Orly Alter, Ph.D.

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https://orcid.org/0000-0002-0418-1078
https://scholar.google.com/citations?user=RKh11ecAAAAJ&hl=en

Orly Alter is a Utah Science, Technology, and Research associate professor of bioengineering and human genetics at the Scientific Computing and Imaging Institute [1] and the Huntsman Cancer Institute at the University of Utah, the principal investigator of a National Cancer Institute's Physical Sciences in Oncology project [2,3], and the chief technology officer and a co-founder of Eigengene, Inc. [4,5] Alter received her Ph.D. in applied physics at Stanford University and her B.Sc. magna cum laude in physics at Tel Aviv University. Her Ph.D. thesis on "Quantum Measurement of a Single System," which was published by Wiley [6,7,8], is recognized as crucial to quantum computing and gravitational wave detection [9,10,11].

Inventor of the "eigengene" [12,13,14,15], Alter formulates comparative spectral decompositions, physics-inspired multi-tensor [16,17] generalizations [18,19,20,21,22] of the singular value decomposition, to (i) compare and integrate any data types, of any number and dimensions, and (ii) scale with data sizes. Her models (iii) are interpretable in terms of known biology and batch effects and (iv) correctly [23] predict [24,25,26,27,28] previously unknown mechanisms [29,30]. By validating a genome-wide pattern of DNA copy-number alterations in brain [31,32,33,34,35] tumors as the best predictor of survival, her retrospective clinical trial [36,37] proved that the models (v) discover accurate, precise, and actionable genotype-phenotype relationships, (vi) are relevant to populations based upon whole genomes of small cohorts, and (vii) can be validated. She discovered this, and patterns in lung [38,39], nerve, ovarian [40,41,42,43,44,45], and uterine tumors, in public data. Such alterations were recognized in cancer, yet repeated previous attempts to associate them with outcome failed, demonstrating that Alter's algorithms are uniquely suited to personalized medicine.

1. https://alterlab.org/in_the_news/Johnson_SCI_News_2010_Feature.pdf
2. https://alterlab.org/physics_of_cancer/
3. https://physics.cancer.gov/research-funding/utah
4. https://eigengene.com/
5. https://linkedin.com/company/eigengene
6. https://onlinelibrary.wiley.com/doi/book/10.1002/9783527617128
7. https://alterlab.org/publications/Alter_Yamamoto_Wiley_2001.pdf
8. https://alterlab.org/presentations/Alter_Ph.D._Dissertation_1999_Slides.pdf
9. https://alterlab.org/in_the_news/Ripin_APS_News_1998_Feature.pdf
10. https://aps.org/publications/apsnews/199808/damop.cfm
11. https://alterlab.org/in_the_news/Thorne_et_al_PRD_2003_Citation.pdf
12. https://alterlab.org/publications/Alter_et_al_ATG_V_1999_Abstract.pdf
13. https://osti.gov/servlets/purl/803995
14. https://doi.org/10.1073/pnas.97.18.10101
15. https://en.wiktionary.org/wiki/Citations:eigengene
16. https://doi.org/10.1073/pnas.0509033102
17. https://doi.org/10.1073/pnas.0709146104
18. https://doi.org/10.1073/pnas.0530258100
19. https://alterlab.org/publications/Ponnapalli_et_al_MMDS_2006_Abstract.pdf
20. https://doi.org/10.1371/journal.pone.0028072
21. https://alterlab.org/research/highlights/pone.0028072_Highlight.pdf
22. https://doi.org/10.1371/journal.pone.0121396
23. https://doi.org/10.1038/msb.2009.70
24. https://alterlab.org/publications/Alter_et_al_MNBWS_2004.pdf
25. https://doi.org/10.1073/pnas.0406767101
26. https://doi.org/10.1371/journal.pone.0018768
27. https://doi.org/10.1073/pnas.0604756103
28. https://doi.org/10.1371/journal.pone.0078913
29. https://doi.org/10.1073/pnas.0607650103
30. https://alterlab.org/in_the_news/Alter_ILAS_Bulletin_2005_Feature.pdf
31. https://doi.org/10.1063/1.5037882
32. https://doi.org/10.1158/1538-7445.AM2018-4262
33. https://doi.org/10.1371/journal.pone.0164546
34. https://doi.org/10.1371/journal.pone.0030098
35. https://alterlab.org/research/highlights/pone.0030098_Highlight.pdf
36. https://doi.org/10.1063/1.5142559
37. https://eurekalert.org/news-releases/477030
38. https://doi.org/10.1063/1.5099268
39. https://doi.org/10.1158/1538-7445.AM2018-4267
40. https://eurekalert.org/news-releases/866753
41. https://alterlab.org/in_the_news/Atkins_NAE_WTOP_Radio_2015_Feature.mp3
42. https://nae.edu/File.aspx?id=134900&File.mp3
43. https://thepathologist.com/issues/0615/big-data-hidden-knowledge/
44. https://alterlab.org/in_the_news/Pavlou_Pathologist_2015_Feature.pdf
45. https://doi.org/10.1158/1557-3265.OVCA15-A60
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