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More specifically, the subject of the research falls within the following two categories: 1. ... through outstanding research, excellent education and the integration of ... Thematic Year: Scientific and Engineering Appl. of Algebraic Topology. Academic Visitor ... July 2007. Cancer Research Center, CIC-CSIC Salamanca, Spain.
Mariel Vazquez Curriculum Vitae 415-338-2071 – [email protected] – http://math.sfsu.edu/mariel Contact

San Francisco State University Department of Mathematics, 928 Thornton Hall 1600 Holloway Ave., San Francisco, CA 94132

Research Interests

My research lies at the interface of mathematics, polymer physics and molecular biology. I specialize on the use of topological tools to study DNA. More specifically, the subject of the research falls within the following two categories: 1. DNA topology Topics: mechanism of site-specific recombination and topoisomerase action, packing of chromosomes in human cells and in viral capsids. Tools: knot theory, low-dimensional topology and Monte Carlo simulations 2. Chromosomal aberrations and cancer Topics: Analysis of genomic data of cancer patients; repair pathways Tools: Biophysical models; computational homology.

Awards

Mohammed Dahleh Distinguished Lectureship 2014 This award has been created to honor the memory, innovative spirit, and contributions of Mohammed Dahleh to our scientific community and to the University of California, Santa Barbara. Awardees are selected based on their pioneering work, extraordinary accomplishments, and promise for exceptional contributions. Awardees are invited to deliver the Mohammed Dahleh Distinguished Lecture at UCSB in the second half of the academic year. Presidential Early Career Award for Scientists and Engineers

2012

PECASE is the U.S. government's highest honor for researchers in the early stages of their careers. PECASE recipients are selected for their pursuit of innovative research at the frontiers of science and technology and their commitment to community service. Federal departments and agencies nominate researchers whose early accomplishments show the greatest promise for keeping America at the cutting edge of science and engineering. I was nominated by the National Science Foundation. PECASE award citation: “Mariel Vazquez is being honored for excellent interdisciplinary and international research at the interface of mathematics and biology, and for creativity and dedication to recruiting, training, and mentoring, and helping students from underrepresented groups achieve their goals.” Emerging Scholar, named by Diverse Magazine

2012

NSF CAREER Award 2011 The Faculty Early Career Development (CAREER) Program is a Foundationwide activity that offers the National Science Foundation's most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of Mariel Vazquez

Curriculum Vitae

education and research within the context of the mission of their organizations. Such activities should build a firm foundation for a lifetime of leadership in integrating education and research. Professional Experience

Associate Professor of Mathematics San Francisco State University, San Francisco

August 2011 – Present

Assistant Professor of Mathematics San Francisco State University, San Francisco

August 2005 –2011

Postdoctoral Fellow August 2000 – August 2005 Mathematics Department U.C. Berkeley, Berkeley, CA Faculty Mentor: Rainer Sachs Visiting Assistant Professor AY2000–June 2003 Mathematics Department U.C. Berkeley, Berkeley, CA Graduate Research Assistant August 1995-July 2000 Mathematics Department, Florida State University, Tallahassee, FL Advisor: De Witt Sumners Graduate Teaching Assistant June-July 1999 Mathematics Department, Florida State University, Tallahassee, FL Teaching Assistant 1992-1995 Mathematics Department, Faculty of Sciences, UNAM, Mexico City, Mexico Visiting Positions Long Term Visitor

September 2013– June 2014 Institute for Mathematics and its Applications, Minneapolis, MN Thematic Year: Scientific and Engineering Appl. of Algebraic Topology Academic Visitor June 2007; June-August 2006 Biochemistry Department, University of Oxford, Oxford, UK Host: David J. Sherratt Projects: Modeling topological simplification by Xer recombination; DNA decatenation by Xer/FtsK Visiting Scholar January – December 2006 Mathematics Department U.C. Berkeley February 2008 – February 2009 Faculty Hosts: Rainer Sachs, Alexandre Chorin Long Term Visitor August – December 2007 Institute for Mathematics and its Applications, Minneapolis, MN Thematic Year: Mathematics of Molecular and Cell Biology Academic Visitor July 2007 Cancer Research Center, CIC-CSIC Salamanca, Spain Host: Jesus Perez-Losada Project: Detecting chromosomal aberrations using SKY Academic Visitor July-September 2008 Molecular Biology Department, CID/CSIC, Barcelona, Spain Host: Joaquim Roca

Mariel Vazquez

Curriculum Vitae

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Project: DNA packaging in bacteriophages: extraction and purification of different topological forms of DNA by high-resolution 2D gel electrophoresis. Education

PhD in Mathematics December 2000 Florida State University, Tallahassee, FL Dissertation: Tangle analysis of Site-specific Recombination: Gin and Xer systems; Advisor: De Witt Sumners B.Sc. in Mathematics April 1995 National University of Mexico (UNAM), Mexico City, Mexico Thesis: Applications of Knot Theory to the Study of DNA Advisor: Max Neumann French High School Diploma June 1989 Lycée Franco-Mexicain, Mexico City, Mexico Diplôme du Baccalauréat de l’Enseignement du 2nd Degré en C-série: Mathématiques et Sciences Physiques

Scholarships and Exxon Mobil Project NExT Fellowship Fellowships 2003

2002-

Agencies: Mathematical Association of America/ Exxon Mobil Fund PMMB/Burroughs Wellcome Doctoral fellowship 1997-2000 Agencies: Program in Mathematics and Molecular Biology (PMMB): Burroughs Wellcome Fund (1997-1998); NSF (1999-2000) Doctoral Studies Scholarship to Florida State University 1995-2000 Agency: General Direction of Academic Personnel Affairs, UNAM, Mexico Undergraduate research Fellowship Institute of Mathematics, UNAM, Mexico Publications

Legend:

Published

Peer-reviewed publications and monographs

1993-1995

† indicates undergraduate student co-author * indicates graduate student co-author Smith†, Smith*, indicate the stage of Smith’s career when the research was conducted.

33. Shimokawa, K., Ishihara, K., Grainge, I., Sherratt, D., and Vazquez, M., FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner (2013) Proceedings of the National Academy of Sciences USA Nov 11 [Epub ahead of print]; SI movie Press Release 32. Ishihara, K., Shimokawa, K. and Vazquez, M., Site-specific recombination modeled as a band surgery: Applications to Xer Recombination (2013) in Discrete and Topological Models in Molecular Biology (Eds. Jonoska Nataša; Saito, Masahico) Natural Computing Series, Mariel Vazquez

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Springer ISBN 978-3-642-40192-3 [Book Chapter] 31. Brasher, R. Scharein, RG. and Vazquez, M., New biologically motivated knot table (2013) Biochemical Society Transactions 41(2):606-611 30. Darcy, IK. and Vazquez, M., Determining the topology of stable proteinDNA complexes (2013) Biochemical Society Transactions 41(2):601-605 29. Ishihara, K., Scharein, R., Diao, Y., Arsuaga, J., Vazquez, M., and Shimokawa, K., Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice, J. of Phys. A: Math Theor. (2012) 45: 065003 28. Arsuaga, J., Diao, Y., Kaplan, T., and Vazquez, M, The effects of density on the topological structure of the mitochondrial DNA from trypanosomes, Journal of Mathematical Biology (2012) 64(6): 1087-1108 27. Soteros, C., Ishihara, K., Shimokawa, K., Szafron, M., and Vazquez, M., Signed Unknotting Number and Knot Chirality Discrimination via Strand Passage, Progress of Theoretical Physics Supplement (2011) 191: 78-95 26. Portillo, J.*, Diao, Y., Scharein, R., Arsuaga, J., and Vazquez, M., On the mean and variance of the writhe of random polygons, J. of Phys. A: Math Theor. (2011) 44: 275004 25. Shimokawa, K., and Vazquez, M., DNA and Knot Theory (Japanese), (2011) Sugaku 63(2): 237-242 Expository paper Note: The English version will appear in “Sugaku Expositions” (AMS). 24. DeWoskin, D.*, Climent, J., Cruz-White, I., Vazquez, M., Park, C., and Arsuaga, J, Applications of Computational Homology to Prediction of Treatment Response in Breast Cancer Patients, Topology and its Applications (2010) 157 (1): 157-164. 23. Scharein, R., Ishihara, K.*, Arsuaga, J., Diao, Y., Shimokawa, K., and Vazquez, M., Bounds for minimal step number of knots in the simple cubic lattice, J. Phys. A :Math. Theor. (2009) 42: 475006. 22. Darcy, I. , Luecke, J. and Vazquez, M., Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex, Algebraic and Geometric Topology (2009) 9: 2247-2309. Note: A preprint can be accessed from the IMA preprint series. 21. Arsuaga, J., Diao, Y., and Vazquez, M., Mathematical Methods in DNA Topology: Applications to Chromosome Organization and Site-specific Mariel Vazquez

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Recombination, Mathematics of DNA Structure, Function and Interactions (eds C.J. Benham, S. Harvey, W.K. Olson, D.W. Sumners and D. Swigon), Springer Science + Business Media, LLC, New York, (2009) pp.7-36. 20. I. Grainge, M. Bregu, M. Vazquez, V. Sivanathan*, SYP Ip and DJ Sherratt, Unlinking chromosome catenanes in vivo by site-specific recombination, EMBO Journal (2007) 26(19): 4228-38. 19. T. Blackstone†, P. McGuirk†, C. Liang*, J. Roca, J. Arsuaga, and M. Vazquez, The role of writhe in DNA condensation, Proceedings of the International Workshop on Knot Theory for Scientific Objects, Ed. A. Kawauchi, OCAMI studies (2007) Vol. 1(2): 239-250. 18. W. Zheng†, C. Galloy, B. Hallet, and M. Vazquez, The tangle model for site-specific recombination: a computer interface and the Tnpl-IRS recombination system, Proceedings of International Workshop on Knot Theory for Specific Objects, Ed. A. Kawauchi, OCAMI studies (2007) Vol. 1(2): 251-271. 17. X. Hua†, B. Raghavan†, D. Nguyen†, J. Arsuaga and M. Vazquez, Random State Transitions of Knots: a first step towards modeling unknotting by type II topoisomerases, Topology and its applications 157(7):1381-1397. 16. Ardanza-Trevijano, S., Arsuaga, J., Crespo J. A., Extremiana, J. I., Hernandez, L.J., Rivas, M. T. , Roca, J., Vazquez, M, Topological Invariants in DNA, Fullerenes and the Theory of Social Choice (Spanish), La Gaceta de la Real Sociedad Matematica Española (2007) 10(3) :611-632.

15. J. Arsuaga, M. Vazquez, P. McGuirck†, S. Trigueros, D.W. Sumners, J. Roca, DNA knots reveal a chiral organization of DNA in phage capsids, Proc. Natl. Acad.Sci. USA (2005) 102(26):9165-9169 14. S. Vives, B. Loucas, M. Vazquez, D. Brenner, R.K. Sachs, L. Hlatky, M. Cornforth, J. Arsuaga, SCHIP: Statistics of Chromosome Interphase Positioning, Bioinformatics (2005) 21(14): 3181-3182. 13. M. Vazquez, S.D. Colloms, D.W. Sumners, A unique mechanism for Xer recombination is suggested by tangle analysis, J. Mol. Biol. (2005) 346:493504 12. D. Levy*, M. Vazquez, M. Cornforth, B. Loucas, R.K. Sachs, J. Arsuaga, Comparing DNA damage processing pathways by computer analysis of chromosome painting data, J. Comp. Biol. (2004) 11(4): 626-641 Mariel Vazquez

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11. J. Arsuaga, K. Greulich-Bode, M. Vazquez, P. Hahnfeldt, D.J. Brenner, R.K. Sachs, L. Hlatky Chromosome spatial clustering expressed through radiogenic aberrations, International Journal of Radiation Biology (2004) 80(7): 507-515 10. M. Vazquez, D.W. Sumners, Tangle Analysis of Gin Recombination, Math. Proc. Camb. Phil. Soc. (2004) 136: 565-582 9. J. Arsuaga, R.Tam, M. Vazquez, D.W. Sumners, S. Harvey, Investigation of viral DNA packaging using molecular mechanics models, Journal of Biophysical Chemistry (2002) 101-102(1):475-484 8. M. Vazquez, K.M. Greulich-Bode, J. Arsuaga, M.N. Cornforth, M. Bruckner, R.K. Sachs, L. Hlatky, M. Molls, P. Hahnfeldt, Computer analysis of mFISH chromosome aberration data uncovers an excess of very complex metaphases, International Journal of Radiation Biology (2002) 78:1103-1116 7. M.N. Cornforth, K.M. Greulich-Bode, B.D. Loucas, J. Arsuaga, M. Vazquez, R.K. Sachs, M. Bruckner, M. Molls, P. Hahnfeldt, L. Hlatky, D.J. Brenner, Chromosomes are predominantly located randomly with respect to each other in interphase human cells, Journal of Cell Biology (2002) 159(2): 237-244. See Chromosomal Cliques by A.W. Dove, J. Cell Biology (2002) 159(2): 199 6. R.K. Sachs, J. Arsuaga, M. Vazquez, P. Hahnfeldt, L. Hlatky, Using Graph Theory to Analyze Chromosome Aberrations, Radiation Research (2002) 159(5): 556-567

5. L. Hlatky, R.K.Sachs, M. Vazquez, M.N. Cornforth, Radiation-induced chromosome aberrations: insights gained from biophysical modeling, Bioessays (2002)24:714-723 4. Y. Saka† and M. Vazquez, TangleSolve: topological analysis of sitespecific recombination, Bioinformatics (2002) 18: 1011-1012 3. J. Arsuaga, M. Vazquez, S. Trigueros*, D.W. Sumners, J. Roca, Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids, Proc. Natl. Acad. Sci. USA (2002) 99(8):5373-5377 2. S. Trigueros*, J. Arsuaga, M.E. Vazquez, D.W. Sumners, J. Roca, Novel Display of knotted DNA molecules by two-dimensional gel electrophoresis, Nucleic Acids Research (2001) 29(13):e67 Software

1. M.E. Vazquez, Knots and DNA, Revista Situs (1995) IMATE, UNAM. Mariel Vazquez

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Published peer-reviewed extended abstracts and non-reviewed conference proceedings 3. Shimokawa, K, Ishihara*, K., and Vazquez, Tangle Analysis of DNA catenane unlinking by the Xer/FtsK system, M. Bussei Kenkyu (Kyoto) (2001) 76: 1-50. (Accepted Nov 2008) 2. Nguyen DV.*, Vazquez, M., Hua X†, Raghavan, B. †, Shayefar N. †, Slaga J. †, Portillo J. † Modeling DNA unknotting by type II topoisomerases, Journal of Investigative Medicine (2007) 55 (1): S93-S93 2007 1. Hua, X.* and Vazquez, M., Modelling State Transitions in Knot Space Motivated by Type II Topoisomerse Action, Proceedings of the International Workshop on Knot Theory for Scientific Objects, Knot Theory for Scientific Objects Ed. A. Kawauchi, OCAMI studies (2007) 1(2):273-276. I have overseen the development of a series of computational tools and userfriendly software where all the research in our group is reported, documented and/or disseminated. TangleSolve, java-based software used in the analysis of site-specific recombination. Available at: http://ewok.sfsu.edu/TangleSolve/ Knotplot extensions: Knotplot is computer software developed by Rob Scharein who is currently a postdoc in my group. Rob has developed new software related to my projects and has incorporated them into Knotplot. These tools are then distributed, free of charge, to students and collaborators, and members of the larger scientific community who request them. Grants Current

NIH 1R01GM109457-01 Reconstruction of 3D Genome Architecture from Chromatin Conformation Capture Data UCSF Principal Investigator Mark Segal; co-investigator Ahituv Nadav SFSU Principal Investigator Javier Arsuaga; co-inv. Mariel Vazquez Press release NSF 942514985 (M. Vazquez, PI) National Science Foundation; CAREER: Topological mechanism of DNA unlinking by the XerCD-FtsK system Period of funding: 5/1/2011-4/30/2016; Amount: $599,944 NSF 0818647 (J. Arsuaga, PI; M. Vazquez, Co-PI; Y. Diao, Co-PI) National Science Foundation; Collaborative Research: Topological characterization of DNA Organization in Bacteriophages. Period of funding 08/28/09 –08/27/12; Amount: $720,000 (two institutions)

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Past Federal

NIH 2P20MD000544-06 (A. Corrigan/B. Macher, PI/PD) National Center on Minority Health and Health Disparities, NI Multiscale analysis of CGH arrays from breast cancer patients using computational algebraic topology. Period of funding: 10/02/08 – 10/01/13; Subproject Amount: $365,000 Role: Project leader with J. Arsuaga (Math, SFSU). NIH T34GM08574 (F. Bayliss, PI) NIH Minority Access to Research Careers (MARC) National Institutes of Health (NIH) Period of funding: 6/1/2007-5/31/2012 20% RRT per year, 2008-2012 for J. Arsuaga or M Vazquez Role: instructor in honors Computing/Math course. NIH MBRS SCORE S06 GM 052588 (Marquez-Magana, PD; Vazquez , PI), Computer analysis of DNA unknotting by Topoisomerase II Period of funding: 01/01/07-12/31/10; Project Amount: $305,000 Role: Pilot Project PI DMS-0938070 (Cheri Shakiban, PI) Modern Mathematics Workshop at SACNAS 6/1/2009 ($36,770 in 1 year) Role: co-organizer of the workshop; helped write the proposal 5S06 GM052588-14 S06 Carry-over Request (PI Marquez-Magana) (Funded: Summer 2009). This grant provided funds to purchase a state of the art biomath server, as well as other computers for use of the SCORE community. Role: Math Biology section project leader (jointly with Dr. J. Arsuaga). 2007 20123550 U56 Mentoring Core - NIH (B. Macher, PI) Role: funded investigator 2005-2007 P20 MD000262, R. Corrigan/B. Macher (PI) NIH/NCMHD RIMI grant $ 16,500 per year for 2 years, plus 20 % release time each semester Description: Biomedical Research at San Francisco The goal of this program is to develop a biomedical research infrastructure at SFSU. Role: funded investigator 2002-2004 Modeling Chromosome Aberrations, Chromatin Structure and Enzymatic Actions, National Science Foundation (DMS 9971169, Creativity Extension), Amount: $ 215,000 Co-author with J. Arsuaga and R.K. Sachs (P.I.)

Other

Faculty mentor for “Creating Momentum through Communicating Mathematics” NSF grant (PI Matt Beck) Role: faculty mentor Mariel Vazquez

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Fall 2007 IMA VIV long-term visitor, Institute of Mathematics and its Applications (IMA) using NSF funds $ 18,000 subcontract to SFSU for Fall 2007, plus travel/subsistence Role: key invited researcher Spring 2007 CCLS Mini-grant (M. Vazquez, PI) ($ 7000). Role: Project leader 2005-2006 Student Enrichment Opportunities, F. Bayliss (PI) SFSU SEO Office 1 month summer salary, 2 wtus MARC mentor allowance. Mariel Vazquez 2004 Mathematical and computational study of topoisomerase II action, Focus-Abengoa Foundation Research Award. 2004 AWM travel grant to attend the Joint AMS-SMM International Meeting

Research Presentations Invited talks at international conferences

Selected invited talks at international meetings: Unlinking DNA replication links by Xer recombination Topological Structures in Computational Biology workshop, December 9-13, 2013 IMA, Minneapolis MN Entanglement in Biology, how nature controls the topology of proteins and DNA November 17-22, 2013 BIRS, Banff, Canada Two 1-hour lectures (TBN) School on Knot Theory and 3-manifolds CIMAT, Guanajuato, Mexico, December 2012 Keynote Lecture: DNA unknotting and unlinking Modern Math Workshop (organized by the 8 NSF Math Institutes, and NIMBioS) Seattle, WA, October 10-11, 2012DNA unknotting and unlinking Topological aspects of DNA function and protein folding Cambridge, UK, September 2012 DNA unlinking by Xer-FtsK Workshop on DNA reactions or DNA Chromosome Dynamics Woodshole MA, Sept 2012 Keynote Lecture: DNA unknotting and unlinking,

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SIAM Life Sciences 2012, San Diego, CA; August 2012 Random Knots and Confinement Considerations MSRI Workshop Connections for Women Discrete Lattice Models in Mathematical Physics and Computing, Berkeley, CA, January 12-13, 2012 DNA unknotting and unlinking, Convexity, Topology, Combinatorics, and Beyond, Workshop in the honor of Luis Montejano, Puerto Vallarta, Mexico; October 3-7, 2011 Plenary Talk: Random knots and confinement considerations Workshop on DNA Knots Mathematical Research Centre (CRM) “Ennio De Giorgi” Scuola Normale Superiore – Pisa, Italy; 15-16 June, 2011 Plenary Talk: DNA Unknotting and Unlinking Workshop on Numerical Knots: Models and Simulations Mathematical Research Centre (CRM) “Ennio De Giorgi” Scuola Normale Superiore – Pisa, Italy; 8-9 June, 2011 DNA unlinking by Xer Recombination, Topological Problems in Molecular Biology, University of Iowa, Iowa City, IA; March 16-20, 2011 Topological analysis of difference topology experiments: applications to a MuDNA complex, Eighth Joint International Meeting of the AMS and the Mexican Mathematical Society, Berkeley, CA; June 2-4, 2010 Modeling DNA unknotting and unlinking, DNA topology workshop, Okinawa Institute of Technology, Okinawa, Japan (November 7, 2009). Plenary talk: Modelling DNA unlinking by Xer recombination Conference on Knots and other Entanglements in Biopolymers: Topological and Geometrical Aspects of DNA, RNA and Protein Structures ICTP, Trieste, Italy September 15-19, 2008 Modelling DNA unknotting and unlinking International workshop on Knots and Macromolecules II. Venice, Italy, March 6-8, 2008 Modelling DNA unknotting and unlinking International Conference on Topology and its Applications, joint with the 4th Japan-Mexico Topology Conference. Kyoto University, Japan, Dec 3-7, 2007 Mariel Vazquez

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Plenary talk: The mathematics of site-specific recombination: 1. difference topology experiments and the Mu tranpososome; 2. DNA unlinking by XerCD/FtsK, Workshop: Mathematics of DNA Structure, Function and Interactions Institute of Mathematics and its Applications, Minneapolis, MN September 16-21, 2007 Modeling DNA topology simplification, Banff International Research Station Banff, Canada; May 21 - 25, 2007 Mathematical and Computational Modeling of chromosomal rearrangements. Institute of Genomic Sciences, UNAM, Cuernavaca, Mexico, April 2007 Tangle Analysis of the mu transpososome, International Workshop on Knot Theory for Scientific Objects, Osaka City University, Japan, March 2006 Enzymes that change the topology of DNA, Third Japan Mexico Joint Meeting on Topology and its Applications, Oaxaca, Mexico December 2004 Using Graph Theory to Analyze Chromosome Aberrations, Combinatorial Biology Symposium, SMB Meeting, Ann Arbor, MI July 2004 Invited talks at National Conferences

Selected invited talks at National conferences: BSN-BSC Deep Dive into Mentoring Student mentor and Speaker at two professional development sessions: 1. Academic Achievement: Career timeline & influences. The real deal. How careers are shaped by a combination of achievement, ambition, personal factors, opportunity, assistance, advice and luck. 2. Professional Development session on Communicating science to K-12 students, educators, the press and the public. March 15th – 16th, 2013 Monterey, CA Keynote Address Sonia Kovalevsky Math Day UT Austin, Austin,

April 20th, 2013

Keynote Lecture: DNA unlinking by Xer recombination Undergraduate Research Conference at the Interface of Biology and Mathematics November 16-17, 2013 NIMBioS, Knoxville, TN Keynote Lecture: DNA unknotting and unlinking Mariel Vazquez

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Modern Math Workshop (organized by the 8 NSF Math Institutes, and NIMBioS) Seattle, WA, October 10-11, 2012 The XerCD-FtsK system unlinks replication catenanes in a stepwise manner. Special Session on Measures of Entanglement of Macromolecules and their Applications (#57A) at the Joint Mathematics Meetings New Orleans, LA, January 2011 Plenary: DNA linking and unlinking by site-specific recombination Biology and Mathematics in the Bay Area (BaMBA) Day 2010 Stanford University, Stanford, CA, November 20, 2010 Modeling DNA unlinking Blackwell Tapia conference, Molecular Biosciences Institute, Ohio State University, Columbus, OH, November 2010 Modeling DNA unknotting and unlinking Life on the Edge in a Sustainable World: Working at the Interface of Biology, Chemistry, Mathematics; SACNAS National Meeting, Anaheim CA Oct., 2010 DNA unknotting, topoisomerases, bacteriophages, Special Session on Physical Knotting and Linking and its Applications, AMS Spring Central Section Meeting, Macallester College, St Paul MN, April 10-11, 2010 Multiscale analysis of CGH arrays from breast cancer patients using computational algebraic topology, RIMI advisory committee meeting Talk given jointly by Javier Arsuaga and Mariel Vazquez, May 2009 Topological Analysis of Enzymatic Actions. SumnersFest: a Conference on Low-Dimensional Topology and Applications to Molecular Biology and Biomedical Mathematics. May 4-5, 2007 Tallahassee, FL DNA rearrangements and multigraphs, Bay Area Discrete Math Day, UC Davis October 2005 Graphs and DNA Rearrangements, Special Session on Discrete Models in Biology, Southeast Section AMS Meeting, East Tennessee State University, Johnson City, TN October 2005 Mathematical and experimental analysis of Xer recombination, joint with J.Bath, Special Session on Mathematical Sciences Contributions to the Biomedical Sciences, AMS JMM, Atlanta, GA January 2005 Plenary: Topological analysis of enzymatic actions: DNA link formation by Xer recombination and DNA unknotting by type II topoisomerase, Knots in Mariel Vazquez

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Washington XIX: Topology in Biology II, Washington DC, Nov. 2004 Genome Comparisons Allowing Complex Rearrangements, AWM Workshop, Siam Meeting, Portland, OR July 2004 Tutorial: Introduction to DNA recombination, Special session: DNA Topology, 948th AMS Meeting, U.T. Austin October 1999 Invited departmental colloquia

Selected departmental colloquia outside SFSU, including internationally (Indicated by #). Selected colloquia are: DNA unknotting and unlinking Mathematics Department, UC Berkeley; November 8, 2012 The topological complexity of DNA: models of unknotting. Mathematics Institute, National University of Mexico (UNAM), UAM, Mexico City, November 24-25, 2009. Knots and DNA, MathCamp 2009, University of Puget Sound, Tacoma WA Mathematical and computational modeling of DNA rearrangements. Colloquium Series Frontiers in Genomics. Institute of Genomic Sciences, UNAM, Cuernavaca, Mexico, April 2007 Topological Analysis of Enzymatic Actions, Mathematics Colloquium Series, CSU Chico (March 2007); Sonoma State University (March 2007); Santa Clara University (Feb. 2007); San Jose State University (2006). Topological analysis of enzymatic actions, DNA link formation by Xer recombination and DNA unknotting by type II topoisomerases. Joint Math and CS colloquium, University of Connecticut. March 2005 Using graph theory to analyze chromosome aberrations. Math colloquium, George Washington University February 2005 Topological analysis of enzymatic actions: site- specific recombinases and type II topoisomerases, Math colloquium, Dartmouth College, Drexel University, University of Utah, Arizona State University, UC Merced, University of North Carolina Chapel Hill, San Francisco State University, University of Utah, February 2005

Departmental Seminars (outside SFSU)

Selected invited seminar talks: DNA Unknotting and Unlinking Mathematical Biology Seminar, UC Davis Math. Dept.; October 10, 2011

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DNA Unknotting and Unlinking Mathematical and Computational Biology Seminar, UC Berkeley Math. Dept.; April 27, 2011 DNA unknotting, topoisomerases and bacteriophages, Statistics and genomics Seminar, UC Berkeley, March 4, 2010 The mathematics of site-specific recombination, Applied Mathematics Seminar, University of Minnesota, November 15, 2007 Modeling DNA unknotting by Type II topoisomerases, Mathematics of Molecular and Cellular Biology Seminar, Institute for Mathematics and its Applications, University of Minnesota, October 26, 2007 DNA topology, Topology Seminar, UC Davis, November 15, 2006 DNA Rearrangements and Multigraphs, Stanford Biological Modeling Club, Stanford University, Palo Alto, CA April 2006 Modeling DNA Unknotting by TypeII Topoisomerases, Applied Math Seminar, UC Berkeley May 2004 Topological Analysis of Site-specific Recombination, Statistics and Genomics Seminar, Statistics Dept., U.C. Berkeley, Nov. 2002 Quantitative analysis of M-FISH chromosome aberration data, Institute f¨ur Humangenetik/TUM, Technical University of Munich June 2002 DNA knots used to analyze an enzymatic action, Applied Math. Seminar,Department of Mathematics, U.C. Berkeley, September 2001 Tangle analysis of Xer site-specific recombination, Department of Biochemistry, University of Oxford June 2000 Tangle analysis of site-specific recombination, Institute of Biomedical and Life Sciences, University of Glasgow June 2000 Knot theory used as a tool to understand an enzymatic action, Geometry Seminar, CIMAT, Guanajuato, Mexico December 1998 Contributed presentations

Mariel Vazquez

Selected contributed presentations: International Conferences DNA unknotting and unlinking Knots and Links: From Form to Function, ESF Math. Conference in partnership with EMS and CRM-Pi Mathematical Research Centre (CRM) “Ennio De Giorgi” Curriculum Vitae

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Scuola Normale Superiore – Pisa, Italy; 2-8 July 2011 Poster: K. Shimokawa, K. Ishihra. I. Grainge, D.J. Sherratt, M. Vazquez, The XerCD-FtsK system unlinks replication catenanes in a stepwise manner, 12th Workshop on Site-Specific Recombination, Transposition and Chromosome Dynamics, Ile d’Oleron, France, Sept. 19-24, 2010 Poster: I. Darcy, J. Luecke, M. Vazquez, Topological analysis of difference topology experiments: applications to the Mu transpososome, 3rd Workshop on Mathematical Virology, Ambleside UK, August 16-20, 2010 Poster: I. Darcy, J. Luecke, M. Vazquez, Topological analysis of difference topology experiments: applications to the Mu transpososome, 2nd ASM Conference on Mobile DNA, Montreal Canada, April 24-28, 2010 Poster: Tangle analysis suggests a unique mechanism for Xer recombination, joint with Colloms, S.D., Saka, Y. † and Sumners D.W.; Workshop on Sitespecific Recombination, Genetic Transposition and DNA dynamics, Oxford, UK, September, 2002 Poster: Computer simulations suggest an early form of instability in irradiated human lymphocytes, joint with Arsuaga F.J., Sachs R.K., Hahnfeldt P., Hlatky L.R.; RECOMB 2001, Montreal, Canada April 2001 National Conferences Poster:Genome Comparison Allowing Complex Rearrangements, joint with Dan Levy* and Rainer Sachs; Geometry, Algebra and Phylogenetic Trees, Harvey Mudd College, Claremont, CA October 2004 Poster:Genome Comparison Allowing Complex Rearrangements, joint with Dan Levy* and Rainer Sachs; RECOMB, San Diego, CA April 2004 Talk: DNA knots in the classroom, joint with J. Arsuaga; Mathfest, Boulder August, 2003 Poster: Tangle analysis reveals a unique mechanism for Xer recombination, joint with Sumners, D.W.; Keystone Symposium: Molecular Mechanisms of DNA replication and recombination, Snowbird, UT January 2002 Poster: Tangle analysis of Xer site-specific recombination, joint with Sumners D.W.; Quantitative Challenges in the Post-Genomic Sequence Era. A Workshop and Symposium. San Diego, CA January 2000 Poster: Tangle analysis of Gin recombination joint with Sumners D.W.; PMMB VI: Understanding Structure. Santa Fe, NM January 1999 Mariel Vazquez

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Teaching Courses

Math301 Exploration and Proof – [GWAR] Fall 2009, 2010, 2012 GWAR: Before graduating, undergraduate students must complete the CSU Graduation Writing Assessment Requirement (GWAR). Students are eligible to fulfill GWAR by taking a GWAR designated course in their department. Math301 is one of two GWAR designated courses in the Math Department.

Math 414-01/ Math714-01 Spring 2007-2011 Analyzing DNA Topology with Mathematical and Computational Methods International Course: OIST Okinawa DNA topology course Okinawa Institute of technology November 1st-6th, 2009 I taught two modules of this course: 1. Mathematical models for topoisomerase (3 hours), Leaders: Mann and Vazquez; 2. 4-plats and Rational Tangles (3 hours), Leaders: Vazquez and Darcy. Audience: 20-30 PhD students, postdocs and young investigators from Japan, China, Korea, India, Irak, Switzerland, UK, USA Math 890-04 Spring 2007 Seminar on Modern Mathematical Methods in Molecular Biology Math325 Linear Algebra Math228 Calculus III

Fall 2006 Fall 2005; Spring 2006

Math195 (UC Berkeley) Spring 2003 Analyzing DNA topology with Mathematical and Computational Methods, joint with Dr. Javier Arsuaga. Math128a Numerical Analysis Spring 2001 Mathematics Department, UC Berkeley Math113 Abstract Algebra Mathematics Department, UC Berkeley

Fall 2000

Short-Course: The topology of DNA (8 hours). Summer 1999 VI Summer School, CIMAT. Co-taught with D.W. Sumners and J. Arsuaga. MAC-1113 Analytic Trigonometry Summer 1999 Mathematics Department, FSU Teaching Assistant 1992-1995 Two upper division courses and one course on General Mathematics for Biologists, Mathematics Department, UNAM K-12

Mariel Vazquez

San Francisco Math Circles Elementary school program Elementary Program Class instructor Curriculum Vitae

Spring 2012-Spring 2013

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Knot theory and DNA topology June 10, 2010 Lycée Français la Pérouse Course length 2 hours Audience: twenty 1st grade students in the class of Sylvain Pelletier Topology of DNA at Mathcamp 07/28-31/09 (co-taught with Dr. J. Arsuaga) Place: University of Puget Sound, Tacoma, Washington Course length: 8 hours spread over 4 days. The Canada/USA Mathcamp is a five-week-long summer program for talented high-school students interested in mathematics. Audience: 15 high-school students (15-18 years old). Mentoring Masters theses committees

In progress: Crista Moreno Computational analysis of Xer recombination Committee: M. Vazquez, chair Brian Cruz DNA packing in bacteriophage capsids Committee: M. Vazquez, chair

Expected Spring 2014

Expected Spring 2014

Michael Steiner Analyzing gene pathways using computational homology Committee: J. Arsuaga, chair; M. Vazquez, Nils Baas Completed Hong Guo Strand-passage on worm-like chains Committee: M. Vazquez, chair Mousa Rebouh Computational Homology and breast cancer Committee: M. Vazquez, chair; J. Arsuaga; M. Nicolau

Fall 2012

Katrina Wono Tangle Analysis of the TnpI-IRS recombination system Committee: M. Vazquez, chair; J. Arsuaga, K. Shimokawa

Fall 2012

Raymond Cavalcante Committee: J. Arsuaga, chair; M. Vazquez; JH Mao Tatsiana Maskalevich Algebraic statistics on testing chromosome proximity Mariel Vazquez

Spring 2013

Curriculum Vitae

Summer 2012

Spring 2011

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Committee: S. Hosten, chair; J. Arsuaga; M. Vazquez Juliet Portillo DNA unknotting by type II topoisomerases: a study of writhe Committee: M. Vazquez, chair; J. Arsuaga, R. Scharein

Summer 2010

Ido Heskia Summer 2010 Testing Proximity Effect Hypothesis for Chromosomes using Algebraic Statistics Committee: S. Hosten, chair; J. Arsuaga; M. Vazquez Jennifer Lopez Spring 2010 TangleSolve: A Topological Tool Used in the Analysis of Site-Specific Recombination Committee: M. Vazquez, chair; J. Arsuaga Zoe Talbot Spring 2010 A study o BFACF entropy and biological application of self-avoiding polygons in Z3. Committee: M. Vazquez, chair; Y. Cheung, K. Okada Daniel Dewoskin Summer 2009 Developments of Techniques in Computational Homology for Multidimensional Analysis of CGH Profiles from Primary Breast Tumors Committee: J. Arsuaga, Chair; C. Park (UCSF); Mariel Vazquez Allen Menglin Chen Fall 2007 X Chromosome Suggests Pronounced Early Human Population Structure Master of Science in Applied Mathematics, UC Berkeley Committee: Rainer K. Sachs, Chair; Mariel Vazquez; Lior Pachter Candice Price Coloring invariant and tangles Committee: Mariel Vazquez, Chair; J Arsuaga; S. Hosten

Undergraduate Theses

Fall 2006

Nicholas Normandin Construction of Lattice Knots from the Gauss Code Applied Math Project I and II (Math 696 and Math 697)

Spring 2009

Juliet Portillo Average writhe of polygons in the simple cubic lattice Applied Math Project I and II (Math 696 and Math 697)

Fall 2006

Miki Suga Spring 2005 DNA Unknotting by Type II Topoisomerases: Modeling DNA knots in Solution using the BFACF Algorithm Mariel Vazquez

Curriculum Vitae

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Mathematics honors thesis, UC Berkeley

Student Awards

Several of my students have received fellowships through the following federal and private programs. National Institutes of Health: MARC, MBRS-RISE; MS/PhD Bridge; RIMI fellows. National Science Foundation: UBM, LS-AMP Bridge Private and other funding: Genentech Fellowship, Berkeley SURF scholarship, Berkeley URAP summer fellowship Students: Candice Price and Alejandro Samaniego (LS-AMP Bridge program); Janella Slaga (NIH Marc); Juliet Portillo (NIH-RISE; Genentech), Jennifer Lopez (NIH RISE); Zoe Talbot (UBM); Mousa Rebouh (RIMI); Mela Hardin (NIH Bridge); Yannan Shen (Berkeley SURF scholar); Michael Jun, Diana Nguyen, Nathan Shayefar and Yuki Saka (URAP summer stipend), Katrina Wono and Brian Cruz (NSF CM2 fellowship).

Students mentored Highschool

Undergraduate

High school Student: Sandeep Peddada Lynbrook High School Presented his research at the California State Science Fair (March 2010), won 2nd place in the Individual Biotechnology Project category. The following SFSU undergraduate students have conducted research under my supervision: Juliet Portillo (Applied Math), Andrew Herrmann (Math); Nicholas Normandin (Applied Math), Jeff Halperin (Statistics), Janella Slaga (Applied Math), Mousa Rebouh (Math), Zoe Talbot (Math), Alejandro Samaniego (Math) Note: They were all involved in student presentations at our mathematical biology group meetings and at the COSE student showcase. All but one have presented their research in poster form or as a talk in regional conferences. Alejandro Samaniego, Juliet Portillo, Mousa Rebouh, and Zoe Talbot presented at national meetings. Nick Normandin presented at an international meeting. I have mentored the following UC Berkeley undergraduates through the undergraduate research apprenticeship program (URAP): Yuki Saka (Math), Tatiana Yarmola (Math), Phillip Davidson (math), Diana Nguyen (MCB, premed), Brian Nguyen (UC Leads program, UCSD), Christopher Lin (Math, CS), Yannan Shen (Math), James Costa (Math), Nathan Shayefar (CS); Itamar Landau (Math and Physics), Wenjing Zheng (Math), Stephanus Jasin (CS) and Miki Suga (Math), Barath Raghavan (CS), Xia Hua (Math, UC Berkeley and Hong Kong University), Kevin He (Math), Michael Jun (Math),

Mariel Vazquez

Curriculum Vitae

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Priya Kshirsagar (Math), Thomas Schuster (Physics)

Graduate

Post-docs/ Research Techs Student output

Candice Price (Math MS, SFSU), Ben Dalziel (CS, SFSU), Xia Hua (Math, MIT), Zoe Talbot (Math MS, SFSU), Jennifer Lopez (Math MS, SFSU), Juliet Portillo (Math MS, SFSU), Mela Hardin (Math MS, SFSU), Jonathan Terhorst (Math MS, SFSU), Mousa Rebouh, Katrina Wono (Math MS, SFSU); Brian Cruz (Math), Hong Guo (Math), Crista Moreno (Math) Note: Four of these students (4 female) have completed masters thesis under my supervision; five students have these in progress. The remaining students have worked with me on research projects for more than 3 months. Rob Scharein (post-doc); Xia Hua, Itamar Landau, Nathan Shayefar, Allen Chen, Reuben Brasher (Research Techs) My students have presented their research at national and international meetings, and within the university.

Service to the Community Referee

I have served as referee for the following journals: Journal of Knot Theory and its Ramifications, Bioinformatics, BMC Bioinformatics, Bulletin of Mathematical Biology, Applied Mathematics and Computation, Journal of Mathematical Physics, Proceedings of the National Academies of Sciences, Transactions of the Royal Society. Grant reviewer

Organization of Scientific meetings, workshops and symposia

I have attended review panels (e.g. DMS/NIGMS) at the National Science Foundation (NSF). I have served as ad-hoc reviewer for the NSF and the Biotechnology and Biological Sciences Research Council (UK). Since 2008, I have reviewed workshop, working group and postdoc applications for the National Institute for Mathematical and Biological Synthesis (NIMBioS). BaMBA VIII: Biology and Mathematics in the Bay Area Organizing Committee: L. Pachter, S. Khuri, P. Koehl, M.Vazquez UC Berkeley; November 2012 A Mathematical Invitation to Knot Theory Organizing Committee: D. Karp, M. Vazquez, R. Wilson SACNAS meeting, Seattle, WA; October 2012 Special Session on Knotting in Linear and Ring Polymer Models (#1078) Organizers: Tetsuo Deguchi, Ken Millett, Eric Rawdon, Mariel Vazquez AMS Spring Western Sectional Meeting; Honolulu, Hawaii; March 3-4 2012 Special Session on Measures of Entanglement of Macromolecules and their Applications (#57A)

Mariel Vazquez

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Joint Mathematics Meetings; New Orleans, LA; January 2011 Modern Mathematics Workshop; SACNAS meetings (2009 Dallas TX; 2010 Anaheim CA) This workshops on contemporary research in mathematics are sponsored by all the US-based Math Institutes (http://www.mathinstitutes.org/diversity/sacnas.html) SIAM mini-symposium: New trends in Mathematical Biology Annual Joint Mathematics Meetings of the AMS and the MAA San Francisco, CA; January, 2010 BaMBA V: Biology and Mathematics in the Bay Area Organizing Committee: S. Khuri, Michael Levitt, J. Stuart and M.Vazquez University of California Santa Cruz; November 2009 1st San Francisco International meeting on DNA topology Chair of the Organizing Committee San Francisco, CA; April 22-26, 2009. Special Session: Applications of knot theory to the entanglement of biopolymers Meeting #1041 from the American Mathematical Society San Francisco, CA April 24th-25th, 2009 BaMBA III: Biology and Mathematics in the Bay Area Organizing Committee: S. Khuri, P. Koehl, M. Levitt, J. Stuart, M.Vazquez San Jose State University; November 2007 BaMBA I: Biology and Mathematics in the Bay Area Organizing Committee: J. Arsuaga, S. Hosten, B. Sturmfels, M. Vazquez San Francisco State University; November 2005

Service to Governmental Agencies

Board of advisers (BOA) and the Committee to Promote Diversity (CPD) of the NSF National Institute for Mathematical and Biological Synthesis (NIMBioS). Fall 2008-Fall 2012

Service to Public DNA topology booth and Private Bay Area Science Festival Organizations

ATT Park, November 2011 Two times panelist at the Physical Sciences and Mathematics Panel at the Northern California Forum for Diversity in Graduate Education (Fall 2006, Mills College; Fall 2008, UC Berkeley)

Mariel Vazquez

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Student mentor and student presentation judge SACNAS meetings (Kansas City, October 2007; Dallas, TX, October 2009; Anaheim CA, Sept. 2010) Service within the University

I have served in several committees at the department, College and University levels. Other activities: 1. Lecturer at the SFSU student Welcome Days in 2007, 2008, and 2009. The SFSU Welcome days consist of 1 day of activities to welcome the incoming class of students before the start of the Fall semester; 2. Faculty mentor for Fall 2008 Study Abroad Segment III cluster; 3. NSF fellowship grant writing workshop for SFSU students, Summer 2009, Summer 2010; 4. Keynote Speaker, COSE Student Project Showcase.

Professional Societies

American Mathematical Society (AMS), Society for Industrial and Applied Mathematics (SIAM)

Languages

Fluent in Spanish, French and English Reading and comprehension in Italian

Mariel Vazquez

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