Our Publications

Research Publications:

M. N. Ellingham, J. Ellis-Monaghan, “Edge-outer graph embedding and the complexity of the DNA reporter strand problem”, submitted. https://arxiv.org/abs/1710.09048

A. Morse#, W. Adkisson*, J. Greene*, D. Perry*, B. Smith*, G. Pangborn, J. Ellis-Monaghan, “DNA Origami and Unknotted A-trails in Torus Graphs”, submitted. https://arxiv.org/abs/1703.03799

M. Ferrari#, A. Cook*, A. Houlihan*, R. Rouleau*, N. Seeman, G. Pangborn, J. Ellis-Monaghan, “Design formalism for DNA self-assembly of polyhedral skeletons using rigid tiles”, The Journal of Mathematical Chemistry, 56, no. 5 (2018) 1365-1392.

J. Ellis-Monaghan, G. Pangborn, N.C. Seeman, S. Blakeley*, C. Disher,* M. Falcigno*, B.Healy*, A. Morse#, B.Singh*, M. Westland*, “Design tools for Reporter Strands and DNA Origami Scaffold Strands”, Theoretical Computer Science, 671 no. 6 (2017) 69-78.

J. Ellis-Monaghan, A. McDowell, I. Moffatt, G. Pangborn, DNA origami and the complexity of Eulerian circuits with turning costs, Natural Computing, 14 no. 3 (2015) 491-503. (journal / arXiv).

J. Ellis-Monaghan, G. Pangborn, L. Beaudin, D. Miller, N. Bruno, A. Hashimoto, Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs, in Discrete and Topological Models in Molecular Biology, Jonoska & Saito, Eds., pp. 241-270, 2014.

J. Ellis-Monaghan, I. Moffatt, Graphs on Surfaces: Twisted Duality, Polynomials, and Knots. SpringerBriefs in Mathematics, 2013.

J. Ellis-Monaghan, I. Moffatt, Twisted duality for embedded graphs,Transactions of the American Mathematical Society, 364, pp. 1529-1569, 2012.

J. Ellis-Monaghan, I. Moffatt, The Tutte-Potts connection in the presence of an external magnetic field, Advances in Applied Mathematics, 47, 2011. http://arxiv.org/abs/1005.5470

J. Ellis-Monaghan, C. Merino, Graph polynomials and their applications I: the Tutte polynomial, in Structural Analysis of Complex Networks, Matthias Dehmer, ed., Birkhauser, 2010.

J. Ellis-Monaghan, C. Merino, Graph polynomials and their applications II: interrelations and interpretations, in Structural Analysis of Complex Networks, Matthias Dehmer, ed., Birkhauser, 2010.

M. Cox, J. Ellis-Monaghan, T. Hughes, K. Mondanaro, Carbon knots in the octet truss, J. Math. Chem., 43 no. 2 pp. 874-891, 2008.

J. Ellis-Monaghan, Transition polynomials, double covers, and biomolecular computing, Cong. Num., 166, pp. 181-192, 2004.

Pedagogical Publications:

J. Ellis-Monaghan, G. Pangborn, L. Beaudin*, D. Miller*, N. Bruno*, A. Hashimoto*, Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs, in Discrete and Topological Models in Molecular Biology, Jonoska & Saito, Eds. (At Amazon)

J. Ellis-Monaghan, G. Pangborn, An example of practical organization for undergraduate research experiences, PRIMUS, 23 (9), pp. 805-814, 2013.

J. Ellis-Monaghan, G. Pangborn, Using DNA self-assembly design strategies to motivate graph theory concepts, Math. Model. Nat. Phenom., 6 (6), pp. 96-107, 2011.

Student Publications:

Jake Girard, Andrew Gilbert, Dan Lewis, Mary Spuches, Design optimization for DNA nanostructures, American Journal of Undergraduate Research, 10 (1), 2011.

Tyler Hotte, Miranda LaRocque, Design Techniques for the DNA Cubic Lattice, in press, American Journal of Undergraduate Research.

Mary Falcigno, Katelyn Heath, Tiling and Threading of Polyhedra, manuscript.

Thomas Dickerson, Jacob Girard, Brian Goodhue, Daniel Koch, Andrew Parent, Mary Spuches, Self-Assembly Strategies in the Octet Truss, manuscript.

Available Software:

Crystal Turtlebug is available for download on SourceForge.

Octet Truss Tile Finder is available for download on Google Code.

Python implementation - finding optimal Eulerian Circuits with Turning Costs