FunSpec: a web-based cluster interpreter for yeast. - Mark D. Robinson; Jörg Grigull; Naveed Mohammad; Timothy R. Hughes (BMC Bioinform., 2002)

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)

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 (ISMB (Supplement of Bioinformatics), 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 (Pacific Symposium on Biocomputing, 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 (RECOMB, 2005)

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)

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. - Xiaoyu Chen; Timothy R. Hughes; Quaid Morris (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Considerations in the identification of functional RNA structural elements in genomic alignments. - Tomas Babak; Benjamin J. Blencowe; Timothy R. Hughes (BMC Bioinform., 2007)

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 (NIPS, 2008)

Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. - Benjamin J. Blencowe; Steven E. Brenner; Timothy R. Hughes; Quaid Morris (Pacific Symposium on Biocomputing, 2009)

Predicting the binding preference of transcription factors to individual DNA k-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)

G+C content dominates intrinsic nucleosome occupancy. - Desiree Tillo; Timothy R. Hughes (BMC Bioinform., 2009)

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)

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)

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)

RBPDB: a database of RNA-binding specificities. - Kate B. Cook; Hilal Kazan; Khalid Zuberi; Quaid Morris; Timothy R. Hughes (Nucleic Acids Res., 2011)

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. - Carl G. de Boer; Timothy R. Hughes (Nucleic Acids Res., 2012)

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; et al. (Nat., 2013)

Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. - Hamed Shateri Najafabadi; Mihai Albu; Timothy R. Hughes (Bioinform., 2015)

Motif comparison based on similarity of binding affinity profiles. - Samuel A. Lambert; Mihai Albu; Timothy R. Hughes; Hamed Shateri Najafabadi (Bioinform., 2016)