Andrew D Smith

phone: (516) 367-8395
fax: (516) 367-8461

Brief Bio

I am a postdoc in Michael Zhang's group at Cold Spring Harbor Laboratory. From 2000 until 2004 I completed my PhD at Faculty of Computer Science, University of New Brunswick. My PhD supervisor was Patricia Evans. The topic of my doctoral dissertation was algorithms and complexity analysis for certain problems of approximate pattern discovery in strings. During 2002 and 2003 I also worked in Elisabeth Tillier's lab at the Ontario Cancer Institute. I attended UNB as an undergrad from 1995 to 2000, completing a BA (major in psychology) and a BCS (Bachelor of Computer Science).

Research Interests

Bioinformatics Software and Resources


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]

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