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Hodges, E., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (September 2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., Xavier, R. J. (August 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.

Niida, A., Smith, A. D., Imoto, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (February 2009) Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics, 10. p. 71. ISSN 1471-2105

Niida, A., Smith, A. D., Imoto, S., Tsutsumi, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (September 2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics, 9. p. 404.

Smith, A. D., Xuan, Z. Y., Zhang, M. Q. (February 2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. Bmc Bioinformatics, 9 (128). ISSN 1471-2105

Kim, T. H., Abdullaev, Z. K., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., Ren, B. (March 2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 128 (6). pp. 1231-1245. ISSN 0092-8674

Martinez, M. J., Smith, A. D., Li, B. L., Zhang, M. Q., Harrod, K. S. (January 2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics, 23 (1). pp. 21-29. ISSN 1367-4803

Schones, D. E., Smith, A. D., Zhang, M. Q. (January 2007) Statistical significance of cis-regulatory modules. Bmc Bioinformatics, 8. p. 16. ISSN 1471-2105

Smith, A. D., Sumazin, P., Zhang, M. Q. (January 2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

Smith, A. D., Sumazin, P., Xuan, Z., Zhang, M. Q. (April 2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A, 103 (16). pp. 6275-80. ISSN 0027-8424 (Print)

Pang, A., Smith, A. D., Nuin, P. A. S., Tillier, E. R. (September 2005) SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics, 6. ISSN 1471-2105

Smith, A. D., Sumazin, P., Das, D., Zhang, M. Q. (June 2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics, 21 Sup. i403-12. ISSN 1367-4803 (Print)

Smith, A. D., Sumazin, P., Zhang, M. Q. (February 2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A, 102 (5). pp. 1560-5. ISSN 0027-8424 (Print)

Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (January 2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)