User:ItsTheDrE/Orly Alter

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. Alter is a co-founder and CTO of Eigengene, Inc. (2016) in addition to to being the principal investigator of a National Cancer Institute's Physical Sciences in Oncology Project (PS-ON).

Early Career
Alter studied a Post-Doctoral Fellowship in Genetics at Stanford University, after being awarded her PhD in applied physics from Stanford in 1999. She had previously graduated with a BSc magna cum laude in physics at Tel Aviv University in 1989. 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.

Later Career
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:

(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.

(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

 * 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).