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.
Any comments are welcome.

Background

• DNA recombination in ciliates and template theory
• Assembly graphs and related concepts

Projects

• Classification of assembly words and graphs
• Assembly numbers and polynomials
• Pathways of DNA recombination proceses via assembly graphs
• Nesting of assembly words and reductions
• Repeated pointer sequences in micronuclear genes
• Macronuclear segments in assembly graphs
• Planarity of assembly graphs
• Linking and writhe of assembly graphs
• Chirality of assembly graphs

Findings

• Tables of assembly graphs for small numbers of rigid vertices were obtained in 2009.
  
• More extended table of assembly words were obtained by Jonathan Burns in 2010.
  His Mathematica program are available here.
• The paper ``Polygonal Hamiltonian paths in regid 4-regular graphs and DNA assembly'',
  contains the following results obtained in 2010-2011.
  • Number of isomorphism classes of assembly words
  • Propserties of the assembly number
  • Properties and computations of the assembly polynomial
  • The number of Hamiltonian sets of polygonal paths

Presentations

• Poster by Natasha Jonoska at Frontiers in Mathematical Biology: NSF-NIH PIs Meeting 2010.
• Handout by Mary Billington at the Undergraduate Research Symposium, USF, 2011
  (winner of the top award `` Georg Kleine Award - Overall Best Oral Presentation'').

Research Groups

• Graduate course (class of Fall 2009)
• Summer research group, 2010
• Summer research group, 2011
• Graduate course (class of Fall 2011)
• Summer research group, 2012

Workshop

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.