Allegra A. Petti, Ph.D.,  McDonnell Genome Institute

Dr. Petti joined the McDonnell Genome Institute in 2013. Her research has focused on understanding the relationship between molecular networks and the phenotypes to which they give rise. She has employed both experimental and computational techniques to investigate how the organization and function of transcriptional, metabolic, and signal transduction networks contribute to normal physiology and disease in yeast and humans. Her current work focuses on the genomics and subclonal evolution of acute myeloid leukemia, and on cancer immunotherapy.

Current research interests include:

  1. Genomics and subclonal evolution of cancer
  2. Identification of tumor-specific neo-epitopes for use in anti-tumor vaccines
  3. Gene regulatory networks in human health and disease
  4. Interaction of gene regulatory and metabolic networks
  5. Contribution of non-coding variation to the development of cancer

Dr. Petti received a B.A. in Biology from Rice University, and a Ph.D. in Genetics from Harvard Medical School. She conducted her postdoctoral research at Princeton University’s Lewis Sigler Institute for Integrative Genomics. Prior to joining MGI, she was a Research Associate/Assistant Professor in the Department of Human Genetics at the University of Chicago.


1. Ceriani, M.F., Darlington, T.K., Staknis, D., Mas, P., Petti, A.A., Weitz, C.J., Kay, S.A. (1999) Light-dependent sequestration of TIMELESS by CRYPTOCHROME. Science, 285(5427): 553-6. PMID: 10417378.
2. Steffen, M., Petti, A., Aach, J., D'haeseleer, P., and Church, G. (2002) Automated modelling of signal transduction networks. BMC Bioinformatics, 3(1): 34-44. PMID: 12413400.
3. Petti, A.A., and Church, G.M. (2005) A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Research, 15(9): 1298. PMID: 16109970.
4. Silverman, S.J., Petti, A.A., Slavov, N.*, Parsons, L., Briehof, R., Thiberge, S.Y., Zenklusen, D., Gandhi, S.J., Larson, D.R., Singer, R.H., Botstein, D. (2010) Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate. Proc. Natl. Acad. Sci., 107(15): 6946-51. PMID: 20335538.
5. Petti, A.A., Crutchfield, C.A., Rabinowitz, J., and Botstein, D. (2011) Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc. Natl. Acad. Sci. Plus., 108(45): E1089-98. PMID: 21734149.
6. Hickman, M.J., Petti, A.A. (co-first authors), Ho-Shing, O., Silverman, S.J., McIsaac, R.S., Lee, T.A., Botstein, D. (2011) Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast. Mol. Biol. Cell., 22(21): 4192-204. PMID: 21900497.
7. McIsaac, R.S., Silverman, S.J., McClean, M.N., Gibney, P.A., Macinskas, J., Hickman, M.J., Petti, A., Botstein, D. (2011) Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Mol. Biol. Cell., 22(22): 4447-59. PMID: 21965290.
8. McIsaac, R.S., Petti, A.A., Bussemaker, H., Botstein D. (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol. Biol. Cell., 23(15): 2993-07. PMID: 22696683.
9. Petti, A.A., McIsaac, R.S., Ho-Shing, O.*, Bussemaker, H., Botstein, D. (2012) Combinatorial Control of Diverse Metabolic and Physiological Functions by Transcriptional Regulators of the Yeast Sulfur Assimilation Pathway. Mol. Biol. Cell., 23(15):3008-24. PMID: 22696679.
10. Stewart C.R., Deery W.J., Egan E.S., Myles B., Petti A.A. (2013) The product of SPO1 gene 56 inhibits host cell division during infection of Bacillus subtilis by bacteriophage SPO1. Virology, 447(1-2): 249-53. PMID: 24210121.
11. Carreno B.M., Magrini V., Becker-Hapak M., Kaabinejadian S., Hundal J., Petti A.A., Ly A., Lie W.R., Hildebrand W.H., Mardis E.R., Linette G. (2015) A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science, Apr 2. pii: aaa3828. [Epub ahead of print]. PMID: 25837513.


title citation publication date
Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies. J Clin Invest. 2017 Oct 2;127(10):3657-3674. doi: 10.1172/JCI93041. Epub 2017 Sep 5. 2017-10-02
Breast Cancer Neoantigens Can Induce CD8+ T-Cell Responses and Antitumor Immunity. Cancer Immunol Res. 2017 Jul;5(7):516-523. doi: 10.1158/2326-6066.CIR-16-0264. Epub 2017 Jun 15. 1970-08-22
Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy. Blood. 2017 Mar 9;129(10):1397-1401. doi: 10.1182/blood-2016-10-745273. Epub 2017 Jan 12.
Decitabine in TP53-Mutated AML. N Engl J Med. 2017 Feb 23;376(8):797-8. doi: 10.1056/NEJMc1616062. 2017-02-23
TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes. N Engl J Med. 2016 Nov 24;375(21):2023-2036. 1970-08-22
RNA splicing is a primary link between genetic variation and disease Science. 2016 Apr 29;352(6285):600-4. doi: 10.1126/science.aad9417. Epub 2016 Apr 28. 2016-04-29
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med. 2016 Jan 29;8(1):11. doi: 10.1186/s13073-016-0264-5. 2016-01-29
Rapid expansion of pre-existing non-leukemic hematopoietic clones frequently follows induction therapy for de novo AML. Blood. 2015 Dec 2. pii: blood-2015-10-677021. [Epub ahead of print] 2015-12-02
Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA. 2015 Aug 25;314(8):811-22. doi: 10.1001/jama.2015.9643. 2015-08-25
A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science. 2015 Apr 2. pii: aaa3828. [Epub ahead of print] 2015-04-02