63 entries « 1 of 2 »

2018

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

A Symmetry Motivated Link Table (submitted) Journal Article

2018.

Links | BibTeX

Moore, A., Vazquez, M.

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

ArXiv e-prints, 2018.

BibTeX

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.

Links | BibTeX

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.

BibTeX

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.

BibTeX

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 ; 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.

Links | BibTeX

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.

BibTeX

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.

BibTeX

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.

BibTeX

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.

Links | BibTeX

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

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.

Links | BibTeX

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.

BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

Darcy, I. K.; Vazquez, M.

Đetermining the topology of stable protein-ĐNA complexes Journal Article

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

Links | BibTeX

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

New biologically motivated knot table Journal Article

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

Links | BibTeX

Rodriguez V, Diao Y.; Arsuaga J.

Percolation phenomena in randomized topological networks. Journal Article

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

BibTeX

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.

Links | BibTeX

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.

BibTeX

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.

BibTeX

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.

BibTeX

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.

Abstract | Links | BibTeX

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.

BibTeX

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.

Links | BibTeX

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.

Abstract | Links | BibTeX

2010

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.

BibTeX

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.

BibTeX

2009

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.

BibTeX

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.

BibTeX

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.

Links | BibTeX

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

2008

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.

BibTeX

2007

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.

Links | BibTeX

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.

Links | BibTeX

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.

BibTeX

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.

BibTeX

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.

BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

BibTeX

2005

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

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.

Links | BibTeX

2004

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.

Links | BibTeX

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.

BibTeX

63 entries « 1 of 2 »