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Timothy R. Hughes
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2010 – 2019
- 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
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
A compendium of RNA-binding motifs for decoding gene regulation. Nat. 499(7457): 172-177 (2013) - 2012
- [j11]Carl G. de Boer
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res. 40(Database-Issue): 169-179 (2012) - 2011
- [j10]Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris
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) - [j8]Sharif Chowdhury, Jason Lloyd-Price
Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst. Biol. 4: 143 (2010) - [j7]Hilal Kazan, Debashish Ray, Esther T. Chan
RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. PLoS Comput. Biol. 6(7) (2010)
2000 – 2009
- 2009
- [j6]Trevis M. Alleyne, Lourdes Peña Castillo
Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinform. 25(8): 1012-1018 (2009) - [j5]Desiree Tillo, Timothy R. Hughes:
G+C content dominates intrinsic nucleosome occupancy. BMC Bioinform. 10: 442 (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
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
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
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
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinform. 3: 35 (2002)
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