Gonzalez, Georgina; Ushakova, Arina; Sazdanovic, Radmila; Arsuaga, Javier Prediction in cancer genomics using topological signatures and machine learning. (English) Zbl 1448.62165 Baas, Nils (ed.) et al., Topological data analysis. Proceedings of the Abel symposium 2018, Geiranger, Norway, June 4–8, 2018. Cham: Springer. Abel Symp. 15, 247-276 (2020). MSC: 62P10 92D20 62M20 62R40 55N31 68T05 PDFBibTeX XMLCite \textit{G. Gonzalez} et al., Abel Symp. 15, 247--276 (2020; Zbl 1448.62165) Full Text: DOI
Liu, P.; Polischuk, R.; Diao, Y.; Arsuaga, J. Characterizing the topology of kinetoplast DNA using random knotting. (English) Zbl 1446.57007 Flapan, Erica (ed.) et al., Topology and geometry of biopolymers. AMS special session on topology of biopolymers, Northeastern University, Boston, MA, USA, April 21–22, 2018. Providence, RI: American Mathematical Society (AMS). Contemp. Math. 746, 17-39 (2020). Reviewer: Claus Ernst (Bowling Green) MSC: 57K10 57Z10 92B99 PDFBibTeX XMLCite \textit{P. Liu} et al., Contemp. Math. 746, 17--39 (2020; Zbl 1446.57007) Full Text: DOI
Ibrahim, L.; Liu, P.; Klingbeil, M.; Diao, Y.; Arsuaga, J. Estimating properties of kinetoplast DNA by fragmentation reactions. (English) Zbl 1422.92105 J. Phys. A, Math. Theor. 52, No. 3, Article ID 034001, 15 p. (2019). MSC: 92D20 92B20 92B15 92E10 82B43 82B27 68U20 81V55 PDFBibTeX XMLCite \textit{L. Ibrahim} et al., J. Phys. A, Math. Theor. 52, No. 3, Article ID 034001, 15 p. (2019; Zbl 1422.92105) Full Text: DOI
Ishihara, Kai; Pouokam, Maxime; Suzuki, Atsumi; Scharein, Robert; Vazquez, Mariel; Arsuaga, Javier; Shimokawa, Koya Bounds for minimum step number of knots confined to tubes in the simple cubic lattice. (English) Zbl 1383.92017 J. Phys. A, Math. Theor. 50, No. 21, Article ID 215601, 28 p. (2017). MSC: 92C10 92D20 57M25 PDFBibTeX XMLCite \textit{K. Ishihara} et al., J. Phys. A, Math. Theor. 50, No. 21, Article ID 215601, 28 p. (2017; Zbl 1383.92017) Full Text: DOI
Arsuaga, Javier; Heskia, Ido; Hoşten, Serkan; Maskalevich, Tatsiana Uncovering proximity of chromosome territories using classical algebraic statistics. (English) Zbl 1347.62226 J. Algebr. Stat. 6, No. 2, 133-149 (2015). MSC: 62P10 62H17 60J22 92D20 PDFBibTeX XMLCite \textit{J. Arsuaga} et al., J. Algebr. Stat. 6, No. 2, 133--149 (2015; Zbl 1347.62226) Full Text: DOI arXiv
Diao, Y.; Hinson, K.; Sun, Y.; Arsuaga, J. The effect of volume exclusion on the formation of DNA minicircle networks: implications to kinetoplast DNA. (English) Zbl 1350.92038 J. Phys. A, Math. Theor. 48, No. 43, Article ID 435202, 13 p. (2015). MSC: 92D20 92C40 92C42 PDFBibTeX XMLCite \textit{Y. Diao} et al., J. Phys. A, Math. Theor. 48, No. 43, Article ID 435202, 13 p. (2015; Zbl 1350.92038) Full Text: DOI Link
Arsuaga, J.; Diao, Y.; Klingbeil, M.; Rodriguez, V. Properties of topological networks of flexible polygonal chains. (English) Zbl 1412.92235 Comput. Math. Biophys. 2, No. 1, 98-106 (2014). MSC: 92D20 57M25 PDFBibTeX XMLCite \textit{J. Arsuaga} et al., Comput. Math. Biophys. 2, No. 1, 98--106 (2014; Zbl 1412.92235) Full Text: DOI
Diao, Y.; Hinson, K.; Kaplan, R.; Vazquez, M.; Arsuaga, J. The effects of density on the topological structure of the mitochondrial DNA from trypanosomes. (English) Zbl 1311.92145 J. Math. Biol. 64, No. 6, 1087-1108 (2012). MSC: 92D20 57M25 92B99 92C42 PDFBibTeX XMLCite \textit{Y. Diao} et al., J. Math. Biol. 64, No. 6, 1087--1108 (2012; Zbl 1311.92145) Full Text: DOI
Arsuaga, Javier; Baas, Nils A.; DeWoskin, Daniel; Mizuno, Hideaki; Pankov, Aleksandr; Park, Catherine Topological analysis of gene expression arrays identifies high risk molecular subtypes in breast cancer. (English) Zbl 1388.92008 Appl. Algebra Eng. Commun. Comput. 23, No. 1-2, 3-15 (2012). MSC: 92C40 92C50 PDFBibTeX XMLCite \textit{J. Arsuaga} et al., Appl. Algebra Eng. Commun. Comput. 23, No. 1--2, 3--15 (2012; Zbl 1388.92008) Full Text: DOI
Ishihara, K.; Scharein, R.; Diao, Y.; Arsuaga, J.; Vazquez, M.; Shimokawa, K. Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice. (English) Zbl 1259.82142 J. Phys. A, Math. Theor. 45, No. 6, Article ID 065003, 24 p. (2012). Reviewer: Guy Jumarie (Montréal) MSC: 82D60 82D25 92D20 57M25 PDFBibTeX XMLCite \textit{K. Ishihara} et al., J. Phys. A, Math. Theor. 45, No. 6, Article ID 065003, 24 p. (2012; Zbl 1259.82142) Full Text: DOI Link
Diao, Y.; Hinson, K.; Arsuaga, J. The growth of minicircle networks on regular lattices. (English) Zbl 1234.92022 J. Phys. A, Math. Theor. 45, No. 3, Article ID 035004, 12 p. (2012). MSC: 92C42 92C40 57M25 PDFBibTeX XMLCite \textit{Y. Diao} et al., J. Phys. A, Math. Theor. 45, No. 3, Article ID 035004, 12 p. (2012; Zbl 1234.92022) Full Text: DOI Link
Blackstone, T.; Scharein, R.; Borgo, B.; Varela, R.; Diao, Y.; Arsuaga, J. Modeling of chromosome intermingling by partially overlapping uniform random polygons. (English) Zbl 1303.92026 J. Math. Biol. 62, No. 3, 371-389 (2011). MSC: 92C37 92D10 52A22 60D05 68U20 PDFBibTeX XMLCite \textit{T. Blackstone} et al., J. Math. Biol. 62, No. 3, 371--389 (2011; Zbl 1303.92026) Full Text: DOI
Portillo, J.; Diao, Y.; Scharein, R.; Arsuaga, J.; Vazquez, M. On the mean and variance of the writhe of random polygons. (English) Zbl 1223.57011 J. Phys. A, Math. Theor. 44, No. 27, Article ID 275004, 19 p. (2011). Reviewer: Jonathan Hodgson (Philadelphia) MSC: 57M25 92B99 PDFBibTeX XMLCite \textit{J. Portillo} et al., J. Phys. A, Math. Theor. 44, No. 27, Article ID 275004, 19 p. (2011; Zbl 1223.57011) Full Text: DOI Link
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. (English) Zbl 1176.92026 Topology Appl. 157, No. 1, 157-164 (2010). MSC: 92C50 55U99 55U10 PDFBibTeX XMLCite \textit{D. DeWoskin} et al., Topology Appl. 157, No. 1, 157--164 (2010; Zbl 1176.92026) Full Text: DOI
Arsuaga, J.; Borgo, B.; Diao, Y.; Scharein, R. The growth of the mean average crossing number of equilateral polygons in confinement. (English) Zbl 1182.92026 J. Phys. A, Math. Theor. 42, No. 46, Article ID 465202, 9 p. (2009). MSC: 92C40 92C05 57M25 60D05 PDFBibTeX XMLCite \textit{J. Arsuaga} et al., J. Phys. A, Math. Theor. 42, No. 46, Article ID 465202, 9 p. (2009; Zbl 1182.92026) Full Text: DOI Link
Varela, R.; Hinson, K.; Arsuaga, J.; Diao, Y. A fast ergodic algorithm for generating ensembles of equilateral random polygons. (English) Zbl 1158.92019 J. Phys. A, Math. Theor. 42, No. 9, Article ID 095204, 14 p. (2009). MSC: 92C40 57M25 PDFBibTeX XMLCite \textit{R. Varela} et al., J. Phys. A, Math. Theor. 42, No. 9, Article ID 095204, 14 p. (2009; Zbl 1158.92019) Full Text: DOI Link
Arsuaga, J.; Diao, Y. DNA knotting in spooling like conformations in bacteriophages. (English) Zbl 1160.92017 Comput. Math. Methods Med. 9, No. 3-4, 303-316 (2008). Reviewer: Claus Ernst (Bowling Green) MSC: 92C40 57M25 92C37 92-08 PDFBibTeX XMLCite \textit{J. Arsuaga} and \textit{Y. Diao}, Comput. Math. Methods Med. 9, No. 3--4, 303--316 (2008; Zbl 1160.92017) Full Text: DOI EuDML
Ardanza-Trevijano, S.; Arsuaga, J.; Crespo, J. A.; Extremiana, J. I.; Hernández, L. J.; Rivas, M. T.; Roca, J.; Vázquez, M. Topological invariants in DNA, fullerenes and the theory of social choice. (Spanish) Zbl 1358.92064 Gac. R. Soc. Mat. Esp. 10, No. 3, 611-632 (2007). MSC: 92D10 57M25 91B14 92E10 PDFBibTeX XMLCite \textit{S. Ardanza-Trevijano} et al., Gac. R. Soc. Mat. Esp. 10, No. 3, 611--632 (2007; Zbl 1358.92064)
Blackstone, T.; McGuirk, P.; Laing, C.; Vazquez, M.; Roca, J.; Arsuaga, J. The role of writhe in DNA condensation. (English) Zbl 1220.92017 Kawauchi, Akio (ed.), Knot theory for scientific objects. Proceedings of the international workshop on knot theory for scientific objects, Osaka, Japan, March 8–10, 2006. Osaka: Osaka Municipal Universities Press (ISBN 978-4-901409-29-2/hbk). OCAMI Studies 1, 239-250 (2007). MSC: 92C37 92C40 68U20 65C20 PDFBibTeX XMLCite \textit{T. Blackstone} et al., OCAMI Stud. 1, 239--250 (2007; Zbl 1220.92017)
Hua, Xia; Nguyen, Diana; Raghavan, Barath; Arsuaga, Javier; Vazquez, Mariel Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases. (English) Zbl 1114.57005 Topology Appl. 154, No. 7, 1381-1397 (2007). Reviewer: Claus Ernst (Bowling Green) MSC: 57M25 60J22 92-XX PDFBibTeX XMLCite \textit{X. Hua} et al., Topology Appl. 154, No. 7, 1381--1397 (2007; Zbl 1114.57005) Full Text: DOI Link
Arsuaga, J.; Blackstone, T.; Diao, Y.; Karadayi, E.; Saito, M. Linking of uniform random polygons in confined spaces. (English) Zbl 1123.57005 J. Phys. A, Math. Theor. 40, No. 9, 1925-1936 (2007). Reviewer: Athanase Papadopoulos (Strasbourg) MSC: 57M25 92C15 62P10 PDFBibTeX XMLCite \textit{J. Arsuaga} et al., J. Phys. A, Math. Theor. 40, No. 9, 1925--1936 (2007; Zbl 1123.57005) Full Text: DOI Link