Mariel Vazquez

Lab

Briggs 15
530-754-0416
mrlvazquez@ucdavis.edu

Research

My research lies at the interface of mathematics, polymer physics, and molecular biology. I specialize in the application of topological tools to study DNA.

My work is currently focused on two lines of inquiry:

1. DNA Topology: the mechanism of site-specific recombination, topoisomerase action, and the packing of chromosomes in human cells and viral capsids; using mathematical tools including know theory, low-dimensional topology, and Monte Carlo simulations.
   
2. Chromosomal Aberrations and Cancer: analysis of cancer genomic data and mechanisms of repair pathways; using biophysical models, graph theory, and topological data analysis.
   

Selected Publications

1. Walker, S., Arsuaga, J., Vazquez, M., Hiltner, L.*, Calderer, M.C. (2019). Liquid crystal model of viral DNA encapsidation. Submitted. arXiv: 1902.09188
2. Cruz, B., Calderer, M.C., Arsuaga, J., Vazquez, M. (2019). Computer simulations show that the bacteriophage packaging motor induces a chiral organization of the genome. Biophysical Journal. Submitted.
3. Moore, A.H., and Vazquez, M. (2019). A note on band surgery and the signature of a knot. arXiv:1806.02440.
4. Moore, A., and Vazquez, M. (2019) Recent advances on the non-coherent band surgery model for site-specific recombination, AMS Contemporary Mathematics. In press. https://arxiv.org/abs/1810.08751 [math.GT]
5. Lidman, T., Moore, A.H. and Vazquez, M. Distance one lens space fillings and band surgery on the trefoil knot. In press. arXiv:1710.07418v2 [math.GT]
6. Pouokam, M.*, Cruz, B., Burgess, S., Segal, M., Vazquez, M., and Arsuaga, J. (2019) The Rabl configuration limits topological entanglement of chromosomes in budding yeast. Scientific Reports. 9 (1): 6795.
7. Witte, S.*, Flanner, M., and Vazquez, M. (2018) A symmetry Motivated Link Table. Symmetry 10: 604 .
8. Stolz, R., Yoshida, M., Brasher, R., Flanner, M., Ishihara, K., Sherratt, D.-J., Shimokawa, K., Vazquez, M. Pathways of DNA unlinking: A story of stepwise simplification, Scientific Reports, 7 (1), pp. 12420, 2017, ISBN: 2045-2322.
9. Ishihara, K., Pouokam, M., Suzuki, A., Scharein, R., Vazquez, M., Arsuaga, J., Shimokawa, K. Bounds for minimum step number of knots confined to tubes in the simple cubic lattice, Journal of Physics A: Mathematical and Theoretical, 50 (21), pp. 215601, 2017.
10. Javier Arsuaga, Reyka Jayasinghe, Robert Scharein, Mark Segal and Vazquez, M., Current theoretical models fail to predict the topological complexity of the human genome, Frontiers in Molecular Biosciences 2, pp.48, 2015
11. Segal, M., Xiong, H., Capurso, D., Vazquez, M., and Arsuaga, J., Reproducibility of Three-Dimensional Chromatin Configuration Reconstructions (2014) Biostatistics, Epub ahead of print, Feb 11.
12. 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 110 (52) 20906-20911; 
Accompanying commentary: Jayaram, M., Mathematical validation of a biological model for unlinking replication catenanes by recombination (2013) PNAS 110 (52) 20854-20855.
13. 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, Springer ISBN 978-3-642-40192-3 [peer- reviewed Book Chapter].
14. Brasher, R. Scharein, R.G., and Vazquez, M., New biologically motivated knot table (2013) Biochemical Society Transactions 41(2): 606-611.
15. Darcy, I.K. and Vazquez, M., Determining the topology of stable protein-DNA complexes (2013) Biochemical Society Transactions 41(2): 601-605.

Honors and Awards

2018 Inaugural Fellow Association for Women in Mathematics

2016 Blackwell Tapia Prize

2014 Mohammed Dahleh Distinguished Lectureship Award, UC Santa Barbara

2012 Presidential Early Career Award for Scientists and Engineers PECASE (White House)

2011 CAREER Award (National Science Foundation)

2014 CAMPOS Faculty Scholar, UC Davis

Department and Center Affiliations

CAMPOS Faculty Director (2019-..)

CAMPOS Faculty Scholar

Department of Mathematics

Department of Microbiology and Molecular Genetics

Professional Societies

American Mathematical Society

Society for Industrial and Applied Mathematics

Association for Women in Mathematics

Teaching Interests

Quantitative methods in structural biology, DNA topology

Last updated: 2019-10-01