Dr. Orly Alter has been an Assistant Professor in the Department of Biomedical Engineering and a Fellow of the Institute for Cellular and Molecular Biology at the University of Texas at Austin since 2004. She was awarded a five-year NSF CAREER Award in 2009,¹  and a five-year National Human Genome Research Institute (NHGRI) R01 grant in 2007.²  In 2005, Dr. Alter was selected to give the Linear Algebra and its Applications Lecture of the International Linear Algebra Society.^3,4  She received a five-year NHGRI Individual Mentored Research Scientist Development Award in 2000. From 1999 to 2003, she was a Sloan Foundation and Department of Energy Postdoctoral Fellow in Computational Molecular Biology in the Department of Genetics at Stanford University.

Dr. Alter received her Ph.D. in Applied Physics at Stanford University in 1999. In her thesis work she established the quantum theoretical limits to the information which can be obtained in the measurement of a single physical system about the system's quantum wavefunction, its time evolution and the classical potentials which shape this time evolution. For this work, she was an American Physical Society Outstanding Doctoral Thesis Research in Atomic, Molecular, or Optical Physics Award Finalist in 1998.⁵  This thesis work was published as a book, titled "Quantum Measurement of a Single System," by Wiley in 2001.⁶  Today Dr. Alter's thesis work is recognized as crucial to the field of gravitational wave detection.⁷

Research in Dr. Alter's Genomic Signal Processing Lab is motivated by recent high-throughput technologies, such as DNA microarrays, which make it possible to record the complete genomic signals that guide the progression of cellular processes. Future discovery and control in biology and medicine will come from the mathematical modeling of such large-scale molecular biological data, just as Kepler discovered the laws of planetary motion by using mathematics to describe trends in astronomical data.⁸

Dr. Alter develops generalizations of the matrix and tensor computations that underlie theoretical physics and uses them to create models from large-scale molecular biological data. She pioneered the use of the matrix singular value decomposition (SVD), generalized SVD (GSVD) and pseudoinverse projection as well as the tensor higher-order SVD (HOSVD) and higher-order eigenvalue decomposition (HOEVD) in comparing and integrating DNA microarray data from, e.g., different studies of the interconnected programs of cell division and cancer. She showed that these mathematical frameworks can represent biological reality: The mathematical variables, patterns uncovered in the data, correlate with activities of cellular elements, such as regulators or transcription factors, that drive the measured genomic signals, and with cellular states where these elements are active. The operations, such as classification, rotation or reconstruction in subspaces of these patterns, simulate experimental observation of the correlations and possibly even the causal coordination of these activities.

Dr. Alter uses her models to predict biological and physical mechanisms that govern the activity of DNA and RNA, including a previously unknown mechanism of regulation that correlates DNA replication initiation with mRNA expression during cell division.⁹  Her recent experimental results verify this computational prediction, demonstrating for the first time that mathematical modeling of microarray data can be used to correctly predict previously unknown cellular mechanisms.¹⁰  This brings biologists a step closer to one day being able to understand and control the inner workings of the cell as readily as NASA engineers plot the trajectories of spacecraft today.¹¹

Dr. Alter's research is cited in hundreds of publications and patents,¹²  is featured in textbooks, and is part of the curriculum of academic courses taught at schools of engineering, natural sciences and medicine. Additional funding for her work comes from the American Institute of Mathematics¹³  and Cancer Research UK.