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Dr Simon Whelan - publications

List of publications


  • D. Money, S. Whelan. (2012). Characterizing the phylogenetic tree-search problem. Systematic Biology, 61, 228-239. eScholarID:155998 | DOI:10.1093/sysbio/syr097
  • 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
  • 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
  • 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
  • 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


  • 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


  • 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
  • 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


  • 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
  • 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). Spatial and Temporal Heterogeneity in Nucleotide Sequence Evolution. Mol. Biol. Evol, 25, 1683-1694. eScholarID:1c7764 | DOI:10.1093/molbev/msn119
  • 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


  • 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
  • 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
  • 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


  • Whelan S. (2006). A review of: "Statistical methods in molecular evolution". Systematic Biology, 55(4), 698-700. eScholarID:1c6288 | DOI:10.1080/10635150600899780
  • 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
  • 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



  • 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


  • 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
  • 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


  • 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
  • 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


  • 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


  • 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