Dr Simon Whelan

Publications

2012
RM. Ames, D. Money, VP. Ghatge, S. Whelan, S. Lovell. (2012). Determining the evolutionary history of gene families. Bioinformatics, 28, 48-55. eScholarID:148058 | DOI:10.1093/bioinformatics/btr592
L. Emery, S. Whelan, KD. Hirschi, JK. Pittman. (2012). Protein phylogenetic analysis of Ca2+/cation antiporters and insights into their evolution in plants. Frontiers in Plant Physiology, 3, 1. eScholarID:149101 | DOI:10.3389/fpls.2012.00001
CP. Klingenberg, S. Duttke, S. Whelan, M. Kim. (2012). Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves. Journal of Evolutionary Biology, 1, 115-129. eScholarID:154746 | DOI:10.1111/j.1420-9101.2011.02410.x
BP. Blackburne, S. Whelan. (2012). Measuring the distance between multiple sequence alignments. Bioinformatics, 28, 495-502. eScholarID:155840 | DOI:10.1093/bioinformatics/btr701
D. Money, S. Whelan. (2012). Characterizing the phylogenetic tree-search problem. Systematic Biology, 61, 228-239. eScholarID:155998 | DOI:10.1093/sysbio/syr097
DA. Liberles, et al. (2012). The interface of protein structure, protein biophysics, and molecular evolution. Protein Science, 21(6), 769-785. eScholarID:161329 | DOI:10.1002/pro.2071
2011
Whelan S, Blackburne BP, Spencer, M. (2011). Phylogenetic substitution models for detecting heterotachy during plastid evolution. Molecular Biology and Evolution, 28, 449-458. eScholarID:102989 | DOI:10.1093/molbev/msq215
2010
S. Whelan, D. Money. (2010). The prevalence of multifurcations in tree-space and their implications for tree-search. Molecular Biology and Evolution, 27, 2674-2677. eScholarID:94890 | DOI:10.1093/molbev/msq163
Gorsi B, Whelan S, and Stringer SE. (2010). Dynamic expression patterns of 6-O endosulfatases during zebrafish development suggest a subfunctionalisation event for sulf2. Developmental Dynamics, 239, 3312-3323. eScholarID:102985 | DOI:10.1002/dvdy.22456
2008
S. Whelan. (2008). Spatial and Temporal Heterogeneity in Nucleotide Sequence Evolution. Mol. Biol. Evol, 25, 1683-1694. eScholarID:1c7764 | DOI:10.1093/molbev/msn119
S. Whelan. (2008). Inferring Trees. In J. Keith (Ed.), Bioinformatics: Data, Sequence Analysis and Evolution. (pp. 287-309). Springer. eScholarID:3c302 | DOI:10.1007/978-1-60327-159-2_14
S. Whelan. (2008). The genetic code can cause systematic bias in simple phylogenetic models. Phil. Trans. R. Soc. B, In press, eScholarID:1c7765 | DOI:10.1098/rstb.2008.0171
Tress ML, Wesselink J-J ,Frankish A, Lopez G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. (2008). Determination and validation of principal gene products. Bioinformatics, 24, 11-17. eScholarID:1c7924 | DOI:10.1093/bioinformatics/btm547
2007
The ENCODE Project Consortium. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816. eScholarID:1c6716 | DOI:10.1038/nature05874
Elliott et al. (2007). Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17, 760-774. eScholarID:1c6717 | DOI:10.1101/gr.6034307
Whelan S. (2007). New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments. Systematic Biology, 56(5), 727-740. eScholarID:1c6963 | DOI:10.1080/10635150701611134
2006
Whelan S. (2006). A review of: "Statistical methods in molecular evolution". Systematic Biology, 55(4), 698-700. eScholarID:1c6288 | DOI:10.1080/10635150600899780
Kosiol C, Bofkin L, Whelan S. (2006). Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome. Journal of biomedical informatics, 39(1), 51-61. eScholarID:1c5079 | PMID:16226061 | DOI:10.1016/j.jbi.2005.08.003
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N. (2006). PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic acids research, 34(Database), D327-31. eScholarID:1c5080 | PMID:16381879 | DOI:10.1093/nar/gkj087
2004
Whelan S, Goldman N. (2004). Estimating the frequency of events that cause multiple-nucleotide changes. Genetics, 167(4), 2027-43. eScholarID:1c5077 | PMID:15342538 | DOI:10.1534/genetics.103.023226
Bofkin L, Whelan S. (2004). Functional needles in a genomic haystack. Heredity, 92(5), 363-4. eScholarID:1c5078 | PMID:15107806 | DOI:10.1038/sj.hdy.6800429
2003
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D. (2003). Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome research, 13, 13-26. eScholarID:1c5074 | DOI:10.1101/gr.844103
Whelan S, de Bakker PIW, Goldman N. (2003). PANDIT: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics (Oxford, England), 19, 1556-1563. eScholarID:1c5075 | DOI:10.1093/bioinformatics/btg188
2002
Waterston et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420(6915), 520-62. eScholarID:1c5076 | PMID:12466850 | DOI:10.1038/nature01262
Goldman N, Whelan S. (2002). A novel use of equilibrium frequencies in models of sequence evolution. Molecular biology and evolution, 19, 1821-1831. eScholarID:1c5073 | DOI:10.1093/oxfordjournals.molbev.a004007
2001
Whelan S, Lio P, Goldman N. (2001). Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends in Genetics, 17, 262-272. eScholarID:1c5071 | DOI:10.1016/S0168-9525(01)02272-7
Whelan S, Goldman N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Molecular biology and evolution, 18, 691-699. eScholarID:1c5072 | DOI:10.1093/oxfordjournals.molbev.a003851
2000
Goldman N, Whelan S. (2000). Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Molecular biology and evolution, 17, 975-978. eScholarID:1c5070
1999
Whelan S, Goldman N. (1999). Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics. Molecular biology and evolution, 16, 1292-1299. eScholarID:1c5068
Hagelburg E, Goldman N, Lio P, Whelan S, Schiefenhovel W, Clegg JB, Bowden DK. (1999). Evidence for mitochondrial DNA recombination in a human population of island melanesia. Proceedings of the Royal Society, London B, 266, 485-492. eScholarID:1c5069 | PMID:10189712 | DOI:10.1098/rspb.1999.0663