Recent Publications ::
Submitted
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 (submitted, June 2009).
Darcy, I. , Luecke, J. and Vazquez, M., Tangle analysis of difference
topology experiments: applications to a Mu protein-DNA complex (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. In
press.
Recent papers published
and in press
- 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, (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
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San Francisco
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