Graphs for DNA Assembly

This web site contains research projects and results on spatial graphs modeling DNA assembly.
The files in this site are work in progress during 2009 - 2013, and will be updated often.
The last modified dates appear in the files.
Any comments are welcome.

Summer Research Opportunities for Undergraduates

There will be summer research groups during Summer 2010 on the topics posted in this web site.
The groups will include a few undergraduate students with summer support.
More information and application processes are posted here.

Background

A pdf file that contains backgound material is available here.
The file is in an early stage of editing, and will be updated often throughout 2009.

Projects and Findings

• Tables of assembly graphs
  • Tables of small numbers of rigid vertices
  • Mathematica programs and results on assembly words by Jonathan Burns
  • Python programs and outputs via Graphviz by Egor Dolzhenko
• Assembly numbers and polynomials
  • Mathematica results on assembly numbers by Jonathan Burns
  • Calculations of assembly polynomials by Egor Dolzhenko (coming soon)
  • Hamiltonian polygonal paths of assembly graphs in the table (preliminary)
• Chirality of assembly graphs
• Linking and writhe of assembly graphs
• Pathways of DNA recombination proceses via assembly graphs

More problems and details are found here.

Research Groups

• Graduate course (class of Fall 2009)
• Summer research group, 2010

People

This material is based upon work partially supported by
the National Science Foundation under Grant No. DMS-0900671.
Any opinions, findings, and conclusions or recommendations
expressed in this material are those of the author(s)
and do not necessarily reflect the views of the National Science Foundation.