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68 entries « 1 of 3 »

2019

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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2018

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

arxiv.org, 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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2017

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.

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2016

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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2015

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.

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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.

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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.

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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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2014

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.

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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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2013

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.

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2012

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.

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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.

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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.

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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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2011

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.

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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 »