Publications

Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z and Zhang MQ (2009)
Updates to the RMAP short-read mapping software.
Bioinformatics, 25(21):2841-2842. [PDF] [Publisher Site]

Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie RW, Wigler M, Hannon GJ and Hicks JB (2009)
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.
Genome Research, 19:1593-1605. [PDF] [Publisher Site]
This article was profiled in the EpiGenie Newsletter.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC and Xavier RJ (2009)
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.
Nucleic Acids Res., 37(14):4587-4602. [PDF] [Publisher Site]

Niida A, Smith AD, Imoto S, Aburatani H, Zhang MQ and Akiyama T (2009)
Gene set-based module discovery in the breast cancer transcriptome.
BMC Bioinformatics, 10:71. [PDF] [Publisher Site]

Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ and Akiyama T (2008)
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
BMC Bioinformatics, 9:404. [PDF] [Publisher Site]

Smith AD, Xuan Z and Zhang MQ (2008)
Using quality scores and longer reads improves accuracy of Solexa read mapping.
BMC Bioinformatics, 9:128. [PDF] [Publisher Site]

Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD and Ren B (2008)
Genome-wide mapping and analysis of active promoters in mouse embryonic
stem cells and adult organs.
Genome Research, 18:46-59. [PDF] [Publisher Site]

Kim TH, Abdullaev Z, Smith AD, Ching KA, Loukinow D, Green RD, Zhang MQ,
Lobanenkov V and Ren B (2007)
Analysis of the vertebrate insulator protein CTCF binding sites in the human genome.
Cell, 128:1231-1245. [PDF] [Publisher Site]

Schones DE, Smith AD and Zhang MQ (2007)
Statistical significance of cis-regulatory modules.
BMC Bioinformatics, 8:19. [PDF] [Publisher Site]

Smith AD, Sumazin P and Zhang MQ (2007)
Tissue-specific regulatory elements in mammalian promoters.
Molecular Systems Biology, 3:73. [PDF] [Publisher Site]

Martinez MJ, Smith AD, Li B, Zhang MQ and Harrod KS (2007)
Computational prediction of novel components of lung transcriptional networks.
Bioinformatics, 23:21-29. [PDF] [Publisher Site]

Smith AD, Sumazin P, Xuan Z and Zhang MQ (2006)
DNA motifs in human and mouse proximal promoters predict tissue specific expression.
PNAS, 103(16):6275-6280. [PDF] [Publisher Site]

Smith AD, Sumazin P, Das D and Zhang MQ (2005)
Mining ChIP-chip data for transcription factor and cofactor binding sites.
Bioinformatics, 21(Suppl 1):i403-i412. [PDF] [Publisher Site]
Presented at the 13th International Conference on Intelligent Systems
for Molecular Biology (ISMB), Detroit, MI, 2005.

Smith AD, Sumazin P and Zhang MQ (2005)
Identifying tissue-specific transcription factor binding sites in vertebrate promoters.
PNAS, 102(5):1560-1565 [PDF] [Publisher Site]
This article was highlighted in Nature Reviews Genetics

Sumazin P, Chen G, Hata N, Smith AD, Zhang T and Zhang MQ (2005)
DWE: Discriminating Word Enumerator.
Bioinformatics 21(1):31-38. [PDF] [Publisher Site]

Pang A, Smith AD, Nuin PAS and Tillier ERM (2005)
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution.
BMC Bioinformatics, 6:236. [PDF] [Publisher Site]

Smith AD, Lui TWH and Tillier ERM (2004)
Empirical models for substitution in ribosomal RNA.
Molecular Biology and Evolution, 21(3):419-427. [PDF] [Publisher Site]

Veerassamy S, Smith A and Tillier ERM (2003)
A transition probability model for amino acid substitutions from BLOCKS.
Journal of Computational Biology, 10(6): 997-1010 [PDF] [Publisher Site]

Evans PA and Smith AD (2003)
Complexity of approximating closest substring problems.
Proceedings of the 14th International Symposium on Fundamentals of Computation Theory (FCT),
LNCS 2751: 210-221 [PDF] [Publisher Site]

Evans PA and Smith AD (2003)
Toward optimal motif enumeration.
Proceedings of the 8th International Workshop on Algorithms And Data Structures (WADS),
LNCS 2748: 47-58 [PDF] [Publisher Site]

Evans PA, Smith AD and Wareham HT (2003)
On the complexity of finding common approximate substrings.
Theoretical Computer Science, 306(1-3): 407-430 [PDF] [Publisher Site]