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68 entries « 2 of 3 »


Diao, Y.; Hinson, K.; Kaplan, R.; Vazquez, M.; Arsuaga, J.

The effects of density on the topological structure of the mitochondrial DNA from trypanosomes Journal Article

Journal of Mathematical Biology, 64 (6), pp. 1087–1108, 2011, ISSN: 1432-1416.

Abstract | Links | BibTeX

Soteros, C., Ishihara, K., Shimokawa, K., Szafron, M., Vazquez, M.

Signed Unknotting Number and Knot Chirality Discrimination via Strand Passage Journal Article

Progress of Theoretical Physics Supplement, 191 , pp. 78-95, 2011.

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Arsuaga, J., Roca, J.; Sumners, D. W.

Emerging Topics in Physical Virology Book Chapter

P. G. Stockley; R. Twarock. (Ed.): Chapter Topology of viral DNA., Imperial College Press., 2010.


DeWoskin, D.; Climent, J.; Cruz-White, I.; Vazquez, M.; Park, C.; Arsuaga, J.

Applications of computational homology to the analysis of treatment response in breast cancer patients Journal Article

Topology and its Applications, 157 (1), pp. 157–164, 2010, ISBN: 0166-8641.

Abstract | Links | BibTeX

Shimokawa, K., Vazquez, M.

DNA and Knot Theory Miscellaneous

Japanese version: The Mathematical Society of Japan; English version:, 2010.



Varela R, Hinson K, Arsuaga J, Diao Y

A fast ergodic algorithm for generating ensembles of polygons. Journal Article

J. Phys A: Math Theor., 42 (095204), 2009.


Arsuaga J, Borgo B, Diao Y; Scharein R

The Average Crossing Number of Equilateral Random Polygons in Confined Volumes. Journal Article

J. Phys. A: Math. Theor., 42 (465202), 2009.


Isabel K Darcy, John Luecke; Mariel Vazquez

Tangle analysis of difference topology experiments: Applications to a Mu protein-DNA complex Journal Article

Algebr. Geom. Topol., 9 (4), pp. 2247-2309, 2009.

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R Scharein; K Ishihara; J Arsuaga; Y Diao; K Shimokawa; M Vazquez

Bounds for the minimum step number of knots in the simple cubic lattice Journal Article

Journal of Physics A: Mathematical and Theoretical, 42 (47), pp. 475006, 2009.

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Arsuaga J,; Diao Y

DNA knotting in Spooling like conformations in Bacteriophages. Journal Article

Journal Computational and Mathematical Methods in Medicine, 9 (3-4), pp. 303-316, 2008.



Grainge, I.; Bregu, M.; Vazquez, M.; Sivanathan, V.; Ip, S. C.; Sherratt, D. J.

Unlinking chromosome catenanes in vivo by site-specific recombination Journal Article

EMBO J., 26 (19), pp. 4228–4238, 2007.

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Hua, X.; Nguyen, D.; Raghavan, B.; Arsuaga, J.; Vazquez, M.

Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases Journal Article

Topol Appl, 154 (7), pp. 1381–1397, 2007.

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Climent, J., Mao, J., Garcia, J. L., Arsuaga, J., Perez-Losada, J.

Characterization of Breast Cancer by Array CGH. Journal Article

Biochemistry and Cell Biology, 85 (4), pp. 497-508, 2007.


Arsuaga, J., Blackstone, T., Diao,Y., Karadayi, E. , Saito, Y.

Linking of Uniform Random Polygons in Confined Spaces. Journal Article

J. Phys. A: Math. Gen., 40 , pp. 1925-1936, 2007.


Arsuaga J, Blackstone T, Diao Y, Karadayi E, Saito Y

Knotting of Uniform Random Polygons in Confined Spaces. Journal Article

J. Phys. A: Math Gen., 40 , pp. 11697-11711, 2007.


Zheng, W, Galloy, C, Hallet, B; Vazquez, M

The tangle model for site-specific recombination: a computer interface and the TnpI-IRS recombination system Inproceedings

A. Kawauchi (Ed.): Knot Theory for Scientific Objects, pp. 251-271, OCAMI studies 2007.

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Ardanza-Trevijano, S, Arsuaga, J, Crespo, JA, Hernandez, LJ, Rivas, MT, Roca, J.; Vazquez, M

Topological invariant DNA Fullerenes and Social Choice Theory Journal Article

The Gazette PSME, 10 (3), pp. 611-632, 2007.

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Blackstone, T., Mcguirk, P., Laing, C.,Vazquez M.; Roca, J.

The role of writhe in DNA condensation Proceeding

Proceedings of International Workshop on Knot Theory for Scientific Objects Universities Press, 1 , 2007.



Vives, S.; Loucas, B.; Vazquez, M.; Brenner, D. J.; Sachs, R. K.; Hlatky, L.; Cornforth, M.; Arsuaga, J.; Hlatky, L.

SCĦIP: statistics for chromosome interphase positioning based on interchange data Journal Article

Bioinformatics, 21 (14), pp. 3181–3182, 2005.

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Arsuaga, J.; Vazquez, M.; McGuirk, P.; Trigueros, S.; Sumners, D.; Roca, J.

ĐNA knots reveal a chiral organization of ĐNA in phage capsids Journal Article

Proc. Natl. Acad. Sci. U.S.A., 102 (26), pp. 9165–9169, 2005.

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Vazquez, M.; Colloms, S. D.; Sumners, D.

Ŧangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway Journal Article

J. Mol. Biol., 346 (2), pp. 493–504, 2005.

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Vives, S. Bradford, L., Vazquez, M., Brenner, D.J., Sachs, R.K., Hlatky, L, Cornforth, M.; Arsuaga, J.

SCHIP: Statistics of Chromosome Interphase Positioning Based on Interchange Data Journal Article

Bioinformatics, 21 (14), pp. 3181-2, 2005.

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Arsuaga, J.; Greulich-Bode, K. M.; Vazquez, M.; Bruckner, M.; Hahnfeldt, P.; Brenner, D. J.; Sachs, R.; Hlatky, L.

Chromosome spatial clustering inferred from radiogenic aberrations Journal Article

Int. J. Radiat. Biol., 80 (7), pp. 507–515, 2004.

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Peter, B., Arsuaga, J., Breier, A., Khodursky, A., Brown, P.,; Cozzarelli N. R.

Genomic analysis of supercoiling sensitive genes in Escherichia coli: responses to topoisomerase inhibition. Journal Article

Genome Biology 5, 11 (R-87.), 2004.


Levy, D.; Vazquez, M.; Cornforth, M.; Loucas, B.; Sachs, R. K.; Arsuaga, J.; Cornforth, M.

Comparing ĐNA damage-processing pathways by computer analysis of chromosome painting data Journal Article

J. Comput. Biol., 11 (4), pp. 626–641, 2004.

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Vazquez, M.; Witt Sumners, D.

Tangle analysis of Gin site-specific recombination Journal Article

Mathematical Proceedings of the Cambridge Philosophical Society, 136 , pp. 565-582, 2004.

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Postow, L., Hardy, C.D., Arsuaga, J.; Cozzarelli, N. R.

Topological domain structure of the Escherichia coli chromosome. Journal Article

Genes Dev, 18 (14), pp. 1766–1779, 2004, ISSN: 0890-9369 (Print); 0890-9369 (Linking).

Abstract | Links | BibTeX


Arsuaga, J.; Tan, R. K.; Vazquez, M.; Sumners, D. W.; Harvey, S. C.

Investigation of viral ĐNA packaging using molecular mechanics models Journal Article

Biophys. Chem., 101-102 , pp. 475–484, 2002.

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Vazquez, M.; Greulich-Bode, K. M.; Arsuaga, J.; Cornforth, M. N.; Bruckner, M.; Sachs, R. K.; Hlatky, L.; Molls, M.; Hahnfeldt, P.

Computer analysis of mFISĦ chromosome aberration data uncovers an excess of very complicated metaphases Journal Article

Int. J. Radiat. Biol., 78 (12), pp. 1103–1115, 2002.

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Sachs, R. K.; Arsuaga, J.; Vazquez, M.; Hlatky, L.; Hahnfeldt, P.

Using graph theory to describe and model chromosome aberrations Journal Article

Radiat. Res., 158 (5), pp. 556–567, 2002.

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68 entries « 2 of 3 »