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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Genevera Allen, Ph.D.

Genevera Allen, Ph.D.

Assistant Professor
Department of Pediatrics-Neurology
Baylor College of Medicine and
the Jan and Dan Duncan Neurological Research Institute,
Texas Children's Hospital

Assistant Professor, Department of Statistics, Rice University

Education:

Ph.D. Statistics, Stanford University

Research Interest:

Statistical modeling of dependencies in high-dimensional biological data.

Dr. Genevera Allen develops mathematical and statistical models for analyzing enormous, complex data sets such as those that are produced by the financial markets or, closer to Dr. Allen’s interests, advanced techniques in neuroimaging, genetics, metabolomics and proteomics. Dr. Allen models the dependence structures in data to better understand their true biological relevance.

For example, functional magnetic resonance imaging (fMRI) can track changes in metabolism of different brain regions in response to cognitive or behavioral tasks in different experimental conditions, or to compare the brain in healthy and disease states. The images are then analyzed to determine whether apparent differences actually reveal changes attributable to the particular experimental activity or abnormality under consideration, as opposed to extraneous patient movements or physiological processes. This analysis is rendered difficult by the complicated dependence structure of the data. Each entity in the image, the voxel, represents a specific location in the brain, and each voxel is measured every couple of seconds. The voxels thus have both spatial and temporal dependencies. By mathematically modeling the spatio-temporal structure directly, one can better understand the biological regions of interest in the brain.

Dr. Allen's specific goal is to develop and apply mathematical and statistical tools in the areas of convex optimization, multivariate analysis, and machine learning to high-dimensional biological data. These tools allow researchers to better separate the biological truth ("signal") from extraneous information ("noise”).

Selected Publications:

  • Allen GI and Maletic-Savatic M. Sparse non-negative generalized PCA with applications to metabolomics. Bioinformatics. 27(21):3029-35 (2011). PubMed
  • Harshman LC, Yu RJ, Allen GI, Srinivas S, Gill HS and Chung GI. Surgical outcomes and complications associated with presurgical tyrosine kinase inhibition for advanced renal cell carcinoma (RCC). Urol Oncol, 31(3):379-85 (2013). PubMed
  • Harshman LC, Bepler G, Zheng Z, Higgins JP, Allen GI and Srinivas S. Ribonucleotide reductase subunit M1 expression in resectable, muscle-invasive urothelial cancer correlates with survival in younger patients. BJU Int, 106(11):1805-11 (2010). PubMed

For more publlications, see listing on PubMed.

Contact Information:

Baylor College of Medicine
Department: Pediatrics-Neurology
Address: Jan and Dan Duncan Neurological Research Institute
at Texas Children's Hospital
1250 Moursund Street, Suite N1365.16
Houston, TX 77030
Phone: 832-824-8879
Fax: 832-825-1251
E-mail: gallen@bcm.edu

Rice University
Department of Statistics
6100 Main St., MS-138
Houston, TX 77005
Office: Duncan Hall 2098
Phone: 713-798-6321
Fax: 713-348-5476
E-mail: gallen@rice.edu

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