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Vazquez, M.E. Knots and DNA, Revista Situs (1995) IMATE, UNAM. Trigueros, S.*, Arsuaga, J., Vazquez, M.E., Sumners, D.W., and Roca, J. Novel Display of knotted DNA molecules by two-dimensional gel electrophoresis, Nucleic Acids Research (2001) 29(13): e67. Arsuaga, J., Vazquez, M., Trigueros, S.*, Sumners, D.W., and Roca, J. Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids, Proc. Natl. Acad. Sci. USA (2002) 99(8): 373-5377. Saka, Y.† and Vazquez, M. TangleSolve: topological analysis of site-specific recombination, Bioinformatics (2002) 18: 1011-1012. Hlatky, L., Sachs, R.K., Vazquez, M., and Cornforth, M.N. Radiation-induced chromosome aberrations: insights gained from biophysical modeling, Bioessays (2002)24:714-723 Sachs, R.K., Arsuaga, J., Vazquez, M., Hahnfeldt, P., and Hlatky, L. Using Graph Theory to Analyze Chromosome Aberrations, Radiation Research (2002) 159(5): 556-567. Cornforth, M.N., Greulich-Bode, K.M., Loucas, B.D., Arsuaga, J., Vazquez, M., Sachs, R.K., Bruckner, M., Molls, M., Hahnfeldt, P., Hlatky, L., and Brenner, D.J., Chromosomes are predominantly located randomly with respect to each other in interphase human cells, Journal of Cell Biology (2002) 159(2): 237-244. Vazquez, M., Greulich-Bode, K.M., Arsuaga, J., Cornforth, M.N., Bruckner, M., Sachs, R.K., Hlatky, L., Molls, M., and Hahnfeldt, P. Computer analysis of mFISH chromosome aberration data uncovers an excess of very complex metaphases, International Journal of Radiation Biology (2002) 78:1103-1116. Arsuaga, J., Tam, R., Vazquez, M., Sumners, D.W., and Harvey, S. Investigation of viral DNA packaging using molecular mechanics models, Journal of Biophysical Chemistry (2002) 101-102(1): 475-484. Vazquez, M., and Sumners, D.W. Tangle Analysis of Gin Recombination, Math. Proc. Camb. Phil. Soc. (2004) 136: 565-582. Arsuaga, J., Greulich-Bode, K., Vazquez, M., Hahnfeldt, P., Brenner, J., Sachs, R.K., and Hlatky, L. Chromosome spatial clustering expressed through radiogenic aberrations, International Journal of Radiation Biology (2004) 80(7): 507-515. Levy, D.*, Vazquez, M., Cornforth, M., Loucas, B., Sachs, R.K., and Arsuaga, J., Comparing DNA damage processing pathways by computer analysis of chromosome painting data, J. Comp. Biol. (2004) 11(4): 626-641. Vazquez, M., Colloms, S.D., and Sumners, D.W. A unique mechanism for Xer recombination is suggested by tangle analysis, J. Mol. Biol. (2005) 346:493-504. Vives, S., Loucas, B., Vazquez, M., Brenner, D., Sachs, R.K., Hlatky, L., Cornforth, M., and Arsuaga, J., SCHIP: Statistics of Chromosome Interphase Positioning, Bioinformatics (2005) 21(14): 3181-3182. Arsuaga, J., Vazquez, M., McGuirck, P.†, Trigueros, S., Sumners, D.W., and Roca, J., DNA knots reveal a chiral organization of DNA in phage capsids, Proc. Natl. Acad.Sci. USA (2005) 102(26):9165-9169. Ardanza-Trevijano, S., Arsuaga, J., Crespo J. A., Extremiana, J. I., Hernandez, L.J., Rivas, M. T., Roca, J., and 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. Hua, X.†, Raghavan, B.†, Nguyen, D.†, Arsuaga, J., and Vazquez, M., Random State Transitions of Knots: a first step towards modeling unknotting by type II topoisomerases, Topology and its applications 157(7):1381-1397 Zheng, W.†, Galloy, C., Hallet, B., and Vazquez, M., 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. Blackstone, T.†, McGuirk, P.†, Liang, C.*, Roca, J., Arsuaga, J., and Vazquez, M., 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. Grainge, I., Bregu, M., Vazquez, M., Sivanathan, V.*, Ip, S.Y.P., and Sherratt, D.J. Unlinking chromosome catenanes in vivo by site-specific recombination, EMBO Journal (2007) 26(19): 4228-38. Arsuaga, J., Diao, Y., and Vazquez, M., Mathematical Methods in DNA Topology: Applications to Chromosome Organization and Site-specific Recombination, 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, (2009) pp. 7-36. 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. 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. 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. Shimokawa, K., and Vazquez, M., DNA and Knot Theory (Japanese), (2011) Sugaku 63(2): 237-242 Expository paper.