# Publications

## 2018 |

A Symmetry Motivated Link Table (submitted) Journal Article 2018. |

A note on band surgery and the signature of a knot (submitted) Journal Article ArXiv e-prints, 2018. |

## 2017 |

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. |

Pathways of DNA unlinking: A story of stepwise simplification Journal Article Scientific Reports, 7 (1), pp. 12420, 2017, ISBN: 2045-2322. |

A Liquid Crystal Model of Viral DNA Encapsidation (submitted) Journal Article ArXiv e-prints, 2017. |

Distance one lens space fillings and band surgery on the trefoil knot ( Algebraic & Geometric Topology, accepted.) Journal Article ArXiv e-prints, 2017. |

## 2016 |

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. |

## 2015 |

Identification of Copy Number Aberrations in Breast Cancer Subtypes using Persistence Topology. Journal Article Microarrays, 4 (3), pp. 339-369, 2015. |

Uncovering Proximity of Chromosome Territories using Classical Algebraic Statistics. Journal Article Journal of Algebraic Statistics., 6 (2), pp. 133-149, 2015. |

The effect of volume exclusion on the formation of DNA minicircle networks. Journal Article J. Phys. A Math Theor., 48 (43), pp. 435202, 2015. |

Current theoretical models fail to predict the topological complexity of the human genome Journal Article Front Mol Biosci, 2 , pp. 48, 2015. |

Orientation of DNA Minicircles Balances Density and Topological Complexity in Kinetoplast DNA Journal Article PLoS ONE, 10 (6), pp. e0130998, 2015, ISBN: 1932-6203. |

## 2014 |

Reproducibility of 3Đ chromatin configuration reconstructions Journal Article Biostatistics, 15 (3), pp. 442–456, 2014. |

Properties of Topological Networks of Flexible Polygonal Chains. Journal Article Mol. Based. Math. Bio., 2 , pp. 98-106, 2014. |

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. |

## 2013 |

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. |

Đetermining the topology of stable protein-ĐNA complexes Journal Article Biochem. Soc. Trans., 41 (2), pp. 601–605, 2013. |

New biologically motivated knot table Journal Article Biochem. Soc. Trans., 41 (2), pp. 606–611, 2013. |

Percolation phenomena in randomized topological networks. Journal Article J. Phys.: Conf. Ser., 454 , pp. 012070, 2013. |

## 2012 |

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. |

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. |

The growth of minicircle networks on regular lattices Journal Article J. of Phys. A: Math. Theor., 45 , pp. 035004, 2012. |

The effect of angle restriction on the topological characteristics of minicircle networks. Journal Article J. Stat. Phys., 146 , pp. 434-445, 2012. |

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. |

## 2011 |

Modeling Chromosome Intermingling Using Overlapping Uniform Random Polygons. Journal Article Journal of Mathematical Biology, 62 (3), pp. 371-89, 2011. |

On the mean and variance of the writhe of random polygons Journal Article J Phys A Math Theor, 44 (27), pp. 275004, 2011. |

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. |

Signed Unknotting Number and Knot Chirality Discrimination via Strand Passage Journal Article Progress of Theoretical Physics Supplement, 191 , pp. 78-95, 2011. |

## 2010 |

Emerging Topics in Physical Virology Book Chapter Stockley, P G; Twarock., R (Ed.): Chapter Topology of viral DNA., Imperial College Press., 2010. |

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. |

DNA and Knot Theory Miscellaneous Japanese version: The Mathematical Society of Japan; English version:, 2010. |

## 2009 |

A fast ergodic algorithm for generating ensembles of polygons. Journal Article J. Phys A: Math Theor., 42 (095204), 2009. |

The Average Crossing Number of Equilateral Random Polygons in Confined Volumes. Journal Article J. Phys. A: Math. Theor., 42 (465202), 2009. |

Tangle analysis of difference topology experiments: Applications to a Mu protein-DNA complex Journal Article Algebr. Geom. Topol., 9 (4), pp. 2247-2309, 2009. |

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. |

## 2008 |

DNA knotting in Spooling like conformations in Bacteriophages. Journal Article Journal Computational and Mathematical Methods in Medicine, 9 (3-4), pp. 303-316, 2008. |

## 2007 |

Unlinking chromosome catenanes in vivo by site-specific recombination Journal Article EMBO J., 26 (19), pp. 4228–4238, 2007. |

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. |

Characterization of Breast Cancer by Array CGH. Journal Article Biochemistry and Cell Biology, 85 (4), pp. 497-508, 2007. |

Linking of Uniform Random Polygons in Confined Spaces. Journal Article J. Phys. A: Math. Gen., 40 , pp. 1925-1936, 2007. |

Knotting of Uniform Random Polygons in Confined Spaces. Journal Article J. Phys. A: Math Gen., 40 , pp. 11697-11711, 2007. |

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. |

Topological invariant DNA Fullerenes and Social Choice Theory Journal Article The Gazette PSME, 10 (3), pp. 611-632, 2007. |

The role of writhe in DNA condensation Proceeding Proceedings of International Workshop on Knot Theory for Scientific Objects Universities Press, 1 , 2007. |

## 2005 |

SCĦIP: statistics for chromosome interphase positioning based on interchange data Journal Article Bioinformatics, 21 (14), pp. 3181–3182, 2005. |

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. |

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. |

SCHIP: Statistics of Chromosome Interphase Positioning Based on Interchange Data Journal Article Bioinformatics, 21 (14), pp. 3181-2, 2005. |

## 2004 |

Chromosome spatial clustering inferred from radiogenic aberrations Journal Article Int. J. Radiat. Biol., 80 (7), pp. 507–515, 2004. |

Genomic analysis of supercoiling sensitive genes in Escherichia coli: responses to topoisomerase inhibition. Journal Article Genome Biology 5, 11 (R-87.), 2004. |