TangleSolve (paper) is a Java applet which implements the tangle method for site-specific recombination. TangleSolve offers an easy to use graphical user interface for analyzing and vizualizing site-specific recombination mechanisms.
The Arsuaga and Vazquez research groups have developed a series of computational tools to model polygonial chains in 3-dimensional space (on and off-lattice) and to explore their conformation space (e.g. BFACF, crankshaft, Hedgehog). We are interested in the following problems:
topological mechanisms of action of enzymes such as type II topisomerases and site-specific recombinases
topological identification of DNA knots (using gauss codes, Dowker codes, polynomial invariants)
Please contact Mariel or Javier for details, and for access to data and/or software. Several of the tools were developed by Rob Scharein and can be interfaced to work within Knotplot
On a separate line of research, in collaboration with the Arsuaga group we have developed software to study intermingling of chromosomes in the cell nucleus, as well as an applet to analyze pairwise interactions between chromosomes (SCHIP, developed jointly with Sergi Vives, paper)
Related software developed in Rainen Sach’s group can be found at this site
Computational Homology and cancer
Finally, we have also worked an application of computational Homology to analyze genomic data from cancer patients (see Javier Arsuaga’s description and images)
The National Science Foundation began supporting ADVANCE initiatives in 2001, and has awarded over $130M in funding for a variety of programs. The most significant efforts seek to create permanent institutional transformation.