1.- Trigueros, S., Arsuaga, J., Vazquez, M., Sumners, D.W., Roca, J. Novel display of knotted DNA molecules by two dimensional gel electrophoresis. Nucleic Acids Research 2001, 29 (13): e67.

2.- Arsuaga, J., Tan, R., Vazquez, M., Sumners, D. W., and Harvey, S. C. Investigation of Viral DNA Packaging Using Molecular Mechanics Models. Biophysical Chemistry 2002, 101-102(1): 475-484.

3.- Arsuaga, J., Vazquez, M., Trigueros, S., Sumners, D. W., and Roca, J. Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proceedings of the National Academy of Science USA 2002, 99(8):5373-5377. [Evaluated by Prof. T. Schlick in Faculty of 1000]

4.- Sachs, R. K., Arsuaga, J., Vazquez, M., Hahnfeldt, P., and Hlatky, L. Using graph theory to analyze chromosome aberrations. Radiation Research 2002, 158 (5): 556-567

5.- Cornforth, M. N., Greulich-Bode, K. M., Loucas, B. D., Arsuaga, J., Vazquez, M., Daye, J., Sachs, R. K., Bruckner,M., Molls, M., Hahnfeldt, P., Hlatky, L., Brenner, D. J. Chromosomes are predominantly located randomly with respect to each other in interphase human cells. The Journal of Cell Biology 2002, 159 (2),237-244. [Evaluated by Prof. M. Matzke in Faculty of 1000]

6.- Vazquez, M., Greulich-Bode, K. M., Arsuaga, J., Cornforth, M. N., Bruckner, M., Sachs, R. K., Hahnfeldt, P., Molls, M., Hlatky, L. Computer analysis of mFISH chromosome aberration data uncovers an excess of very complex metaphases. International Journal of Radiation Biology 2002, 78(12):1103-1115.

7.- Arsuaga, J., Greulich-Bode, K., Vazquez, M., Brukner, M.,Hahnfeldt,P., Brenner, D.J., Sachs, R. and Hlatky, L. Chromosome positioning through radiogenic aberrations. International Journal of Radiation Biology 2004, 80 (7), 507-516.

8.- Postow, L., Hardy, C., Arsuaga, J. and Cozzarelli, N. Topological domain structure of the Escherichia coli chromosome. Genes and Development. 2004 Jul 15;18(14):1766-79. [Evaluated by Prof. U. Schibler in Faculty of 1000]

9.- Levy, D., Vazquez, M., Loucas, B. D., Cornforth, M. N., Sachs, R. K., Arsuaga, J. Comparing DNA damage-processing pathways by computer analysis of chromosome painting data. Journal of Computational Biology (2004), 11(4), 626-641.

10.- Peter, B., Arsuaga, J., Breier, A., Khodursky, A., Brown, P., Cozzarelli, N. Genomic analysis of supercoiling sensitive genes in Escherichia coli: responses to topoisomerase inhibition. Genome Biology 2004 5 (11);R87. Highly Accessed Paper. [Evaluated by Prof. W. Hide in Faculty of 1000]

11.- Vives, S., Loucas, B., Vazquez, M., Brenner, D.J., Sachs, R.K., Hlatky, L., Cornforth, M., and Arsuaga, J. SCHIP: statistics for chromosome interphase positioning based on interchange data. Bioinformatics. 2005 Jul 15;21(14):3181-2.

12.- Arsuaga, J., Vazquez, M., McGuirk*, P., Trigueros, S., Sumners, de W., and Roca, J. DNA knots reveal a chiral organization of DNA in phage capsids. Proceedings National Academy of Sciences U S A. 2005 Jun 28;102(26):9165-9.[Evaluated by Prof. J. Cascarrosa in Faculty of 1000]

13.- Hua*,X., Baghavan*,B., Nguyen*,D., Arsuaga,J. and M. Vazquez Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases. Topology and its Applications (2007) 154; 1381-1397.

14.- Ardanza-Trevijano, S. Arsuaga, J. , Crespo J. A., Extremiana, J. I., Hernandez, L.J., Rivas, M. T. , Roca, J., Vazquez, M. La topologia como herramienta en otros campos. La Gaceta de la Real Sociedad Matematica Espanola (2007) 10.3; 611-632.

15.- Blackstone, T.*, McGuirck, P.*,Laing, C., Vazquez, M., Roca, J. and Arsuaga, J. The role of wr ithe in DNA knotting. Proceedings of International Workshop on Knot Theory for Scientific Objects (2007). OCAMI Studies Volume 1 (2) Osaka Municipal Universities Press; 239-250

16.- Arsuaga, J., Blackstone, T.*, Diao,Y., Karadayi, E. , Saito, Y. Linking of Uniform Random Polygons in Confined Spaces. J. Phys. A: Math. Gen. (2007) 40; 1925-1936

17.- Climent, J., Mao, J., Garcia, J. L., Arsuaga, J., Perez-Losada, J. Characterization of Breast Cancer by Array CGH. Biochemistry and Cell Biology (2007) 85(4); 497-508

18.- Arsuaga, J., Blackstone, T.*, Diao,Y., Karadayi, E. , Saito, Y. Sampling Large Random knots in Confined Spaces. J. Phys. A: Math Gen. (2007) 40; 11697-11711

19.- Arsuaga, J. and Diao Y. DNA knotting in Spooling like conformations in Bacteriophages. Journal Computational and Mathematical Methods in Medicine (2008) 9 (3-4) 303-316

20.- Arsuaga, J. , Diao, Y. and Vazquez, M. DNA topology in recombination and chromosome organization. (Book Chapter) To be included in the volume, Mathematics of DNA Structure, Function and Interactions (eds C.J. Benham, S. Harvey, W.K. Olson, D.W. Sumners and D. Swigon), Springer Science + Business Media, LLC, New York, (2009) special issue of the IMA.

21.- Varela, R., Hinson, K., Arsuaga, J. and Diao, Y. A Fast ergodic algorithm for generating ensembles of random polygons J. Phys A: Math Gen (2009) 42 (9) 095204

22.- Arsuaga, J. , Borgo*, B., Diao, Y. and Scharein, R. The Average Crossing Number of Equilateral Random Polygons in Confined Volumes. J. Phys. A: Math. Theor. 42 (2009) 465202.

23.- Scharein,R., Ishihara,K., Arsuaga,J. , Shimokawa, K., Vazquez, M. Bounds for minimal step number of knots in the simple cubic lattice. J. Phys A: Math. and Theor (2009) 42 (47)475006-457030

24.- Dewoskin, D., Climent, J., Cruz-White, I., Vazquez, M., Park, C.,Arsuaga, J. Using computational homology for prediction of breast cancer response to chemotherapy. Topology and Its Applications (2010) 157 (1) 157-164

25.- Arsuaga, J., Roca, J. and Sumners, D. W. DNA knots and chromosome organization in bacteriophages. (Book chapter) in "Emerging Topics in Physical Virology" Imperial College Press. (2010) Ed: P. Stockley and R. Twarock. pp: 255-288.

26.- Blackstone, T, Scharein, R., Varela, R., Diao, Y., and Arsuaga, J.Modeling Chromosome Intermingling Using Overlapping Uniform Random Polygons Journal of Mathematical Biology (2011) 62(3):371-89.

27.-J. Portillo, Y. Diao, R. Scharein, J Arsuaga and M. Vazquez. On the mean and the variance of the writhe. J. Phys A: Math and Theor. (2011) 44 275004

28.-Diao, Y., Hinson, K., Kaplan, R., Vazquez, M. and Arsuaga J. The effects of minicircle density on the topological structure of the mitochondrial DNA from trypanosomes. The Journal of Mathematical Biology (2012) 64 (6) 1087-108.

29.- Arsuaga, J., Diao, Y. and Hinson, K. The effect of angle restriction on the topological characteristics of minicircle networks. J. Stat. Phys. (2012) 146: 434--445.

30.- Diao, Y. and Hinson, K. and Arsuaga J. The effect of lattice selections on the formation of minicircle networks: applications to kinetoplast DNA from trypanosomes, Journal of Physics A. (2012) 45 035004.

31.- Ishihara,K., Scharein,R., Diao, Y., Arsuaga,J. , Vazquez, M. and Shimokawa, K. Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice. Journal of Physics A. (2012) 45 065003.

32.- Arsuaga,J. ,Baas N., DeWoskin, D., Mizuno, H., and Pankov,A., Park, C. Topological analysis of gene expression arrays identifies high risk molecular subtypes in breast cancer. Applicable Algebra in Engineering, Communication and Computing. Special issue on Computer Algebra in Algebraic Topology and Its Applications (2012) 3-15

33.- Rodriguez, V, Diao, Y. and Arsuaga, J. Percolation phenomena in randomized topological networks. J. Phys.: Conf. Ser. (2013) 454 012070

Coming Soon:

34.- Arsuaga J, Diao Y, Klingbeil M, Rodriguez V. Properties of Topological Networks of Flexible Chains Submitted

35.- Segal M, Xiong H, Capurso D, Vazquez M, Arsuaga J. Reproducibility of Three-Dimensional Chromatin Configuration Reconstructions Submitted

36.- Borrman T, Gonzalez G, Cavalcante R, Park C, Perez-Losada J, Mao JH, Arsuaga J. Identification of periodic patterns in copy number data using topological analysis: a first step in the identification of co-occurring copy number changes in cancer Submitted

*Undergraduate Students