jump to page contentSan Francisco State University  

Mariel Vazquez

 images of SFSU

image coming soon placeholder

Math Department

College of Science and Engineering

SFSU Home

Welcome!

Courses :: Papers and Publications:: Research :: Professional Associations

 

Contact Information

Title:

Assistant Professor

Office Hours:

Tuesday 3:30-4:30, or by appointment

E-mail:

mariel@math.sfsu.edu

Office Phone:

(415) 338-2071

Mailing Address:

San Francisco State University
Department of Mathematics,
Thorton Hall Room #928
1600 Holloway Ave
San Francisco, CA 94132
  
Fifth BaMBA Meeting
               
                November 14, 2009  UC Santa Cruz
The meeting is free (please register on the site) and all are welcome to attend.

The Biology and Mathematics in the Bay Area (BaMBA) meeting is a one-day annual event that takes place in the San Francisco Bay Area. Speakers are leading researchers who discuss applications of mathematics, statistics, and computer science in modern biology.

The goal of the meeting is to encourage dialogue between researchers and students from different disciplines in an atmosphere that promotes the exchange of ideas and viewpoints. The first meeting was hosted by San Francisco State University, the second by the MSRI at Berkeley, the third at San Jose State University, and the fourth at UC Davis. BaMBA V will take place at UC Santa Cruz on November 14, 2009.

Attendance is open to everyone but we expect the majority of the participants from the Bay Area universities (Stanford University, UC Berkeley, UC Santa Cruz, UC San Francisco, San Jose State University, San Francisco State University, University of Santa Clara, etc). In 2008, BaMBA IV attracted more than 100 participants.

Courses Fall09::

Recent Publications ::

        Submitted

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 (accepted, J. Phys. A :Math. Theor.).

Darcy, I. , Luecke, J. and Vazquez, M., Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex (accepted, Algebraic and Geometric Topology). This preprint can also be accessed from the IMA preprint series.

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. In press.

Recent papers published and in press

  • Arsuaga, J., Diao, Y., and Vazquez, M., Mathematical Methods in DNA Topology: Applications to Chromosome Organization and Site-specific Recombination, to be included in the volume, 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) in press.

  • Ardanza-Trevijano, S, Arsuaga, J, Crespo, JA, Hernandez, LJ, Rivas, MT, Roca, J. and Vazquez, M,  Invariantes Topologicos en el ADN, los Fullerenos y la Teoria de Eleccion Social (2007) La Gaceta de la RSME 10(3):611-632

  • Grainge, I, Bregu, M, Vazquez, M, Sivanathan, V, Ip, SC, and Sherratt, DJ, (2007) Unlinking chromosomes catenated in vivo by site-specific recombination EMBO J 26(19):4228-4238

  • Hua, X, Raghavan, B, Nguyen, D,  Arsuaga, J, and Vazquez, M (2007) Random State Transitions of Knots: a first step towards modeling unknotting by type II topoisomerases Topology and its Applications 154(7):1381-1397

  • Zheng, W, Galloy, C, Hallet, B and Vazquez, M, The tangle model for site-specific recombination: a computer interface and the TnpI-IRS recombination system (2007) Proceedings of International Workshop on Knot Theory for Specific Objects, Ed. A. Kawauchi, OCAMI studies 1(2): 251-271(PDF)

  • Blackstone, T, McGuirk, P, Liang, C, Roca, J, Arsuaga, J, Vazquez, M., The role of writhe in DNA condensation (2007) Proceedings of the International Workshop on Knot Theory for Scientific Objects, Ed. A. Kawauchi, OCAMI studies 1(2): 239-250.(PDF)

  • J. Arsuaga, M. Vazquez, P. McGuirck, Trigueros, S., D.W. Sumners, J. Roca DNA knots reveal a chiral organization of DNA in phage capsids; Proc. Natl Acad Sci U.S.A (2005) 102(26):9165-9. (PDF)

  • Vives, S. Bradford, L., Vazquez, M., Brenner, D.J., Sachs, R.K., Hlatky, L, Cornforth, M. and Arsuaga, J.  SCHIP: Statistics of Chromosome Interphase Positioning Based on Interchange Data, Bioinformatics. (2005) 21(14):3181-2 (PDF)

  • M. Vazquez, S.D. Colloms, D.W. Sumners, Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single 3-dimensional topological pathway; J. Mol Biol (2005) 346: 493-504 (PDF)

  • Arsuaga, J., Greulich-Bode, K., Vazquez, M., Brukner, M.,Hahnfeldt,P., Brenner, D.J., Sachs, R. and Hlatky, L. Chromosome positioning through radiogenic aberrations, Int. J. Radiat. Biol. (2004) 80(7):507-15 (PDF)

  • D. Levy, M. Vazquez, B. Loucas, M. Cornforth,  R.K. Sachs, J. Arsuaga, Comparing DNA damage processing pathways by computer analysis of chromosome painting data, J. Comput. Biol. (2004) 11(4): 626-41 (PDF)

  • M. Vazquez, D.W. Sumners, Tangle Analysis of Gin recombination, Math. Proc. Camb. Phil. Soc. (2004) 136:565-582 (PDF)


    Complete list of Publications

top of page

Research Projects/Interests ::

 I am interested in the application of topology and geometry to understand biological processes.

Software ::

TangleSolve: java applet for the mathematical analysis of site-specific recombination

top of page

Professional Associations ::

American Mathematical Society  (AMS)

Mathematical Association of America (MAA)

International Society for Computational Biology (ISCB)

Association for Women in Mathematics (AWM)

 

 
last updated: August 2008
  top of page