Mariel Vazquez

Math Department

College of Science and Engineering

SFSU Home

Welcome!

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

Courses Spring 2010::

• Math414-01/Math714-01: Analyzing DNA topology with Mathematical and Computational Methods (course website)
  

Recent Publications ::

     

Recent papers published and in press

• 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 (2010) Topology and its Applications 157 (1): 157-164
  
  
  
• 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 (2009) J. Phys. A :Math. Theor. 42: 475006.
  
  
• Darcy, I. , Luecke, J. and Vazquez, M., Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex (2009) Algebraic and Geometric Topology 9: 2247-2309. This preprint can also be accessed from the IMA preprint series.
  PDF
  
  
• Arsuaga, J., Diao, Y., and Vazquez, M., Mathematical Methods in DNA Topology: Applications to Chromosome Organization and Site-specific Recombination, (2009) in 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, pp. 7-36.
  
  
• 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
  

Research Funding:

My research is funded by the National Institutes of Health and by the National Science Foundation:

NSF Mathematical Biology (2009-2013)
Topological characterization of DNA organization in bacteriophages
co-PIs Javier Arsuaga (Leading PI; SFSU), Yuanan DIao (co-PI, UNC Charlotte)

NIH MBRS SCORTopoE program (2007-2010)
Computer Analysis of DNA Unknotting by Topoisomerase II

NIH NCMHD RIMI (2008-2013)
Health Disparities Research at San Francisco State University
Multiscale analysis of CGH arrays of breast cancer patients using computational algebraic topology
Co-PI: Javier Arsuaga (SFSU)

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

Professional Associations ::

American Mathematical Society  (AMS)

Mathematical Association of America (MAA)

International Society for Computational Biology (ISCB)

Association for Women in Mathematics (AWM)