63 entries « 1 of 2 »


Witte, S., Flanner, M., Vazquez, M.

A Symmetry Motivated Link Table (submitted) Journal Article


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Moore, A., Vazquez, M.

A note on band surgery and the signature of a knot (submitted) Journal Article

ArXiv e-prints, 2018.



Ishihara, K., Pouokam, M., Suzuki, A., Scharein, R., Vazquez, M., Arsuaga, J., Shimokawa, K.

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

Journal of Physics A: Mathematical and Theoretical, 50 (21), pp. 215601, 2017.

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Stolz, R., Yoshida, M., Brasher, R., Flanner, M., Ishihara, K., Sherratt, D.-J., Shimokawa, K., Vazquez, M.

Pathways of DNA unlinking: A story of stepwise simplification Journal Article

Scientific Reports, 7 (1), pp. 12420, 2017, ISBN: 2045-2322.

Abstract | Links | BibTeX

Arsuaga, J., Calderer, M, Hiltner, L., Vazquez, M.

A Liquid Crystal Model of Viral DNA Encapsidation (submitted) Journal Article

ArXiv e-prints, 2017.


Moore, A., Vazquez, M., Lidman T.

Distance one lens space fillings and band surgery on the trefoil knot ( Algebraic & Geometric Topology, accepted.) Journal Article

ArXiv e-prints, 2017.



Sergio, A.-T., Gonzalez, G., Borrman, T., Garcia, J. L., Arsuaga, J.

Topological Analysis of Amplicon Structure in Comparative Genomic Hybridization (CGH) Data: An Application to ERBB2/HER2/NEU Amplified Tumors Book Chapter

Bac, Alexandra ; Mari, Jean-Luc (Ed.): Computational Topology in Image Context: 6th International Workshop, CTIC 2016, Marseille, France, June 15-17, 2016, Proceedings, pp. 113–129, Springer International Publishing, Cham, 2016, ISBN: 978-3-319-39441-1.

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Arsuaga J., Borrman T., Cavalcante R., Gonzalez G.; Park C

Identification of Copy Number Aberrations in Breast Cancer Subtypes using Persistence Topology. Journal Article

Microarrays, 4 (3), pp. 339-369, 2015.


Arsuaga J., Heskia I., Hosten S.,; Maskalevich T.

Uncovering Proximity of Chromosome Territories using Classical Algebraic Statistics. Journal Article

Journal of Algebraic Statistics., 6 (2), pp. 133-149, 2015.


Diao Y., Hinson K., Sun Y.; Arsuaga J.

The effect of volume exclusion on the formation of DNA minicircle networks. Journal Article

J. Phys. A Math Theor., 48 (43), pp. 435202, 2015.


Arsuaga, J.; Jayasinghe, R. G.; Scharein, R. G.; Segal, M. R.; Stolz, R. H.; Vazquez, M.

Current theoretical models fail to predict the topological complexity of the human genome Journal Article

Front Mol Biosci, 2 , pp. 48, 2015.

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Diao, Y. , Rodriguez, V., Klingbeil, M., Arsuaga, J.

Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA Journal Article

PLoS ONE, 10 (6), pp. e0130998, 2015, ISBN: 1932-6203.

Abstract | Links | BibTeX


Segal, M. R.; Xiong, H.; Capurso, D.; Vazquez, M.; Arsuaga, J.

Reproducibility of 3Đ chromatin configuration reconstructions Journal Article

Biostatistics, 15 (3), pp. 442–456, 2014.

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Arsuaga J., Diao Y, Klingbeil M.; Rodriguez V.

Properties of Topological Networks of Flexible Polygonal Chains. Journal Article

Mol. Based. Math. Bio., 2 , pp. 98-106, 2014.


Ishihara, K., Shimokawa, K., Vazquez, M.

Site-specific recombination modeled as a band surgery: applications to Xer recombination Incollection

Discrete and topological models in molecular biology, pp. 387–401, Springer, Heidelberg, 2014.

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Shimokawa, K.; Ishihara, K.; Grainge, I.; Sherratt, D. J.; Vazquez, M.

FtsK-dependent XerCĐ-dif recombination unlinks replication catenanes in a stepwise manner Journal Article

Proc. Natl. Acad. Sci. U.S.A., 110 (52), pp. 20906–20911, 2013.

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Darcy, I. K.; Vazquez, M.

Đetermining the topology of stable protein-ĐNA complexes Journal Article

Biochem. Soc. Trans., 41 (2), pp. 601–605, 2013.

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Brasher, R.; Scharein, R. G.; Vazquez, M.

New biologically motivated knot table Journal Article

Biochem. Soc. Trans., 41 (2), pp. 606–611, 2013.

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Rodriguez V, Diao Y.; Arsuaga J.

Percolation phenomena in randomized topological networks. Journal Article

J. Phys.: Conf. Ser., 454 , pp. 012070, 2013.



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

Ŧhe effects of density on the topological structure of the mitochondrial ĐNA from trypanosomes Journal Article

J Math Biol, 64 (6), pp. 1087–1108, 2012.

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Arsuaga J , Baas N, DeWoskin D, Mizuno H,; Pankov A, Park C

A topological signature derived from expression profiles for the identification of breast cancer subtypes. Journal Article

Applicable Algebra in Engineering, Communication and Computing, 23 (1), pp. 3-15, 2012.


Arsuaga J, Diao Y; Hinson K,

The growth of minicircle networks on regular lattices Journal Article

J. of Phys. A: Math. Theor., 45 , pp. 035004, 2012.


Arsuaga J, Diao Y; Hinson K

The effect of angle restriction on the topological characteristics of minicircle networks. Journal Article

J. Stat. Phys., 146 , pp. 434-445, 2012.


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

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

Journal of Physics A: Mathematical and Theoretical, 45 (6), pp. 065003, 2012.

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Blackstone, T, Scharein, R., Varela, R., Diao, Y.,; Arsuaga J.

Modeling Chromosome Intermingling Using Overlapping Uniform Random Polygons. Journal Article

Journal of Mathematical Biology, 62 (3), pp. 371-89, 2011.


Portillo, J.; Diao, Y.; Scharein, R.; Arsuaga, J.; Vazquez, M.

On the mean and variance of the writhe of random polygons Journal Article

J Phys A Math Theor, 44 (27), pp. 275004, 2011.

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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.

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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

Stockley, P G; Twarock., R (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.

Abstract | Links | BibTeX


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

Kawauchi, A (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.


63 entries « 1 of 2 »