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Items: 19

1.

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

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

Sci Rep. 2019 May 1;9(1):6795. doi: 10.1038/s41598-019-42967-4.

2.

Pathways of DNA unlinking: A story of stepwise simplification.

Stolz R, Yoshida M, Brasher R, Flanner M, Ishihara K, Sherratt DJ, Shimokawa K, Vazquez M.

Sci Rep. 2017 Sep 29;7(1):12420. doi: 10.1038/s41598-017-12172-2.

3.

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

Arsuaga J, Jayasinghe RG, Scharein RG, Segal MR, Stolz RH, Vazquez M.

Front Mol Biosci. 2015 Aug 21;2:48. doi: 10.3389/fmolb.2015.00048. eCollection 2015.

4.

Reproducibility of 3D chromatin configuration reconstructions.

Segal MR, Xiong H, Capurso D, Vazquez M, Arsuaga J.

Biostatistics. 2014 Jul;15(3):442-56. doi: 10.1093/biostatistics/kxu003. Epub 2014 Feb 11.

5.

FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner.

Shimokawa K, Ishihara K, Grainge I, Sherratt DJ, Vazquez M.

Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):20906-11. doi: 10.1073/pnas.1308450110. Epub 2013 Nov 11.

6.

New biologically motivated knot table.

Brasher R, Scharein RG, Vazquez M.

Biochem Soc Trans. 2013 Apr;41(2):606-11. doi: 10.1042/BST20120278. Review.

PMID:
23514162
7.

Determining the topology of stable protein-DNA complexes.

Darcy IK, Vazquez M.

Biochem Soc Trans. 2013 Apr;41(2):601-5. doi: 10.1042/BST20130004. Review.

PMID:
23514161
8.

Unlinking chromosome catenanes in vivo by site-specific recombination.

Grainge I, Bregu M, Vazquez M, Sivanathan V, Ip SC, Sherratt DJ.

EMBO J. 2007 Oct 3;26(19):4228-38. Epub 2007 Sep 6.

9.

Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases.

Hua X, Nguyen D, Raghavan B, Arsuaga J, Vazquez M.

Topol Appl. 2007 Apr 1;154(7):1381-1397.

10.

DNA knots reveal a chiral organization of DNA in phage capsids.

Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners D, Roca J.

Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9165-9. Epub 2005 Jun 15.

11.

SCHIP: statistics for chromosome interphase positioning based on interchange data.

Vives S, Loucas B, Vazquez M, Brenner DJ, Sachs RK, Hlatky L, Cornforth M, Arsuaga J.

Bioinformatics. 2005 Jul 15;21(14):3181-2. Epub 2005 May 10.

PMID:
15886279
12.

Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway.

Vazquez M, Colloms SD, Sumners D.

J Mol Biol. 2005 Feb 18;346(2):493-504. Epub 2005 Jan 11.

PMID:
15670599
13.

Comparing DNA damage-processing pathways by computer analysis of chromosome painting data.

Levy D, Vazquez M, Cornforth M, Loucas B, Sachs RK, Arsuaga J.

J Comput Biol. 2004;11(4):626-41.

PMID:
15579235
14.

Investigation of viral DNA packaging using molecular mechanics models.

Arsuaga J, Tan RK, Vazquez M, Sumners DW, Harvey SC.

Biophys Chem. 2002 Dec 10;101-102:475-84.

PMID:
12488021
15.

Chromosomes are predominantly located randomly with respect to each other in interphase human cells.

Cornforth MN, Greulich-Bode KM, Loucas BD, Arsuaga J, Vázquez M, Sachs RK, Brückner M, Molls M, Hahnfeldt P, Hlatky L, Brenner DJ.

J Cell Biol. 2002 Oct 28;159(2):237-44. Epub 2002 Oct 28.

16.

Using graph theory to describe and model chromosome aberrations.

Sachs RK, Arsuaga J, Vázquez M, Hlatky L, Hahnfeldt P.

Radiat Res. 2002 Nov;158(5):556-67.

PMID:
12385633
17.

Radiation-induced chromosome aberrations: insights gained from biophysical modeling.

Hlatky L, Sachs RK, Vazquez M, Cornforth MN.

Bioessays. 2002 Aug;24(8):714-23. Review.

PMID:
12210532
18.

TangleSolve: topological analysis of site-specific recombination.

Saka Y, Vázquez M.

Bioinformatics. 2002 Jul;18(7):1011-2.

PMID:
12117800
19.

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.

Arsuaga J, Vázquez M, Trigueros S, Sumners D, Roca J.

Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5373-7.

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