Publications

DNA topology

• 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, Unlinking chromosome catenanes in vivo by site-specific recombination (2007) 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 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 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)
  
  
• S. Ardanza-Trevijano, J. Arsuaga, J.A. Crespo, J.I. Extremiana, L.J. Hernandez, M. Rivas, J. Roca and M. Vazquez, La topologia como herramienta en otros campos (in press) La Gaceta de la Real Sociedad Matematica Espanola. (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)
  
  
• 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)
  
  
• M. Vazquez, D.W. Sumners, Tangle Analysis of Gin recombination, Math. Proc. Camb. Phil. Soc. (2004) 136:565-582 (PDF)
  
  
• J. Arsuaga, R. Tam, M. Vazquez, D.W. Sumners, S. Harvey, Investigation of viral DNA packaging using molecular mechanics models, Journal of Biophysical Chemistry (2002)  101-102(1):475-484 (PDF) 
  
  
• Y. Saka, M. Vazquez, TangleSolve: topological analysis of site-specific recombination, Bioinformatics (2002) 18:1011-1012 (PDF)
  
  
• J. Arsuaga, M. Vazquez, S. Trigueros, D.W. Sumners, J. Roca, Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids, Proc. Natl. Acad. Sci. USA (2002) 99(8):5373-5377 (PDF)
  
  
• S. Trigueros, J. Arsuaga, M.E. Vazquez, D.W. Sumners, J. Roca, Novel display of knotted DNA molecules by two-dimensional gel electrophoresis, Nucleic Acids Research (2001) 29(13):e67 (PDF)
  
  
• M.E. Vazquez, Tangle Analysis of Site-specific Recombination: Gin and Xer systems, PhD Dissertation, Mathematics FSU (2000) 
  
  
• M.E. Vazquez, Knots and DNA, Revista Situs (1995) IMATE, UNAM, Mexico
  
  

• M.E. Vazquez, Applications of Knot Theory to the Study of DNA, B.Sc. Thesis, Mathematics, UNAM (1995)

Radiation Biology

• 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)
  
  
• 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, K.M. Greulich-Bode, J. Arsuaga, M.N. Cornforth, M. Bruckner, R.K. Sachs, P. Hahnfeldt, M. Molls, L. Hlatky, Computer analysis of mFISH chromosome aberration data uncovers an excess of very complex metaphases, International Journal of Radiation Biology (2002) 78:1103-1116 ( PDF)
  
  
• M.N. Cornforth, K.M. Greulich-Bode, B.D. Loucas, J. Arsuaga, M. Vazquez, R.K. Sachs, M. Bruckner, M. Molls, P. Hahnfeldt, L. Hlatky, D.J. Brenner Chromosomes are predominantly located randomly with respect to each other in interphase human cells, Journal of Cell Biology (2002) 159(2):237-244 (PDF)
          Refer also to accompanying commentary: Chromosomal Cliques by A.W. Dove, Journal of Cell Biology (2002) 159(2):199 (PDF)
  
  
• R.K. Sachs, J. Arsuaga, M. Vazquez, P. Hahnfeldt, L. Hlatky, Using Graph Theory to Analyze Chromosome Aberrations, Radiation Research (2002) 159(5):556-567 (PDF)
  
  
• L. Hlatky, R.K.Sachs, M. Vazquez, M.N. Cornforth, Radiation-induced chromosome aberrations: insights gained from biophysical modeling, Bioessays (2002) 24:714-723 (PDF)
  

Manuscripts submitted

• Darcy, I. , Luecke, J. and Vazquez, M., Unlinking chromosome catenaned in vivo by site-specific recombination (submitted October 2007). 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,  submitted May 2008.