In most cases, copyright and all rights therein are retained by the respective publishers. This material may not be copied or reproduced in any form without permission.
In the list below, numbered items are peer-reviewed research papers. I have published 35 articles in total, including work in press. The list below is generally up-to-date, but you can always
check out a list of my publications in PubMed if you think something's missing.
in press
25. Yang Liu, James A. Cotton, Bin Shen, Xiuqun Han, Stephen J. Rossiter and Shuyi Zhang (in press) Convergent sequence evolution between echolocating bats
and dolphins. Current Biology [reprint available soon]
2009
24. Diego San Mauro, Dave Gower, Tim Massingham, Mark Wilkinson, Rafael Zardoya and James A. Cotton (2009) Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1. Systematic Biology 58(4):425-438.
23. Huabin Zhao, Stephen J. Rossiter, Emma C. Teeling, Chanjuan Li, James A. Cotton and Shuyi Zhang (2009) The evolution of color vision in nocturnal mammals. Proc. Natl. Acad. Sci. USA 106(22):8980-8985.
[journal page][PubMed]
22. Kat Gold, James A. Cotton and Angelika Stollewerk (2009). The role of Notch signalling and numb function in mechanosensory organ formation in the spider Cupiennius salei. Developmental Biology 327(1):121-131.
[PubMed]
James A. Cotton and Mark Wilkinson (2009) Supertrees enter the mainstream of phylogenetics. Trends in Ecology and Evolution 24:1-3.
[journal page][PubMed]
2008
21. Angela McCann, James A. Cotton and James McInerney (2008) The Tree of Genomes: An Empirical Comparison of Genome Phylogeny Reconstruction Methods BMC Evolutionary Biology 8:312.
[open-access at BMC][PubMed]
20. Gang Li, Jinhong Wang, Stephen J. Rossiter, Gareth Jones, James A. Cotton and Shuyi Zhang (2008) The hearing gene Prestin reunites echolocating bats. Proc. Natl. Acad. Sci. USA 37:13959-13964.
[PNAS website][PubMed]
James O. McInerney, James A. Cotton and Davide Pisani (2008) The Prokaryotic Tree of Life: Past, Present and Future. Trends in Ecology and Evolution 23(5):276-281.
[journal page][PubMed]
James A. Cotton (2008)
The Impact of Gene Duplication on Human Genome Evolution. article A20841 in Encylopedia of Life Sciences, John Wiley & Sons, Chichester. Also appears in Handbook of Human Molecular Evolution, David N. Cooper and Hildegard Kehrer-Sawatzki, eds.
[ELS article]
19. Kevin J. Peterson, James A. Cotton, James G. Gehling and Davide Pisani (2008)
The Ediacaran Emergence of Bilaterians: Congruence between the Genetic and Geologic Fossil Records. Phil Trans Roy Soc Lond 363(1496):1435-1443.
Also published as a chapter in Animal Evolution: Genomes, Fossils, and Trees M.J. Telford and D.T.J. Littlewood (eds). Oxford University Press.
[Journal page][PubMed][Buy the book on Amazon.co.uk]
18. Julia J. Day, James A. Cotton and Timothy G. Barraclough (2008) Tempo and Mode of Diversification in Lake Tanganyika cichlid fishes PLoS One 3(3):e1730.
[open-access at PLoS One][PubMed]
17. James A. Cotton and Mark
Wilkinson (2008) Quantifying the potential utility of phylogenetic characters. Taxon 57(1):131-136.
[IngentaConnect]
13. Mark Wilkinson, James A. Cotton, Francois-Joseph Lapointe and
Davide Pisani (2007) Properties of supertree methods in the consensus setting. Syst. Biol.
56(2):330-337.
[PubMed][Informaworld]
2006
12. Mark Wilkinson and James A. Cotton (2006) Supertree methods for
building the tree of life:
divide-and-conquer approaches to large phylogenetic problems. pp.61-75 in Towards the Tree of Life: Taxonomy and Systematics of Large and Species Rich Taxa (Hodkinson, T., J. Parnell, and S. Waldren, eds.). Systematic Association special volume, CRC Press.
[Publishers site]
10. James A. Cotton, Claire S.C. Slater and Mark Wilkinson (2006)
Discriminating Supported and Unsupported Relationships in Supertrees using Triplets. Syst. Biol. 55(2):345-350.
[PubMed]
9. K. Kevin Pfister, Paresh R. Shah, Holger Hummerich, Andreas Russ, James Cotton, Azlina Ahmad Annuar, Stephen M. King and Elizabeth M.C. Fisher (2006) Genetic Analysis of the Cytoplasmic Dynein Subunit Families. PLoS Genetics 2(1).
[free online access][PubMed]
2005
8. Mark Wilkinson, Davide Pisani, James A. Cotton and Ian Corfe (2005) Measuring Support and Finding Unsupported Relationships in Supertrees. Syst. Biol. 54(5):823-831
[PubMed]
7. Mark Wilkinson, James A.
Cotton, Chris Creevey, Oliver Eulenstein, Simon R.
Harris, Francois-Joseph Lapointe, Claudine Levasseur, James O.
McInerney, Davide Pisani and Joseph L. Thorley (2005) The Shape of Supertrees to Come: Tree Shape Related Properties of Fourteen Supertree Methods. Syst. Biol. 54(3):419-431
[PubMed]
J. A. Cotton (2005) Analytical methods for detecting paralogy
in molecular datasets. In Methods in Molecular
Evolution: Producing the Biochemical Data, Part B (E. A. Zimmer and E. H.
Roalson, eds.). Methods in Enzymology 395:700-724.
[PubMed]
2004
5. M. Wilkinson, J. A. Cotton and J. L. Thorley (2004) The Information
Content of Trees and their Matrix Representations. Systematic Biology 53(6):989-1001. [RadCon homepage]
4. J. A. Cotton and
R. D. M. Page
(2004) Tangled trees from molecular markers: reconciling conflict between phylogenies to build molecular supertrees. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 107-125. Kluwer Academic, Dordrecht, the Netherlands. [book web site]
2003
3. J. A. Cotton and R. D. M. Page (2003) Gene Tree Parsimony vs. Uninode coding for phylogenetic reconstruction from duplicate genes.
Molecular Phylogenetics and Evolution 29:298-308. [Science Direct fulltext][PubMed]
1. Page, R.D.M. and J. A. Cotton (2001). Vertebrate phylogenomics: reconciled trees and gene duplications. In Russ B. Altman, A. Keith Dunker, Lawrewnce Hunter, Kevin Lauderdale and
Teri E. Klein, (eds.), Proceedings
of the Pacific Syposium on Biocomputing 2002. World Scientific Publishing, Singapore. pp. 536-548. [PSB website][PubMed]
James Cotton (2001). Invertebrate retroelements have borrowed diverse viral envelopes for infection. Genome Biology 2(2):reports0006 [Genome Biology fulltext
]
James Cotton (2001). Techniques commonly applied to the discovery of unknown prokaryotes have now been used to identify new eukaryotic lineages with
in picoplankton. Genome Biology 2(7):reports0016 [Genome Biology fulltext
]
James Cotton (2001). An unusual genetic system has allowed recombination to be recognized in an animal mitochondrial genome. Genome Biology 2(10):reports0034 [Genome Biology fulltext
]
2000
Page, R.D.M. and Cotton, J.A. (2000) GeneTree: a tool for exploring gene family evolution. In D. Sankoff, and J. Nadeau, (eds.), Comparative Genomics: Empirical and Analytical Approaches to Gene Order
Dynamics, Map Alignment, and the Evolution of Gene Families. Kluwer Academic Press, Dordrecht, pp. 525-536. [DCAF website][Book]
James Cotton (2000). DNA libraries from uncultured soil-microbes have revealed insights into the functional and genomic diversity of soil bacteria.
Genome Biology 1(2):reports0060. [Genome Biology fulltext
]
James Cotton (2000). Genome structure confirms the chastity of some ancient asexuals.
Genome Biology 1(3):reports0068 [Genome Biology fulltext
]
James Cotton (2000). A new division of the Archaea could be the most ancient living lineage. Genome Biology 1(6):reports0076 [Genome Biology fulltext
]
