Christopher Tuffley's papers page
Publications and preprints
Search
for me on the arXiv.
Topology

(with Howida al Fran) Distinguishing the generalised knot groups of square and granny knot analogues, J. Knot Theory Ramifications, 28(5):1950035 (2019),
arxiv.org:1810.07853.

Intrinsic linking with linking numbers of specified divisibility,
Ars Mathematica Contemporanea 16(2):331348 (2019),
arXiv:1702.03479.

Some Ramseytype results on intrinsic linking of ncomplexes, Alg. Geom. Topology 13(3):15791612 (2013), arXiv:1112.4558.

Generalized
knot groups distinguish the square and granny knots
(with an appendix by
David Savitt),
Journal of Knot Theory and its Ramifications 18(8):11291157 (2009),
arXiv:0706.1807.

(with Mira Bernstein)
Level
structures on the Weierstrass family of cubics,
Communications in Algebra 35:12491261 (2007),
arXiv:math/0512117.

Connectivity
of finite subset spaces of cell complexes,
Pac. J. Math. 217(1):175179 (2004), arXiv:math/0304086.

Finite
subset spaces of graphs and punctured surfaces,
Alg. Geom. Topology 3:873904 (2003), arXiv:math/0210315.

Finite
subset spaces of graphs and surfaces, Ph.D. dissertation,
UC Berkeley (2003).

Finite
subset spaces of S^1,
Alg. Geom. Topology 2:11191145 (2002), arXiv:math/0209077.
Combinatorics
Mathematical biology

(with Timothy White, Mike Hendy and David Penny)
Correcting the
apparent
mutation rate acceleration at shorter time scales under a JukesCantor model,
Mol. Biol. Evol. 29(12):37033709 (2012),
arXiv:1112.4570.
Note: arXiv version does not completely match published version, which includes some copyrighted material.

(with Atheer Matroud, Mike Hendy and David Bryant)
A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats, in Advances in Bioinformatics and Computational Biology, proceedings of the
7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 1517, 2012. Lecture Notes in Computer Science, 7409:3748.

(with Atheer Matroud and Mike Hendy)
NTRFinder:
a software tool to find nested tandem repeats, Nucleic Acids
Research 40(3):e17 (2012), doi: 10.1093/nar/gkr1070.

(with Atheer Matroud and Mike Hendy)
An
algorithm to solve the motif alignment problem for approximate nested
tandem repeats in biological sequences, Journal of Computational
Biology 18(9):12111218 (2011).
 (with Mike Steel)
Modelling the covarion hypothesis of
nucleotide substitution, Mathematical Biosciences 147:6391 (1998).

Trees and Ps
and things that sneeze: Markov process models of
site substitution, M.Sc. thesis, University of Canterbury (1997).
 (with Mike Steel)
Links between
maximum likelihood and maximum
parsimony under a simple model of site substitution, Bulletin
of Mathematical Biology 59(3):581607 (1997).
Dynamical Systems
Mathematical creative writing
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Last modified 6th November 2019