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Peter Waddell

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Publications

TOP 3
Xijiang Miao; Peter J Waddell; Homayoun Valafar
TALI: local alignment of protein structures using backbone torsion angles.
Paul D Waters; Gauthier Dobigny; Peter J Waddell; Terence J Robinson
LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences.
Peter J Waddell; Hirohisa Kishino; Rissa Ota
Phylogenetic methodology for detecting protein interactions.

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All Publications

2008: Xijiang Miao; Peter J Waddell; Homayoun Valafar
TALI: local alignment of protein structures using backbone torsion angles.
Journal of bioinformatics and computational biology 2008;6(1):163-81.
2008: Paul D Waters; Gauthier Dobigny; Peter J Waddell; Terence J Robinson
LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences.
Methods in molecular biology (Clifton, N.J.) 2008;422():227-37.
2007: Peter J Waddell; Hirohisa Kishino; Rissa Ota
Phylogenetic methodology for detecting protein interactions.
Molecular biology and evolution 2007;24(3):650-9.
2007: Yasuhiro Kitazoe; Hirohisa Kishino; Peter J Waddell; Noriaki Nakajima; Takahisa Okabayashi; Teruaki Watabe; Yoshiyasu Okuhara
Robust time estimation reconciles views of the antiquity of placental mammals.
PloS one 2007;2(4):e384.
2007: Paul D Waters; Gauthier Dobigny; Peter J Waddell; Terence J Robinson
Evolutionary history of LINE-1 in the major clades of placental mammals.
PloS one 2007;2(1):e158.
2005: Peter J Waddell
Measuring the fit of sequence data to phylogenetic model: allowing for missing data.
Molecular biology and evolution 2005;22(3):395-401.
2003: Joshua S Rest; Jennifer Ast; Christopher C Austin; Peter J Waddell; Elizabeth A Tibbetts; Jennifer M Hay; David P Mindell
Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.
Molecular phylogenetics and evolution 2003;29(2):289-97.
2003: Peter J Waddell; Shawn Shelley
Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models.
Molecular phylogenetics and evolution 2003;28(2):197-224.
2002: Yu-Hsin Lin; Peter J Waddell; David Penny
Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires.
Gene 2002;294(1-2):119-29.
2002: Peter J Waddell; Hirohisa Kishino; Rissa Ota
Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.
Genome informatics. International Conference on Genome Informatics 2002;13():82-92.
2001: David L Swofford; Peter J Waddell; J P Huelsenbeck; P G Foster; Paul O Lewis; JS Rogers
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods.
Systematic biology 2001;50(4):525-39.
2001: Peter J Waddell; Hirohisa Kishino; Rissa Ota
A phylogenetic foundation for comparative mammalian genomics.
Genome informatics. International Conference on Genome Informatics 2001;12():141-54.
2000: Peter J Waddell; Hirohisa Kishino; Rissa Ota
Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests.
Molecular biology and evolution 2000;17(12):1988-92.
2000: Rissa Ota; Peter J Waddell; M Hasegawa; H Shimodaira; Hirohisa Kishino
Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters.
Molecular biology and evolution 2000;17(5):798-803.
2000: J Adachi; Peter J Waddell; W Martin; M Hasegawa
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.
Journal of molecular evolution 2000;50(4):348-58.
2000: Peter J Waddell; Hirohisa Kishino
Cluster inference methods and graphical models evaluated on NCI60 microarray gene expression data.
Genome informatics. Workshop on Genome Informatics 2000;11():129-40.
2000: Hirohisa Kishino; Peter J Waddell
Correspondence analysis of genes and tissue types and finding genetic links from microarray data.
Genome informatics. Workshop on Genome Informatics 2000;11():83-95.
1999: David Penny; M Hasegawa; Peter J Waddell; Michael D Hendy
Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.
Systematic biology 1999;48(1):76-93.
1999: Peter J Waddell; Y Cao; J Hauf; M Hasegawa
Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant.
Systematic biology 1999;48(1):31-53.
1999: Peter J Waddell; Y Cao; M Hasegawa; David P Mindell
Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework.
Systematic biology 1999;48(1):119-37.
1999: Peter J Waddell; N Okada; M Hasegawa
Towards resolving the interordinal relationships of placental mammals.
Systematic biology 1999;48(1):1-5.
1998: Y Cao; Peter J Waddell; Norihiro Okada; Masami Hasegawa
The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates.
Molecular biology and evolution 1998;15(12):1637-46.
1998: Ying Cao; Axel Janke; Peter J Waddell; M Westerman; O Takenaka; S Murata; Norihiro Okada; S Pääbo; Masami Hasegawa
Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders.
Journal of molecular evolution 1998;47(3):307-22.
1997: Peter J Waddell; M A Steel
General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites.
Molecular phylogenetics and evolution 1997;8(3):398-414.
1997: Peter J Waddell; David Penny; T Moore
Hadamard conjugations and modeling sequence evolution with unequal rates across sites.
Molecular phylogenetics and evolution 1997;8(1):33-50.
1996: P J Lockhart; A W Larkum; M Steel; Peter J Waddell; David Penny
Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(5):1930-4.
1995: David Penny; M Steel; Peter J Waddell; Michael D Hendy
Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens.
Molecular biology and evolution 1995;12(5):863-82.