%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.net/


%% Created for Gavin A Huttley at 2020-04-22 14:57:59 +1000 


%% Saved with string encoding Unicode (UTF-8) 



@article{2009.Huttley.000,
	Author = {Huttley, Gavin},
	Date-Modified = {2020-04-22 14:50:31 +1000},
	Journal = {Australian Journal of Zoology},
	Pages = {167},
	Title = {{Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?}},
	Url = {https://www.publish.csiro.au/?paper=ZO09049},
	Volume = {57},
	Year = {2009}}

@article{2008.Lindsay.000,
	Author = {Lindsay, Helen and Yap, Von Bing and Ying, Hua and Huttley, Gavin A},
	Date-Modified = {2020-04-22 14:48:44 +1000},
	Journal = {Biol Direct},
	Pages = {52},
	Title = {{Pitfalls of the most commonly used models of context dependent substitution.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/19087239},
	Volume = {3},
	Year = {2008}}

@article{2007.Knight.000,
	Author = {Knight, R and Maxwell, P and Birmingham, A and Carnes, J and Caporaso, J G and Easton, B C and Eaton, M and Hamady, M and Lindsay, H and Liu, Z and Lozupone, C and McDonald, D and Robeson, M and Sammut, R and Smit, S and Wakefield, M J and Widmann, J and Wikman, S and Wilson, S and Ying, H and Huttley, G A},
	Date-Modified = {2020-04-22 14:47:50 +1000},
	Journal = {Genome Biol},
	Pages = {R171},
	Title = {{PyCogent: a toolkit for making sense from sequence.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/17708774},
	Volume = {8},
	Year = {2007}}

@article{2011.Ying.000,
	Author = {Ying, H and Huttley, G},
	Date-Modified = {2020-04-22 14:52:21 +1000},
	Journal = {Genome Biology and Evolution},
	Pages = {938},
	Title = {{Exploiting CpG hypermutability to identify phenotypically significant variation within human protein-coding genes}},
	Url = {https://academic.oup.com/gbe/article/doi/10.1093/gbe/evr021/578802},
	Volume = {3},
	Year = {2011}}

@article{2015.Kaehler.000,
	Author = {Kaehler, Benjamin D and Yap, Von Bing and Zhang, Rongli and Huttley, Gavin A},
	Date-Modified = {2020-04-22 14:57:11 +1000},
	Journal = {Systematic Biology},
	Pages = {281--93},
	Title = {{Genetic distance for a general non-stationary Markov substitution process.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/25503772},
	Volume = {64},
	Year = {2015}}

@misc{2012.Huttley.000,
	Author = {Huttley, Gavin A and Yap, Von Bing},
	Title = {{Robust estimation of natural selection using parametric codon models}},
	Year = {2012}}

@article{2010.Yap.000,
	Author = {Yap, Von Bing and Lindsay, Helen and Easteal, Simon and Huttley, Gavin},
	Date-Modified = {2020-04-22 14:51:30 +1000},
	Journal = {Molecular Biology and Evolution},
	Pages = {726--734},
	Title = {{Estimates of the effect of natural selection on protein-coding content}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/19815689},
	Volume = {27},
	Year = {2010}}

@article{2010.Caporaso.000,
	Author = {Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Pe{\~{n}}a, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and Huttley, Gavin A and Kelley, Scott T and Knights, Dan and Koenig, Jeremy E and Ley, Ruth E and Lozupone, Catherine A and McDonald, Daniel and Muegge, Brian D and Pirrung, Meg and Reeder, Jens and Sevinsky, Joel R and Turnbaugh, Peter J and Walters, William A and Widmann, Jeremy and Yatsunenko, Tanya and Zaneveld, Jesse and Knight, Rob},
	Date-Modified = {2020-04-22 14:50:56 +1000},
	Journal = {Nat Methods},
	Pages = {335--336},
	Title = {{QIIME allows analysis of high-throughput community sequencing data.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/20383131},
	Volume = {7},
	Year = {2010}}

@article{2008.Caporaso.000,
	Author = {Caporaso, J G and Smit, S and Easton, B C and Hunter, L and Huttley, G A and Knight, R},
	Date-Modified = {2020-04-22 14:48:18 +1000},
	Journal = {BMC Evol Biol},
	Pages = {327},
	Title = {{Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/19055758},
	Volume = {8},
	Year = {2008}}

@article{2011.Epps.000,
	Author = {Epps, Julien and Ying, Hua and Huttley, Gavin},
	Date-Modified = {2020-04-22 14:52:01 +1000},
	Journal = {Biology Direct},
	Pages = {21},
	Title = {{Statistical methods for detecting periodic fragments in DNA sequence data}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/21527008},
	Volume = {6},
	Year = {2011}}

@article{2008.Schranz.000,
	Author = {Schranz, Harold W and Yap, Von Bing and Easteal, Simon and Knight, Rob and Huttley, Gavin A},
	Date-Modified = {2020-04-22 14:49:48 +1000},
	Journal = {BMC Bioinformatics},
	Pages = {550},
	Title = {{Pathological rate matrices: from primates to pathogens.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/19099591},
	Volume = {9},
	Year = {2008}}

@article{2010.Sammut.000,
	Author = {Sammut, Raymond and Huttley, Gavin},
	Date-Modified = {2020-04-22 14:51:15 +1000},
	Journal = {J Mol Evol},
	Pages = {147--159},
	Title = {{Regional Context in the Alignment of Biological Sequence Pairs.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/21107551},
	Volume = {72},
	Year = {2010}}

@article{2008.Oscamou.000,
	Author = {Oscamou, Maribeth and McDonald, Daniel and Yap, Von Bing and Huttley, Gavin and Lladser, Manuel and Knight, Rob},
	Date-Modified = {2020-04-22 14:49:14 +1000},
	Journal = {BMC Bioinformatics},
	Pages = {511},
	Title = {{Comparison of methods for estimating the nucleotide substitution matrix}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/19046431},
	Volume = {9},
	Year = {2008}}

@article{2012.Bellani.000,
	Author = {Bellani, M and Epps, J and Huttley, G},
	Date-Modified = {2020-04-22 14:54:10 +1000},
	Journal = {Proc. IEEE Workshop on Genomic Signal Processing and Statistics},
	Title = {{A Comparison of Periodicity Profile Methods for Sequence Analysis}},
	Url = {https://ieeexplore.ieee.org/document/6507731},
	Year = {2012}}

@article{2004.Butterfield.000,
	Author = {Butterfield, A and Vedagiri, V and Lang, E and Lawrence, C and Wakefield, M J and Isaev, A and Huttley, G A},
	Date-Modified = {2020-04-22 14:46:26 +1000},
	Journal = {BMC Bioinformatics},
	Pages = {1},
	Title = {{PyEvolve: a toolkit for statistical modelling of molecular evolution}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/14706121},
	Volume = {5},
	Year = {2004}}

@article{2013.Verbyla.000,
	Author = {Verbyla, Klara L and Yap, Von Bing and Pahwa, Anuj and Shao, Yunli and Huttley, Gavin A},
	Date-Modified = {2020-04-22 14:56:37 +1000},
	Journal = {PLoS ONE},
	Pages = {e69187},
	Title = {{The embedding problem for Markov models of nucleotide substitution}},
	Url = {https://pubmed.ncbi.nlm.nih.gov/23935949/},
	Volume = {8},
	Year = {2013}}

@inproceedings{2007.Easton.000,
	Author = {Easton, B and Maxwell, P and Isaev, A and Huttley, G A},
	Booktitle = {Proceedings of the 5th Asia-Pacific Bioinformatics Conference},
	Editor = {Chin, Chin},
	Pages = {195--204},
	Publisher = {Imperial College Press},
	Title = {{A probabilistic method to identify compensatory substitutions for pathogenic mutations}},
	Volume = {5},
	Year = {2007}}

@article{2017.Kaehler.000,
	Author = {Kaehler, Benjamin D and Yap, Von Bing and Huttley, Gavin A},
	Date-Modified = {2020-04-22 14:57:45 +1000},
	Journal = {Genome Biology and Evolution},
	Pages = {134--149},
	Title = {{Standard codon substitution models overestimate purifying selection for non-stationary data}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/28175284},
	Volume = {9},
	Year = {2017}}

@article{2010.Ying.000,
	Author = {Ying, Hua and Epps, Julian and Williams, Rohan and Huttley, Gavin},
	Date-Modified = {2020-04-22 14:51:42 +1000},
	Journal = {Mol Biol Evol},
	Pages = {637--649},
	Title = {{Evidence that localised variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/19843619},
	Volume = {27},
	Year = {2010}}

@article{2015.Maitip.000,
	Author = {Maitip, Jakkrawut and Trueman, Holly E and Kaehler, Benjamin D and Huttley, Gavin A and Chantawannakul, Panuwan and Sutherland, Tara D},
	Date-Modified = {2020-04-22 14:57:28 +1000},
	Journal = {Insect biochemistry and molecular biology},
	Pages = {72--9},
	Title = {{Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/25712559},
	Volume = {59},
	Year = {2015}}

@article{2004.Huttley.000,
	Author = {Huttley, Gavin A},
	Date-Modified = {2020-04-22 14:47:24 +1000},
	Journal = {Mol Biol Evol},
	Pages = {1760--1768},
	Title = {{Modeling the impact of DNA methylation on the evolution of BRCA1 in mammals.}},
	Url = {https://www.ncbi.nlm.nih.gov/pubmed/15190129},
	Volume = {21},
	Year = {2004}}
