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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.
Peer-reviewed publications
21. 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.
20. 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
19. 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
18. 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 (2007) Topology
and its
applications 157(7):1381-1397
17. 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)
16. 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)
15. 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)
14. 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)
13. 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)
12. M. Vazquez, D.W. Sumners, Tangle Analysis of Gin
recombination, Math. Proc. Camb. Phil. Soc. (2004) 136:565-582 (PDF)
11. 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)
10. 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)
9. 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)
8. Y. Saka, M. Vazquez,
TangleSolve: topological
analysis of site-specific recombination, Bioinformatics (2002)
18:1011-1012 (PDF)
7. 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)
6. 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)
5. 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)
4. 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)
3. 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)
2. 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)
1. M.E. Vazquez, Knots and DNA, Revista Situs
(1995)
IMATE, UNAM, Mexico
Theses
M.E. Vazquez, Tangle Analysis of Site-specific
Recombination: Gin and Xer systems, PhD Dissertation, Mathematics
FSU (2000)
M.E. Vazquez, Applications
of Knot Theory to the Study of DNA, B.Sc. Thesis, Mathematics, UNAM(1995)