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Orly Alter, Ph.D. Assistant Professor

Orly Alter, Ph.D.

Assistant Professor
Department of Biomedical Engineering
Fellow, Institute for Cellular and Molecular Biology

• Curriculum Vitae
• Department of Biomedical Engineering
  Institute for Cellular and Molecular Biology
  The University of Texas at Austin
  1 University Station A4800
  Austin, Texas 78712-0159
  (512) 471-7939 (phone)
  (512) 471-2149 (fax)
  
• Lab Website
• Office Hours: By appointment

Research Interests

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.¹

Dr. Alter, who holds a Ph.D. in Applied Physics, develops generalizations of the matrix and tensor computations that underlie theoretical physics and pioneers their use in creating models from data from different studies of the interconnected programs of cell division and cancer. She 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.²  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.³  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.⁴

Dr. Alter's research is cited in hundreds of publications and patents, is featured in textbooks, and is part of the curriculum of academic courses taught at schools of engineering, natural sciences and medicine.⁵  Funding for this research comes from the National Human Genome Research Institute,⁶  the National Science Foundation,⁷  the American Institute of Mathematics⁸  and Cancer Research UK.

Selected Publications

• L. Omberg, J. R. Meyerson, K. Kobayashi, L. S. Drury, J. F. X. Diffley and O. Alter, "Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression," Nature Molecular Systems Biology 5, article 312 (October 2009) (supplemental material at http://www.bme.utexas.edu/research/orly/verification_of_prediction/). To read the press release, go to: http://www.engr.utexas.edu/news/articles/200910131769/.
• L. Omberg, G. H. Golub and O. Alter, "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), pp. 18371-18376 (November 2007) (supplemental material at http://www.bme.utexas.edu/research/orly/HOSVD/).
• O. Alter, "Genomic Signal Processing: From Matrix Algebra to Genetic Networks," in Microarray Data Analysis: Methods and Applications, edited by M. J. Korenberg (Humana Press, Totowa, 2007), pp. 17-59. 
• O. Alter, "Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data," Proceedings of the National Academy of Sciences 103 (44), pp. 16063-16064 (October 2006)
  (reprint at http://www.bme.utexas.edu/research/orly/publications/PNAS_Commentary_2006.pdf).
• O. Alter and G. H. Golub, "Singular Value Decomposition of Genome-Scale mRNA Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band Broadening," Proceedings of the National Academy of Sciences 103 (32), pp. 11828-11833 (August 2006) (supplemental material at http://www.bme.utexas.edu/research/orly/harmonic_oscillator/).
• O. Alter and G. H. Golub, "Reconstructing the Pathways of a Cellular System from Genome-Scale Signals Using Matrix and Tensor Computations," Proceedings of the National Academy of Sciences 102 (49), pp. 17559-17564 (December 2005) (supplemental material at
  http://www.bme.utexas.edu/research/orly/network_decomposition/).
• O. Alter and G. H. Golub, "Integrative Analysis of Genome-Scale Data Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription," Proceedings of the National Academy of Sciences 101 (47), pp. 16577-16582 (November 2004) (supplemental material at http://www .bme.utexas.edu/research/orly/pseudoinverse/).
• O. Alter, P. O. Brown and D. Botstein, "Generalized Singular Value Decomposition For Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms," Proceedings of the National Academy of Sciences 100 (6), pp. 3351-3356 (March 2003) (supplemental material at http://genome-www.stanford.edu/GSVD/ and at http://www.bme.utex as.edu/research/orly/GSVD/).
• T. Nielsen, R. B. West, S. C. Linn, O. Alter, M. A. Knowling, J. O'Connell, S. Zhu, M. Fero, G. Sherlock, J. R. Pollack, P. O. Brown, D. Botstein and M. van de Rijn, "Molecular Characterisation of Soft Tissue Tumours: a Gene Expression Study," Lancet 359 (9314), pp. 1301-1307 (April 2002) (supplemental material at http://genome-www.stanford.edu/sarcoma/).
• O. Alter, P. O. Brown and D. Botstein, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling," Proceedings of the National Academy of Sciences 97 (18), pp. 10101-10106 (August 2000) (supplemental material at http://genome-www.stanford.edu/SVD/ and at http://www.bme.utexas.edu/research/orly/SVD/PNAS_2000/).
• O. Alter and Y. Yamamoto, Quantum Measurement of a Single System (Wiley, New York, 2001).
• Publications in Genetics
• Publications in Physics