Genomics • epigenetics • bionformatics • gene regulation • cancer
The overarching goal of my research program is to improve the survival of patients with cancers of the stomach and esophagus. We are focused on understanding the role of coding and non-coding somatic mutations together with alterations to the chromatin landscape in the progression of these cancers to metastasis. In addition, we are developing bioinformatic approaches to interpret the function of non-coding genomic alterations to regulatory elements in cancer initiation and progression.
Mehdi T, Bailey SD, Guilhamon P, Lupien M. C3D: a tool to predict 3D genomic interactions between cis-regulatory elements. Bioinformatics. 2018. (in press).
Bailey SD, Desai K, Kron KJ, Mazrooei P, Sinnott-Armstrong NA, Treloar AE, et al. Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer. Nat Genet. 2016;48(10):1260-6. PMID: 27571262.
Bailey SD, Virtanen C, Haibe-Kains B, Lupien M. ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. Bioinformatics. 2015;31(18):3057-9. PMID: 25995231.
Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, et al. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun. 2015;2:6186. PMID: 25645053.
Zhang X, Bailey SD, Lupien M. Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'. Trends Genet. 2014;30(4):140-9. PMID: 24661571.