Colin N. Dewey 1406 Navellier St El Cerrito, CA 94530 (510) 541-3481 [email protected] http://www.eecs.berkeley.edu/~cdewey

EDUCATION Ph.D. University of California, Berkeley Electrical Engineering and Computer Sciences Computational and Genomic Biology Designated Emphasis December 2006 (expected) GPA: 3.97/4.0

Algorithms for the alignment of multiple whole genomes

Lior Pachter (chair), Richard Karp, Michael Eisen

Examination areas: algorithms, molecular biology,

B.S. University of California, Berkeley Electrical Engineering and Computer Sciences, High Honors May 2001 GPA: 3.91/4.0, Major GPA: 4.0/4.0

RESEARCH Algorithms for problems in . INTERESTS Alignment algorithms for multiple whole genome sequences. Applications of computational geometry and to genomics.

RESEARCH 2001- University of California, Berkeley EXPERIENCE present Graduate Student Dissertation research on methods for multiple alignment of whole genomes. Specific methods developed for construction of multiple genome homology maps and parametric alignment of whole genomes.

2005 National Center for Biotechnology Information (NCBI), (Summer) National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD Scientific Visitor Conducted molecular evolution research in Dr. Eugene Koonin’s group.

2004- ENCODE Project Consortium present Member International effort to identify all functional elements in the human genome. Identified vertebrate genomic segments orthologous to human segments. Constructed and analyzed genomic multiple alignments.

Colin N. Dewey – Curriculum Vitae – Page 1 of 5 2004 International Chicken Genome Sequencing Consortium Member Constructed a whole genome orthology map for five genomes.

2004 Rat Genome Sequencing Project Consortium Member Constructed a whole genome orthology map for human, mouse, and rat. Identified and validated novel genes through comparative gene prediction.

2002 Mouse Genome Sequencing Consortium Member Analyzed and evaluated comparative gene prediction methods.

2000-2002 Agilent Laboratories, Palo Alto, CA (Summers) Intern Designed and constructed PC boards for a fluid control system. Designed control and translation software for a laser ablation system.

1999 Lawrence Berkeley National Laboratory, Berkeley, CA (Summer) Student Assistant Developed software for analysis of high performance computing systems.

HONORS/ 2003 Howard Hughes Medical Institute (HHMI) AWARDS Predoctoral Fellowship in Biological Sciences Honorable Mention

2003 National Science Foundation (NSF) Graduate Research Fellowship Honorable Mention

2001-2002 U.S. Department of Education Graduate Assistance in Areas of National Need Fellowship

2001 National Science Foundation (NSF) Graduate Research Fellowship Honorable Mention

2001- Phi Beta Kappa present

1999-2001 Honors Program, Electrical Engineering and , Unversity of California, Berkeley Breadth area in molecular biology

1999- Eta Kappa Nu present Electrical and Computer Engineering Honor Society

1998 University of California, Berkeley Edward Frank Kraft Scholarship Prize

Colin N. Dewey – Curriculum Vitae – Page 2 of 5 PUBLICATIONS 2006 C. Dewey, P. Huggins, K. Woods, B. Sturmfels, and L. Pachter (2006) Parametric alignment of Drosophila genomes. PLoS In press.

C. Dewey and L. Pachter (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics 15:R51-R56.

S. Lall, D. Grün, A. Krek, K. Chen, Y. Wang, C. Dewey, P. Sood, T. Colombo, N. Bray, P. MacMenamin, H. Kao, K. Gunsalus, L. Pachter, F. Piano and N. Rajewsky (2006) A genome-wide map of conserved microRNA targets in C. elegans. Current Biology 16:460–471.

2005 C. Dewey and K. Woods “Parametric Sequence Alignment.” Algebraic Statistics for Computational Biology. Ed. L. Pachter and B. Sturmfels. Cambridge University Press, November 2005. 193-205.

2004 International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.

The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia of DNA Elements) Project. Science 306:636-640.

C. Dewey, J.Q. Wu, S. Cawley, M. Alexandersson, R. Gibbs and L. Pachter (2004) Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Research, 14:661-664.

Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.

2002 Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.

WORKS C. Dewey, I. Rogozin, and E. Koonin, Compensatory relationship between SUBMITTED splice sites and exonic splicing signals depending on the length of vertebrate introns.

N. Beerenwinkel, C. Dewey, and K. Woods, Parametric inference of recombination with an application to HIV-1 circulating recombinant forms.

WORKS IN C. Dewey and L. Pachter. Mercator: multiple whole-genome orthology map PREPARATION construction. http://bio.math.berkeley.edu/mercator/

Colin N. Dewey – Curriculum Vitae – Page 3 of 5 CONFERENCES 2005 ENCODE Workshop, Hinxton, UK ATTENDED Multiple-species alignment analysis group

Clay Mathematics Institute Workshop, Cambridge, MA Algebraic Statistics for Computational Biology

ENCODE Consortium Meeting, Gaithersburg, MD

ENCODE Data Analysis Workshop, Rockville, MD Multiple-species alignment analysis group.

2004 Cold Spring Harbor Laboratory Meeting, Cold Spring Harbor, NY The Biology of Genomes Poster: Construction of orthology maps for multiple whole genomes

TALKS 2006 Statistics and Genomics Seminar, UC Berkeley, (4/6) Whole-genome alignments and polytopes for comparative genomics

PROFESSIONAL 2005- International Society for Computational Biology (ISCB) AFFILIATIONS present

TEACHING 2003 Department of Computer Science, UC Berkeley EXPERIENCE (Fall) Graduate Student Instructor Led two discussion and two laboratory sections for a computer science course (CS61A). Graded laboratory reports and exams.

1999 Reader (Spring) Graded homework assignments for a computer science course (CS61A). Met with students to evaluate projects.

COURSEWORK Computer Science data structures, efficient and randomized algorithms, computational geometry, machine architecture, low-level/assembly programming, computer graphics, digital design, , cryptography, statistical learning theory, statistical natural language processing

Computational Biology statistical genetics, algorithms for computational biology, algebraic statistics for computational biology

Biological Sciences organic chemistry, general biochemistry and molecular biology, advanced genetics

Colin N. Dewey – Curriculum Vitae – Page 4 of 5 RESEARCH Lior Pachter, Ph.D. REFERENCES Associate Professor of Mathematics 1081 Evans Hall Department of Mathematics University of California, Berkeley Berkeley, CA 94720 Tel. (510) 642-2028 Fax (510) 642-8204 [email protected]

Bernd Sturmfels, Ph.D. Professor of Mathematics and Computer Science 925 Evans Hall Department of Mathematics University of California, Berkeley Berkeley, CA 94720 Tel. (510) 642-4687 Fax (510) 642-8204 [email protected]

Eugene V. Koonin, Ph.D. Senior Investigator National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda, MD 20894 Tel. (301) 435-5913 Fax (301) 435-7794 [email protected]

TEACHING Michael Clancy REFERENCE Senior Lecturer 779 Soda Hall Department of Computer Science University of California, Berkeley Berkeley, CA 94720 Tel. (510) 642-7017 Fax (510) 642-5775 [email protected]

Colin N. Dewey – Curriculum Vitae – Page 5 of 5