Aimée Dudley
Ph.D., Genetics
Harvard Medical School, 1999
Email:
Dr. Aimée Dudley earned her Ph.D. in genetics at Harvard Medical School. Her graduate work in Dr. Fred Winston´s laboratory helped decipher mechanisms by which transcription factors regulate gene expression. As a postdoctoral fellow in Dr. George Church´s laboratory (Harvard Medical School), she collaboratively developed experimental and computational methods to probe the structure of genetic networks using high-throughput analysis of gene function and regulation. These methods include a spotted glass microarray system, which uses experimental and computational methods to improve data accuracy and comparability, and a simple, cost-effective method for large-scale phenotype analysis in yeast. One application of the phenotyping technique was a systems genetics study focusing on the relatively common, but poorly understood phenomenon of pleiotropy, in which a mutation in a single gene produces multiple traits. She also collaborated with Dr. Daphne Koller (Stanford University) to develop new methods for using gene expression data gathered from populations of individuals to uncover the mechanisms by which genetic changes perturb the gene regulatory network.
Areas of Research:
Systems genetics
Understanding the structure and systems level properties of genetic networks is a key component of accurate and predictive models of an organism´s behavior and response to environmental perturbation. What is the degree to which gene functions are independent or highly connected? How often are functions re-used to allow the cell to respond to distinct developmental or environmental cues? Does evolution favor specific network properties?
Projects in the lab related systems genetics include:
- genomic methods for analyzing complex genetic traits
- analysis of systems level properties in natural populations
- development and application of "synthetic biology" methods for genome re-engineering
Post-transcriptional gene regulation
Although the importance of posttranscriptional regulation is now well-documented, many of the pathways involved and the signals that activate them are not well understood. These mechanisms are required for diverse biological processes and have been implicated in a number of diseases. Because many of these processes are conserved across evolution, we are using a systems biology approach in yeast to identify the factors and decipher their functions.
Projects in the lab related to posttranscriptional regulatory networks include:
- genomic and proteomic analysis of a computationally predicted post-transcriptional regulatory network
- genomic and proteomic analysis of condition specificity of post-transcriptional regulation
- identification of new post-transcriptional regulatory factors
Spatial and temporal dynamics
Despite their importance in nearly all biological processes, the impact of spatial and temporal effects on the levels, modification states, and interactions of cellular components (RNA, protein, and metabolites) are greatly understudied in systems level analyses.
Projects in the lab related to spatial and temporal dynamics include:
- genomic and proteomic approaches to studying the dynamics of protein and RNA sub-cellular localization
- microfluidics and high throughput microscopy approaches to studying the spatial and temporal dynamics of sub-cellular localization
Key collaborations outside ISB:
George Church
Department of Genetics
Harvard Medical School
Daphne Koller
Computer Science Department
Stanford University
Daniel Segrè
Department of Biology
Department of Biomedical Engineering
Boston University
Carl Hansen
Physics and Astronomy
Electrical and Computer Engineering
University of British Columbia
Key collaborations at the ISB:
Ruedi Aebersold
John Aitchison
David Galas
Tim Galitski
Ilya Shmulevich
Grants and contracts:
N.I.H./ N.H.G.R.I. Genome Scholar and Faculty Transition Award K22 (2007-2009)
NIH/ NHBLI Seattle Proteomic Center Pilot Project (2007-2008)
Awards:
U.S. Department of Energy Alexander Hollaender Distinguished Postdoctoral Fellowship (2000-2002)
A complete CV and publication list can be found here.
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