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User:ItsTheDrE/Orly Alter

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In her Genomic Signal Processing Lab, Alter creates mathematical models by arranging the data in multi-dimensional tables known as tensors. She then develops algorithms to uncover patterns in these data structures, and is able to relate these patterns to mechanisms that govern the activity of DNA and RNA in the cell.

Orly Alter is a US-Israeli Utah Science, Technology and Research (USTAR) Associate Professor of Bioengineering and Human Genetics at the Scientific Computing and Imaging Institute and Huntsman Cancer Institute, University of Utah.[1] Alter is a co-founder and CTO of Eigengene, Inc. [2] (2016) in addition to to being the principal investigator of a National Cancer Institute's Physical Sciences in Oncology Project (PS-ON).[3]

Early Career

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Alter studied a Post-Doctoral Fellowship in Genetics at Stanford University, after being awarded her PhD in applied physics from Stanford in 1999[4]. She had previously graduated with a BSc magna cum laude in physics at Tel Aviv University in 1989.[4] Her PhD thesis, supervised by Professor Yoshihisa Yamamoto entitled " Impossibility of Determining the Quantum Wavefunction of a Single System and Fundamental Limit to External Force Detection", was published into a book by Wiley and is highly regarded in the field of quantum computing and gravitational wave detection, being a finalist in the American Physical Society, Division of Atomic, Molecular and Optical Physics (DAMOP) Thesis Award in 1998.[5][6]

In her Genomic Signal Processing Lab, Alter develops new mathematical methods that are uniquely suited for personalized medicine.

Later Career

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As the inventor of Eigengene, Alter's work focuses on formulating comparative spectral decompositions, physics-inspired multi-tensor generalisations of the singular value decomposition regarding genomic data to:[7][8][9][10]

(i) Compare and integrate any data types of any number and dimension and (ii) scale with data sizes.

(iii) Make models interpretable in terms of known biology and batch effects and (iv) correctly predict previously unknown mechanisms.[11][12][13]

(v) Discover accurate, precise, and actionable genotype-phenotype relationships, which (vi) are relevant to populations based upon whole genomes of small cohorts and (vii) can be validated.

Notable Publications

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  • Aiello, K. A., et al. (2018). "Mathematically universal and biologically consistent astrocytoma genotype encodes for transformation and predicts survival phenotype." APL Bioengineering 2(3).
  • Alter, O., et al. (2000). "Singular value decomposition for genome-Wide expression data processing and modelling." Proceedings of the National Academy of Sciences of the United States of America 97(18): 10101-10106.
  • Bohen, S. P., et al. (2003). "Variation in gene expression patterns in follicular lymphoma and the response to rituximab." Proceedings of the National Academy of Sciences of the United States of America 100(4): 1926-1930.
  • Nielsen, T. O., et al. (2002). "Molecular characterisation of soft tissue tumours: A gene expression study." Lancet 359(9314): 1301-1307.
  • Omberg, L., et al. (2009). "Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression." Molecular Systems Biology 5.
  • Ponnapalli, S. P., et al. (2020). "Retrospective clinical trial experimentally validates glioblastoma genome-wide pattern of DNA copy-number alterations predictor of survival." APL Bioengineering 4(2).

References

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  1. ^ "ORLY ALTER - Research - Faculty Profile - The University of Utah". faculty.utah.edu. Retrieved 2023-03-08.
  2. ^ "Orly Alter PhD". cbtn.org. Retrieved 2023-03-08.
  3. ^ "University of Utah PS-OP– PS-ON - NCI". physics.cancer.gov. 2021-09-16. Retrieved 2023-03-08.
  4. ^ a b "ORLY ALTER - Home - Faculty Profile - The University of Utah". faculty.utah.edu. Retrieved 2023-03-08.
  5. ^ Alter, Orly; Yamamoto, Yoshihisa (2001-07-05). Quantum Measurement of a Single System (1 ed.). Wiley. doi:10.1002/9783527617128. ISBN 978-0-471-28308-9.
  6. ^ "DAMOP Thesis Award". aps.org. Retrieved 2023-03-08.
  7. ^ Alter, Orly; Brown, Patrick O.; Botstein, David (2000-08-29). "Singular value decomposition for genome-wide expression data processing and modeling". Proceedings of the National Academy of Sciences. 97 (18): 10101–10106. doi:10.1073/pnas.97.18.10101. ISSN 0027-8424. PMC 27718. PMID 10963673.{{cite journal}}: CS1 maint: PMC format (link)
  8. ^ Omberg, Larsson; Golub, Gene H.; Alter, Orly (2007-11-20). "A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies". Proceedings of the National Academy of Sciences. 104 (47): 18371–18376. doi:10.1073/pnas.0709146104. ISSN 0027-8424. PMC 2147680. PMID 18003902.{{cite journal}}: CS1 maint: PMC format (link)
  9. ^ Alter, Orly; Golub, Gene H. (2005-12-06). "Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations". Proceedings of the National Academy of Sciences. 102 (49): 17559–17564. doi:10.1073/pnas.0509033102. ISSN 0027-8424. PMC 1308929. PMID 16314560.{{cite journal}}: CS1 maint: PMC format (link)
  10. ^ Ponnapalli, Sri Priya; Saunders, Michael A.; Loan, Charles F. Van; Alter, Orly (2011-12-22). "A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms". PLOS ONE. 6 (12): e28072. doi:10.1371/journal.pone.0028072. ISSN 1932-6203. PMC 3245232. PMID 22216090.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  11. ^ Omberg, Larsson; Meyerson, Joel R; Kobayashi, Kayta; Drury, Lucy S; Diffley, John F X; Alter, Orly (2009-01). "Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression". Molecular Systems Biology. 5 (1): 312. doi:10.1038/msb.2009.70. ISSN 1744-4292. PMC 2779084. PMID 19888207. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  12. ^ Alter, Orly; Golub, Gene H. (2004-11-23). "Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription". Proceedings of the National Academy of Sciences. 101 (47): 16577–16582. doi:10.1073/pnas.0406767101. ISSN 0027-8424. PMC 534520. PMID 15545604.{{cite journal}}: CS1 maint: PMC format (link)
  13. ^ Alter, Orly (2006-10-31). "Discovery of principles of nature from mathematical modeling of DNA microarray data". Proceedings of the National Academy of Sciences. 103 (44): 16063–16064. doi:10.1073/pnas.0607650103. ISSN 0027-8424. PMC 1637536. PMID 17060616.{{cite journal}}: CS1 maint: PMC format (link)
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