Curriculum Vitae September 2005

Jeffrey Chuang Assistant Professor Department of Biology, Boston College

Address: Boston College - Department of Biology Email: [email protected] 140 Commonwealth Avenue – Higgins 444B Phone: (617) 552-0804 Chestnut Hill, MA 02467 Fax: (617)552-2011

EDUCATION Dates Institution and Location Degree Major 06/96 Harvard University B.A. Chemistry and Physics Cambridge, MA 06/2001 Massachusetts Institute of Technology Ph. D. Physics Cambridge, MA

PROFESSIONAL EMPLOYMENT

09/2005 to present Assistant Professor, Department of Biology Boston College 9/2001-7/2005 Postdoctoral Fellow, Department of Biochemistry and Biophysics University of California, San Francisco, CA 09/1996-06/2001 Graduate research assistant, Theoretical Condensed Matter Physics Massachusetts Institute of Technology, Cambridge, MA

HONORS AND AWARDS National Science Foundation Postdoctoral Fellowship in Interdisciplinary 2003-2005 Informatics 2001-2002 National Institutes of Health Biochemistry Postdoctoral Fellowship 1997-1999 National Science Foundation Graduate Fellowship 1996-1997 MIT Karl Taylor Compton Graduate Fellowship for Theoretical Physics 1996 Phi Beta Kappa, Harvard University 1992 Silver medalist (USA), International Chemistry Olympiad

RESEARCH INTERESTS Computational approaches to comparative genomics, gene regulation, and molecular evolution.

PROFESSIONAL ORGANIZATIONS Member of International Society for Computational Biology Member of American Association for the Advancement of Society Member of American Physical Society Member of Sigma Xi scientific research society

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LECTURES AND SEMINARS

Massachusetts Institute of Technology, Computational Biology Seminar (2005). Insights from Comparative Genomics: From Genome Organization to Regulatory Complexity Boston College, Department of Physics (2005). Computational Approaches in Comparative Genomics New York University, Department of Biology (2005). Insights from Comparative Genomics: From Genome Organization to Regulatory Complexity Boston College, Department of Biology (2005). Insights from Comparative Genomics: From Genome Organization to Regulatory Complexity Bauer Center for Genomics Research (2005). Insights from Comparative Genomics: From Genome Organization to Regulatory Complexity Rice University, Department of Bioengineering (2005). Insights from Comparative Genomics: From Genome Organization to Regulatory Complexity Intelligent Systems for Molecular Biology Workshop on Biopathways, Glasgow, Scotland (2004). Functional Significance of Spatial Variations in Mutation Rates: Mammals and Yeast. UCSF Research in Progress Seminar Series (2003). Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome Europolymer Conference, Gargnano, Italy (2002). Multiple Point Adsorption in a Heteropolymer Gel and the Tanaka Approach to Imprinting American Physical Society March Meeting, Minneapolis, Minnesota (2001). Free Energy Self-Averaging in Protein-Sized Random Heteropolymers National Institute of Standards and Technology, Gaithersburg, Maryland (2001). Entropic Slowdowns in Aggregation and Translocation of Biopolymers 84th Statistical Mechanics Conference at Rutgers University (2000). Free Energy Self-Averaging in Protein-Sized Random Heteropolymers

POSTERS AND EXHIBITS

Intelligent Systems for Molecular Biology Conference (2004). Mutation Rates in Rodents and Human are Correlated. UCSF Tetrad Retreat (2004). Mutation Rates in Rodents and Human are Correlated. UCSF Biophysics Retreat (2004). Mutation Rates in Rodents and Human are Correlated. UCSF Biophysics Retreat (2003). Mutation Rates in Rodents and Humans. UCSF Tetrad Retreat (2002). Mutational Hot and Cold Spots in the Human Genome. UCSF Biophysics Retreat (2001). Searching for Regulatory Elements in the Caulobacter Crescentus Genome. Enrico Fermi Summer School in Protein Folding and Design (2000). Free Energy Self-Averaging in Protein-Sized Random Heteropolymers. Biophysical Society Annual Conference (2000), with Prof. Thomas Chou, UCLA. Protein-Induced Bending in Membranes. American Physical Society March Meeting (1999). Topological Repulsion between Polymer Globules. Discover Magazine awards at Epcot Center (1998). Smart Gels.

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PUBLICATIONS

C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome Research 15, 205 (2005). “Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.”

Jeffrey H. Chuang and H. Li. “Regional Mutation Rates are Conserved in Rodents and Humans.” In preparation.

Jeffrey H. Chuang and H. Li, PLOS Biology 2, e29 (2004). "Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome."

K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Macromolecular Symposia 207, 1 (2004). “Multiple Contact Adsorption of Target Molecules by Heteropolymer Gels.”

K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Progress in Polymer Science 28, 1489 (2003). “Multiple Point Adsorption in a Heteropolymer Gel and the Tanaka Approach to Imprinting: Experiment and Theory.”

Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001). “Anomalous Dynamics of Translocation.”

H. Hiratani, C. Alvarez-Lorenzo, Jeffrey Chuang, O. Guney, A. Yu.Grosberg, and T. Tanaka, Langmuir, 17, 4431 (2001). “Effect of Reversible Cross-linker, N,N'-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels.”

Jeffrey Chuang, A. Yu. Grosberg, and M. Kardar, Physical Review Letters, 87, 078104 (2001). “Free Energy Self-Averaging in Protein-Sized Heteropolymers.”

T. Enoki, Jeffrey Chuang, T. Tanaka, A. Yu. Grosberg, et al., Physical Review Letters, 85, 5000 (2000). “Frustrations in Polymer Gels and Their Minimization through Molecular Imprinting.”

Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka, Journal of Chemical Physics 112, 6434 (2000). “Topological Repulsion between Polymer Globules.”

STUDENTS MENTORED

Michael Stromberg Fall 2005 Rotation Student

MISCELLANEOUS ACTIVITIES

The Dallas Morning News - One of two fellows selected by the American Association for the Advancement of Science and the American Physical Society to report on science news, as part of a fellowship to improve public understanding of science. Published news articles on topics including evolutionary biology, acoustics, geology, traffic flow, inorganic chemistry, and space exploration (1997).

Science and Health Partnership - Taught a series of computational biology and genetics classes to students at Wallenberg High School, in an outreach program between UCSF and the San Francisco school district (2002).

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