Curriculum Vitae AM Moses

August 10

CURRICULUM VITAE

A. BIOGRAPHICAL INFORMATION

1. PERSONAL

Name: Alan Moses

Home Address: 160 Baldwin St., Unit 414 Toronto, ON M5T 3K7 CANADA +1 416 506 1639

University Address: Department of Cell and Systems , University of Toronto 25 Willcocks St. Toronto ON M5S 3B2 CANADA Lab: +1 416 978 5563 Office: +1 416 946 3980

Email: [email protected]

2. DEGREES

Ph. D., Biophysics 2005 University of California, Berkeley “Molecular of transcriptional regulation”, supervisor Michael Eisen

B. A., Biophysics, Astronomy 2000 Columbia University

3. EMPLOYMENT

Assistant Professor Department of Cell & Systems Biology University of Toronto 2008 – present

Graduate Faculty, Full Member Graduate Program in Cell & Systems Biology University of Toronto 2008 – present

Cross-Appointment & Graduate Faculty, Full Member Graduate Program in Ecology & Evolutionary Biology Curriculum Vitae AM Moses

University of Toronto 2008 – present

Cross-Appointment & Graduate Faculty, Full Member Department of Computer Science University of Toronto 2008 – present

Sanger Postdoctoral Fellow Informatics Division Wellcome Trust Sanger Institute 2005 – 2008

Graduate Research Assistant Lawrence Berkeley National Laboratory 2001 – 2005

Teaching Assistant “Radiation and Life.” Columbia University 2000

Summer Undergraduate Fellow Center for Studies in Physics and Biology Rockefeller University 1999

Teaching Assistant “Introduction to Molecular Biology for non-scientists.” Columbia University 1999

4. HONOURS

Awards: 2007 National Science Foundation travel fellowship 2005-2007 Sanger Institute Postdoctoral Fellowship 2005 Keystone Symposia travel scholarship 2004 ISCB travel fellowship award 2000 Graduated magna cum laude, Columbia University 2000 Elected Phi Beta Kappa 1996-2000 Dean’s List, Columbia College 1999 Summer Research Fellowship, Rockefeller University

Special Recognition of Published Research: Curriculum Vitae AM Moses

3 Publications have received ‘Highly Accessed’ designations from BioMed Central, and 5 have been selected by faculty of 1000 .

5. PROFESSIONAL AFFILIATIONS AND ACTIVITIES

Guest Associate Editor: 2008 PLoS

Journal Reviewer (Past 6 Years): PLoS Computational Biology, PLoS Genetics, PLoS One, Phil. Trans. R. Soc. B: Biol. Sci., Molecular Biology and Evolution, Journal of Molecular Evolution, PROTEINS: Structure, Function, Bioinformatics, Journal of Theoretical Biology, Algorithms for Molecular Biology, BMC bioinformatics, BMC , BMC Evolutionary Biology, Bioinformatics, ISMB 2009, RECOMB 2009, PSB 2010

Memberships: cis-regulatory evolution working group, National Evolutionary Synthesis Center, Durham NC, USA 2007

Society for Molecular Biology and Evolution (2008-present)

International Society for Computational Biology (2004, 2007)

Genetics Society (2006)

B. ACADEMIC HISTORY

6. A. RESEARCH ENDEAVOURS

Evolution of Regulatory Sequences and Networks -Evolution of phsophorylation sites, transcription factor binding sites -Computational tools for regulatory sequence analysis

B. RESEARCH AWARDS (grants, contracts, fellowships) during preceding 5 years

“Functional variation in ultra-high-throughput sequence data” Canadian Institutes of Health Research (CIHR) Alan Moses 2009-2010 $79,650

“Bridging comparative, population and functional genomics” Genome Canada/Genome Quebec Curriculum Vitae AM Moses

Thomas Bureau 2009-2012 $4,750,961

“Evolution of regulatory sequences and systems” Connaught Foundation Alan Moses 2008-2009 $10,000

“Evolution of regulatory sequences and systems” Natural Sciences and Engineering Research Council of Canada (NSERC) Alan Moses 2008-2012 $117,850

“Evolution of regulatory sequences and systems” Canada Foundation for Innovation (CFI)/ Ontario Research Fund (ORF) Alan Moses 2008-2010 $230,000

“Computational analysis of regulatory sequences” Wellcome Trust Alan Moses 2005-2007 $100,000

C. SCHOLARLY AND PROFESSIONAL WORK

7. Refereed publications

1. Nguyen Ba AN, Moses AM (2010). Evolution of characterized phosphorylation sites in budding yeast. Mol Biol Evol. Apr 5. 2. Fraser HB, Moses AM, Schadt EE. (2010) Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc Natl Acad Sci U S A. Jan 28 3. Moses AM (2009) Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites BMC Evol Biol. 2009,9:28 4. Nguyen Ba AN, Pogoutse A, Provart N, Moses AM. (2009) NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics. Jun 29;10:202 5. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ. (2009) Population genomics of domestic and wild yeasts. Nature. Feb 11. 6. Moses AM, Durbin R, (2008) Inferring selection on amino acid preference in protein domains. Mol. Biol. Evol. Dec 18. 7. Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta- Curriculum Vitae AM Moses

Vidal A, Bolund L, Wang J, Durbin R. TreeFam: 2008 Update. (2008) Nucleic Acids Res. Jan;36(Database issue):D735-40. Epub 2007 Dec 1. 8. Moses AM, Liku ME, Li JJ, Durbin R. Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. (2007) Proc Natl Acad Sci U S A. Nov 6;104(45):17713-8. 9. Shultzaberger RK, Chiang DY, Moses AM, Eisen MB. Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis.(2007) PLoS ONE. Nov 21;2(11):e1199. 10. Moses AM, Hériché JK, Durbin R. (2007) Spatial clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biology. 8(2):R23. 11. Pennacchio LA, Ahituv N, Moses AM, Prabhakar A, Nobrega M, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. (2006) In Vivo Enhancer Analysis of Human Conserved Noncoding Sequences. Nature. Nov 23;444(7118):499-502 12. Moses AM, Pollard D, Nix DA, Iyer VN, Li XY, Biggin MD and Eisen MB. (2006) Large-scale turnover of functional transcription factor binding sites in . PLoS Computational Biology. Oct 13;2(10) 13. Pollard D, Iyer VN, Moses AM and Eisen MB (2006) Whole Genome Phylogeny of the Drosophila melanogaster Species Subgroup: Widespread Discordance with Species Tree & Evidence for Incomplete Lineage Sorting. PLoS Genetics. 2(10). 14. Pollard DA, Moses AM, Iyer VN and Eisen MB. (2006) Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics. Aug 14;7(1):376 15. Wang QF, Prabhakar S, Wang Q, Moses A, Chanan S, Brown M, Eisen M, Cheng JF, Rubin E, Boffelli D. (2006) Primate-Specific Evolution of an LDLR Enhancer. Genome Biology. Aug 2;7(8):R68 16. Moses AM, Chiang DY, Pollard DA, Iyer VN and Eisen MB (2004) MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biology, 5(12):R98 17. Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M and Eisen MB. (2004) Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi. PLoS Biology Nov 9;2(12):e398 18. Moses AM, Chiang DY and Eisen MB (2004). Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures. Pacific Symposium on Biocomputing. 19. Moses AM, Chiang DY, Kellis M, Lander ES and Eisen MB (2003). Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evolutionary Biology 3(19). Curriculum Vitae AM Moses

20. Chiang DY, Moses AM, Kellis M, Lander ES and Eisen MB (2003). Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biology 4(7):R43.

8. Non-Refereed Publications

Moses AM, Sinha S (2009) Regulatory Motif Analysis Bioinformatics: Tools and Applications (Edwards D, Stajich J,Hansen D)Springer Biomedical and Life Sciences collection.

Intelligent Design: playing with the building blocks of biology (2005) Berkeley Science Review 5:1

Back to the future (2002) Berkeley Science Review 2:2

Life: wanted dead or alive (2002) Berkeley Science Review 2:1

Evolution is not a tautology (2001) Berkeley Science Review 1:1

9. Manuscripts/publications, etc. in preparation and submitted to publishers

10. Presentations at Meetings and Symposia

“Modeling the evolution of a classic genetic switch” Society for Molecular Biology and Evolution, 2010 Lyon, France

“Evidence for large numbers of weakly selected mutations in genome-scale variation data” Society for Molecular Biology and Evolution, 2008 Barcelona, Spain

“Bioinformatics of protein regulatory modules: predicting cyclin-dependent kinase targets based on clustering of consensus motifs” at Intelligent Systems for Molecular Biology / European Conference on Computational Biology 2007 Vienna

“Bioinformatics of protein regulatory modules” at Genome Informatics, 2006 Hinxton UK

“Evolution of Simple Transcription Networks” at Systems and Biology, 2005 Keystone USA

“Position specific variation in the rate of evolution in transcription factor binding sites” at Society for Molecular Biology and Evolution, 2003 Newport Beach, USA

Curriculum Vitae AM Moses

11. Invited Lectures

“Evolution of Regulatory Networks and Sequences” institute de biologie integrative et des systemes, Laval University, Quebec QC, April, 2010

“Biological Information and Evolution” Populations, Evolution Physics, Jan. 2010 Aspen, USA

“Biological Information and Evolution” Origins Institute, McMaster University, Hamilton ON, Sept. 2009

“Selection and Function in Population Genomics” at the Genomic Sciences Program Seminar, University of Wisconsin-Madison, Madison USA 2008

“Clusters of cyclin-dependent kinase consensus sites: regulatory modules in proteins?” at the Bioinformatics Seminar Series, University of Manchester, Manchester UK 2007

“Molecular evolution of transcription factor binding sites” at the Ecology and Evolution Seminar Series, University of Chicago, Chicago USA 2005

D. LIST OF COURSES (in preceding 5 years)

12. Undegraduate Teaching:

CSB498 Cell & Systems Biology Independent Research 2010 Gianni Castiglione 2010 Selam Yohannes 2009-2010 Christos Josephides 2008-2009 Alex Nguyen-Ba 2008 Collin Claridge

2008-9 CSB435 University of Toronto “Regulatory networks and systems in molecular biology”

2009 CSB349 University of Toronto “Eukaryotic Gene Expression”

13. Theses supervised: 2009-present, Alex Nguyen Ba, MSc Student, Department of Cell & Systems Biology, University of Toronto 2009-present, Andy Lai, MSc Student, Department of Cell & Systems Biology, University of Toronto Curriculum Vitae AM Moses

2008-present, Louis-Francois Handfield, PhD Student, Computer Science, University of Toronto

14. Other teaching and lectures given (in preceding 5 years):

2009 EEB461 molecular evolution and phylogenetics, University of Toronto “Regulatory Evolution”

2009 MMG1016H comparative genomics, University of Toronto “Regulatory Evolution”

2006 Bioinformatics training course, Hangzhou, China “Evolutionary mixtures for phylogenetic motif-finding"

Graduate Student Committees: JingJing Du Ecology & Evolutionary Biology (Belinda Chang) 2008-2009 Lee Zamparo Computer Science (Zhaolei Zhang) 2009-present Shobhit Jain Computer Science (Gary Bader) 2009-present Carl de Boer Molecular Genetics (Tim Hughes) 2009-present Nisa Dar Molecular Genetics (John Parkinson) 2009 Rohan Patel Cell & Systems Biology (Nick Provart) 2009-present Carman Yea Cell & Systems Biology (David Guttman) 2010-present Jessica Yang Cell & Systems Biology (David Guttman) 2010-present Matt Doering Cell & Systems Biology (Elizabeth Edwards) 2010-present Kristin Ancevicius Cell & Systems Biology (Tim Westwood) 2010-present

Graduate Student Examination Committees: Ron Ammar Cell & Systems Biology (Nicholas Provart) M.Sc. 2008 Trevis Alleyne Molecular Genetics (Tim Hugues) M.Sc. 2008 JingJing Li Molecular Genetics (Zhaolei Zhang) Reclass exam Dea Shahinas Cell & Systems Biology (Dinesh Christendat) M.Sc. 2008 Honour McCann Ecology & Evolutionary Biology (David Guttman) Ph.D. Proposal Julian Northey Cell & Systems Biology (Peter McCourt) Ph.D. approval Jian Zou Molecular Genetics (Brenda Andrews) Ph.D. Defense Adriana Caragea Cell & Systems Biology (Thomas Berleth) Ph.D. Transfer David Wade-Farley Computer Science (Quaid Morris) M.Sc. 2009 Kayvan Mirhadi Cell & Systems Biology (M. Abouhaider) M.Sc. 2009 Heather Wheeler Cell & Systems Biology (Malcolm Campbell) Ph.D. Proposal Ryan Austin Cell & Systems Biology (Nicholas Provart) Ph.D. 2009

E. ADMINISTRATIVE POSITIONS

Organizer of Genome Biology & Bioinformatics Retreat 2009

Curriculum Vitae AM Moses

Cell & Systems Biology Undergraduate Committee 2009-10

Systems Biology Faculty Search Committee 2009

Cell & Systems Biology Departmental Seminar Committee 2008-10