Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

Background

Orly Alter is a Utah Science, Technology, and Research (USTAR) associate professor of bioengineering and human genetics at the Scientific Computing and Imaging Institute1  and the Huntsman Cancer Institute at the University of Utah, the principal investigator of a National Cancer Institute (NCI) Physical Sciences in Oncology project,2  and the chief technology officer (CTO) and a co-founder of Eigengene, Inc.3,4  Inventor of the "eigengene,"5,6,7  she pioneered the matrix8,9,10  and tensor11,12  modeling of molecular biological data, which, as she demonstrated, can (i) compare and integrate different, e.g., multi-omic, data types; (ii) scale with data sizes; (iii) be interpreted in terms of the known biology and batch effects underlying the data; and (iv) correctly predict previously unknown and experimentally verifiable physical,13,14,15  cellular,16,17,18,19  and evolutionary20,21  mechanisms.22,23,24  Her successful retrospective clinical trial25,26  provided a proof of principle that her recently formulated and developed physics-inspired multi-tensor27,28,29,30  generalizations of the singular value decomposition additionally can (v) discover accurate, precise, and actionable genotype-phenotype relationships; (vi) prove relevant to populations based upon whole genomes of small cohorts; and (vii) be validated in clinical trials.

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-Interscience as a book,45,46,47,48  is recognized today as crucial to the field of gravitational wave detection.49,50 

Research Interests

Postdoctoral and Graduate Positions at the Genomic Signal Processing Lab

NCI U01 CA-202144: Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics

Alter's trial experimentally validated a genome-wide pattern of DNA copy-number alterations found in glioblastoma brain31,32,33,34,35,36  tumors as a predictor of life expectancy statistically more accurate than and independent of age, which has been the best indicator for 70 years. She discovered this pattern, and patterns similarly predicting survival and response to treatment of patients with neuroblastoma nerve cancer and lung,37,38  ovarian,39,40,41,42,43,44  and uterine adenocarcinoma cancers, by modeling data from NCI databases. Researchers have recognized copy-number alterations as a hallmark of cancer for more than a century and have observed them in these tumors for decades. However, previous attempts to associate the tumors' copy numbers with the patients' outcome failed, including studies of the same data that used other artificial intelligence and machine learning methods. This demonstrates that Alter's multi-tensor decompositions are uniquely suited for personalized medicine.

  • 26th Annual Meeting of the Society for Neuro-Oncology (SNO) (Boston, November 18–21, 2021).
  • Decade of the Physical Sciences in Oncology Network (PS-ON) at the National Cancer Institute (NCI) Virtual Symposium (September 21–23, 2020).