Orly Alter, Ph.D.
Assistant Professor |
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Orly Alter, Ph.D.
Assistant Professor
Department of Biomedical Engineering
Fellow, Institute for Cellular and Molecular Biology
- 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
In her Genomic Signal
Processing Lab at UT Austin, Dr.
Orly Alter and her students use generalizations of mathematical frameworks
that have proven successful in describing the physical world to model large-scale
molecular biological data, such as DNA microarray data. DNA microarrays
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 these data. To
this end, Dr. Alter built the first predictive models of DNA microarray
data using matrix computations. She demonstrated the ability of her models
to predict previously unknown biological principles with a prediction of
a novel mechanism of regulation that correlates DNA replication initiation
with cell cycle-regulated mRNA expression. This research work is cited
in hundreds of scientific papers and several textbooks. It has become a
part of the academic core curriculum in courses in mathematics and molecular
biology.
In 2007 Dr.
Alter has been awarded more than $1.5 million in an R01 Grant from the National
Human Genome Research Institute (NHGRI). This grant will support a five-year
project in her lab, titled "Tensor Computations For Modeling Large-Scale
Molecular Biological Data: From Discovery of Patterns to Discovery of Principles
of Nature."
Dr.
Alter's goal is to enable better understanding and ultimately also control
of life processes on the molecular level. Her models may become the foundation
of a future in which biological systems are modeled as physical systems are
today. The predicted mechanism of regulation may be at the basis of a future
where the cell cycle and cancer can be controlled.
Selected Publications
- 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. (reprint at http://www.bme.utexas.edu/research/orly/publications/PNAS_Commentary_2006.pdf).
- 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)
- 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
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