34. Segal, M., Xiong, H., Capurso, D.,
Vazquez, M., and Arsuaga, J.,
Vazquez, M., Curriculum Vitae 6
Reproducibility of Three-Dimensional Chromatin Configuration
Reconstructions (2014) Biostatistics, Epub ahead of print, Feb
11.
32. 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 [Book Chapter]
29. K. Ishihara, R. Scharein, Y. Diao, J.
Arsuaga, M. Vazquez, and K.Shimokawa,
Bounds for the minimum step number of knots confined to
slabs in the simple cubic
lattice (2012) J.Phys
A.: Math. Theor. 45: 065003
28. Soteros, C., Ishihara, K., Shimokawa,
K., Szafron, M., and Vazquez, M., Signed Unknotting
Number and Knot Chirality Discrimination via Strand
Passage, Progress of Theoretical Physics
Supplement, Proceedings of the Conference “Statistical
Physics and Topology of Polymers with Ramifications to
Structure and Function of DNA and Proteins, YITP, Kyoto, 2-6
August 2010
27. Diao, Y., Hinson, K., Kaplan, T.,
Vazquez, M, and Arsuaga, J.,The
effects of density on the topological structure of the
mitochondrial DNA from trypanosomes, Journal of
Mathematical Biology, in
press, online DOI:
10.1007/s00285-011-0438-0
26. Portillo, J.*, Diao, Y., Scharein,
R., Arsuaga, J., and Vazquez, M., On
the mean and varaince of the writhe of random
polygons, J.
of Phys. A: Math Theor. 44 (2011) 275004
25. Shimokawa, K., and Vazquez,
M., DNA and Knot Theory (in
Japanese), Sugaku (2010) 62, The Mathematical Society of
Japan (Expository paper) Note:
The
English version will appear in “Sugaku Expositions”
(AMS)
24. 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 (2010) Topology
and its Applications 157 (1): 157-164
23. 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(2009) J.
Phys. A :Math. Theor. 42: 475006
22. Darcy, I. , Luecke, J. and
Vazquez, M., Tangle analysis of
difference topology experiments: applications to a Mu
protein-DNA complex (2009) Algebraic and Geometric
Topology 9: 2247-2309. This preprint can also be
accessed from the IMA preprint series. PDF
21. Arsuaga, J., Diao, Y., and
Vazquez, M., Mathematical Methods in
DNA Topology: Applications to Chromosome Organization and
Site-specific Recombination, (2009) 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, pp. 7-36
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, (2007) Unlinking chromosomes catenated
in vivo by site-specific recombination EMBO
J 26(19):4228-4238
18. 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
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. 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)
14. 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)
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. 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)
11. 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)
10.M. Vazquez, D.W.
Sumners, Tangle Analysis of Gin recombination,
Math. Proc. Camb. Phil. Soc. (2004) 136:565-582 (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
