Amanda Kedaigle, Ph.D.

Year of Graduation: 

2018

Advisors/Lab: 

Prof. Ernest Fraenkel

Current Position: 

Computational Biology I, Broad Institute, Cambridge, MA

Thesis Title: Intergrating Omics Data: A New Software Tool and its Use in Implicating Therapeutic Targets in Huntington's Disease

 

Publications while at MIT: 

 

1.Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice.

Kedaigle AJ, Reidling JC, Lim RG, Adam M, Wu J, Wassie B, Stocksdale JT, Casale MS, Fraenkel E, Thompson LM.Hum Mol Genet. 2020 Jan 15;29(2):202-215. doi: 10.1093/hmg/ddz264.PMID: 31696228

 

2. Bioenergetic deficits in Huntington's disease iPSC-derived neural cells and rescue with glycolytic metabolites.

HD iPSC Consortium.Hum Mol Genet. 2020 Jul 21;29(11):1757-1771. doi: 10.1093/hmg/ddy430.PMID: 30768179 Free PMC article.

 

3. Turning omics data into therapeutic insights.

Kedaigle A, Fraenkel E.Curr Opin Pharmacol. 2018 Oct;42:95-101. doi: 10.1016/j.coph.2018.08.006. Epub 2018 Aug 24.PMID: 30149217 Free PMC article. Review.

 

4. Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data.

Kedaigle AJ, Fraenkel E.Methods Mol Biol. 2018;1711:13-26. doi: 10.1007/978-1-4939-7493-1_2.PMID: 29344883 Free PMC article.

 

5. PCSF: An R-package for network-based interpretation of high-throughput data.

Akhmedov M, Kedaigle A, Chong RE, Montemanni R, Bertoni F, Fraenkel E, Kwee I.PLoS Comput Biol. 2017 Jul 31;13(7):e1005694. doi: 10.1371/journal.pcbi.1005694. eCollection 2017 Jul.PMID: 28759592 Free PMC article.

 

6. Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits.

Lim RG, Quan C, Reyes-Ortiz AM, Lutz SE, Kedaigle AJ, Gipson TA, Wu J, Vatine GD, Stocksdale J, Casale MS, Svendsen CN, Fraenkel E, Housman DE, Agalliu D, Thompson LM.Cell Rep. 2017 May 16;19(7):1365-1377. doi: 10.1016/j.celrep.2017.04.021.PMID: 28514657 Free PMC article.

 

7. Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice.

HD iPSC Consortium.Nat Neurosci. 2017 May;20(5):648-660. doi: 10.1038/nn.4532. Epub 2017 Mar 20.PMID: 28319609 Free PMC article.

 

8. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.

Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E.PLoS Comput Biol. 2016 Apr 20;12(4):e1004879. doi: 10.1371/journal.pcbi.1004879. eCollection 2016 Apr.PMID: 27096930 Free PMC article.