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Welcome!
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Courses :: Papers and
Publications:: Research :: Professional Associations
Contact
Information
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Title:
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Assistant
Professor
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Office Hours:
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Tuesday
3:30-4:30, or by appointment
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E-mail:
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mariel@math.sfsu.edu
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Office Phone:
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(415) 338-2071
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Mailing Address:
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San Francisco
State University
Department of Mathematics,
Thorton Hall Room #928
1600 Holloway Ave
San Francisco, CA 94132
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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.
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Courses Fall09::
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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

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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

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Professional Associations
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American Mathematical Society (AMS)
Mathematical Association of America (MAA)
International Society for Computational Biology (ISCB)
Association for Women in Mathematics (AWM)
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| last updated:
August 2008 |
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