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February 26, 2013
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February 8, 2013
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February 8, 2013
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UC Davis ADVANCE
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CAMPOS
Center for the Advancement of Multicultural Perspectives on Science

November 21, 2013
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CRN
Capital Resource Network

October 2, 2014
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ICCI
Inclusive Campus Climate

November 21, 2013
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M&NI
Mentorship & Networking

November 21, 2013
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P&PRI
Policy & Practices Review

November 21, 2013
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SSRI
Social Sciences Research

April 26, 2016
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Software

Overview

Software

April 16, 2015

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.

Other software

DNA Toplogy  

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:

  1. properties of circular chains in confinement (e.g. DNA packing in bacteriophages, formation of the trynanosome mini-circle network)
  2. topological mechanisms of action of enzymes such as type II topisomerases and site-specific recombinases
  3. 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

Chromosome Positioning

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)

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April 16, 2015
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April 16, 2015
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April 16, 2015
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April 16, 2015
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NSF ADVANCE Program

February 13, 2013

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. 

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© 2015 UCDavis Advance, All Rights Reserved.

July 26, 2012
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The UC Davis ADVANCE Program is supported by NSF Cooperative Agreement HRD 1209235

April 18, 2013
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Logo design by Carlos Jackson, assistant professor in the Chicana/o Studies Program and Art Department.

April 18, 2013
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