References
Disclaimer: This is by no means a comprehensive list of references, but it is a good starting point for the interested reader. Please e-mail Mariel (mariel@math.berkeley.edu) if you would like to see a reference added to this list, or if you would like more information about any of the following topics:
[K1] Dale Rolfsen, Knots and links, Publish or Perish, Inc., Houston, 1976.
[K2] Jay R. Goldman and Louis Kauffman, Rational tangles, Advances in Applied Mathematics 18 (1997), 300-332.
[K3] Colin C. Adams, The Knot Book, W.H. Freeman and Company, New York, 1994.
[T1] De Witt Sumners, Untangling DNA, The Mathematical Intelligencer 12 (1990), 71-80.
[T2] Claus Ernst and De Witt Sumners, A calculus for rational tangles: applications to DNA recombination., Math. Proc. Camb. Phil. Soc. 108 (1990), 489-515
[T3] De Witt Sumners, Claus Ernst, Nicholas R. Cozzarelli, and Sylvia J. Spengler, Mathematical analysis of the mechanisms of DNA recombination using tangles, Quarterly Reviews of Biophysics 28 (1995), 253-313.
[T4] Mariel Vazquez, Tangle analysis of site-specific recombination: Gin and Xer systems, PhD Dissertation, Mathematics, Florida State University (2000).
[T5] De Witt Sumners, Claus Ernst, Nicholas R. Cozzarelli, and Sylvia J. Spengler, Mathematical analysis of the mechanisms of DNA recombination using tangles, Quarterly Reviews of Biophysics 28 (1995), 253-313.
[T6] Isabel Darcy, Biological Distances on DNA Knots and Links: Applications to XER recombination Knots in Hellas '98, Vol. 2 (Delphi). J. Knot Theory Ramifications, 10 (2001), no. 2, 269--294
[T7] Untangling DNA, The Mathematical Intelligencer 12 (1990), 71-80.
[S1] Roland Kanaar, Anke Klippel, Eugene Shekhtman, Regine Kahmann, Jan M. Dungan and Nicholas R. Cozzarelli, Processive recombination by the phage Mu Gin system: Implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action, Cell 62 (1990), 353-366
[S2] Nancy J. Crisona, Roland Kanaar, Tania N. Gonzalez, E. Lynn Zechiedrich, Anke Klippel, and Nicholas R. Cozzarelli, Processive recombination by wild-type Gin and an enhancer-independent mutant insight into the mechanisms of recombination selectivity and strand exchange, Journal of Molecular Biology 243 (1994), 437-457.
[S3] Sean D. Colloms, Jonathan Bath, and David J. Sherratt, Topological selectivity in Xer site-specific recombination, Cell 88 (1997), 855-864.
[S4] F. Cornet, B. Hallet, and David J. Sherratt, Xer recombination in Escherichia coli, Journal of Biological Chemistry 270 (1997), no. 35, 21927-21931.
[S5] Jonathan Bath, Sean D. Colloms and David J. Sherratt, Topology of Xer recombination on catenanes produced by lambda integrase, Journal of Molecular Biology 289 (1999), 873-883.
[S6] Grainge et al, Geometry of site alignment during Int family recombination: antiparallel synapsis by the Flp recombinase, Journal of Molecular Biology 298 (2000), no. 5, 749-764
Maintained by Yuki Saka ysaka@uclink.berkeley.edu