, Timothy R. Hughes

Bioinform., 2015

2013

A compendium of RNA-binding motifs for decoding gene regulation.

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

Nat., 2013

2012

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.

Carl G. de Boer, Timothy R. Hughes

Nucleic Acids Res., 2012

2011

RBPDB: a database of RNA-binding specificities.

Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, Timothy R. Hughes

Nucleic Acids Res., 2011

2010

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins.

Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris

PLoS Comput. Biol., 2010

Information propagation within the Genetic Network of Saccharomyces cerevisiae.

Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro

BMC Syst. Biol., 2010

FuncBase : a resource for quantitative gene function annotation.

John E. Beaver, Murat Tasan, Francis D. Gibbons, Weidong Tian, Timothy R. Hughes, Frederick P. Roth

Bioinform., 2010

2009

G+C content dominates intrinsic nucleosome occupancy.

Desiree Tillo, Timothy R. Hughes

BMC Bioinform., 2009

Predicting the binding preference of transcription factors to individual DNA <i>k</i>-mers.

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

Bioinform., 2009

Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization.

Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

A mixture model for the evolution of gene expression in non-homogeneous datasets.

Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris

Proceedings of the Advances in Neural Information Processing Systems 21, 2008

2007

Considerations in the identification of functional RNA structural elements in genomic alignments.

Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes

BMC Bioinform., 2007

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

Xiaoyu Chen, Timothy R. Hughes, Quaid Morris

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data.

Brendan J. Frey, Quaid Morris, Timothy R. Hughes

J. Comput. Biol., 2006

2005

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model.

Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes

Proceedings of the Research in Computational Molecular Biology, 2005

GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data.

Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes

Proceedings of the Biocomputing 2005, 2005

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data.

Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004

MyMed: A database system for biomedical research on MEDLINE data.

Kimberly N. Lewis, Mark D. Robinson, Timothy R. Hughes, Christopher W. V. Hogue

IBM Syst. J., 2004

2002

FunSpec: a web-based cluster interpreter for yeast.

Mark D. Robinson, Jörg Grigull, Naveed Mohammad, Timothy R. Hughes

BMC Bioinform., 2002