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68 entries « 1 of 3 »


Pouokam, M., Cruz, B., Burgess, S., Segal, M., Vazquez, M., Arsuaga, J.

The Rabl configuration limits topological entanglement of chromosomes in budding yeast. Journal Article

Scientific Reports, 9 (1), pp. 6795, 2019, ISBN: 2045-2322.

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Walker, S., Arsuaga, J., Calderer, C., Hiltner, L., Vazquez, M.

Fine Structure of Viral dsDNA Encapsidation Journal Article

ArXiv e-prints(Condensed Matter - Soft Condensed Matter, submitted), 2019.

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

Distance one lens space fillings and band surgery on the trefoil knot Journal Article

ArXiv e-prints( Algebraic & Geometric Topology, accepted.), 2019.

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Ibrahim, L., Liu, P., Klingbeil, M., Diao, U., Arsuaga, J.

Estimating properties of kinetoplast DNA by fragmentation reactions Journal Article

Journal of Physics A: Mathematical and Theoretical, 52 (3), 2018.

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Moore, A., Vazquez, M.

Recent advances on the non-coherent band surgery model for site-specific recombination Journal Article Forthcoming, Forthcoming, ("to appear in Contemporary Mathematics issue on the AMS Special Session on Topology of Biopolymers).

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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.

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

A Symmetry Motivated Link Table Journal Article

Symmetry, 10 , pp. 604, 2018.

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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.

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

A Liquid Crystal Model of Viral DNA Encapsidation (submitted) 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 and 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.

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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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68 entries « 1 of 3 »