Simon Whelan, Ph.D. - Publications

Affiliations: 
Evolutionary Biology Uppsala University, Uppsala, Uppsala län, Sweden 
Area:
Molecular Evolution

40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Md Mukarram Hossain AS, Blackburne BP, Shah A, Whelan S. Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty. Genome Biology and Evolution. 7: 2102-16. PMID 26139831 DOI: 10.1093/gbe/evv127  1
2015 Talavera D, Lovell SC, Whelan S. Covariation Is a Poor Measure of Molecular Coevolution. Molecular Biology and Evolution. PMID 25944916 DOI: 10.1093/molbev/msv109  1
2015 Money D, Whelan S. GeLL: a generalized likelihood library for phylogenetic models. Bioinformatics (Oxford, England). 31: 2391-3. PMID 25725494 DOI: 10.1093/bioinformatics/btv126  1
2015 Whelan S, Allen JE, Blackburne BP, Talavera D. ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models. Systematic Biology. 64: 42-55. PMID 25209223 DOI: 10.1093/sysbio/syu062  1
2014 García-Pereira MJ, Carvajal-Rodríguez A, Whelan S, Caballero A, Quesada H. Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers. Molecular Phylogenetics and Evolution. 76: 102-9. PMID 24631855 DOI: 10.1016/j.ympev.2014.03.001  1
2014 Allen JE, Whelan S. Assessing the state of substitution models describing noncoding RNA evolution. Genome Biology and Evolution. 6: 65-75. PMID 24391153 DOI: 10.1093/gbe/evt206  1
2013 Blackburne BP, Whelan S. Class of multiple sequence alignment algorithm affects genomic analysis Molecular Biology and Evolution. 30: 642-653. PMID 23144040 DOI: 10.1093/molbev/mss256  1
2012 Emery L, Whelan S, Hirschi KD, Pittman JK. Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants. Frontiers in Plant Science. 3: 1. PMID 22645563 DOI: 10.3389/fpls.2012.00001  1
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, ... ... Whelan S, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/pro.2071  1
2012 Blackburne BP, Whelan S. Measuring the distance between multiple sequence alignments Bioinformatics. 28: 495-502. PMID 22199391 DOI: 10.1093/bioinformatics/btr701  1
2012 Money D, Whelan S. Characterizing the phylogenetic tree-search problem Systematic Biology. 61: 228-239. PMID 22076302 DOI: 10.1093/sysbio/syr097  1
2012 Klingenberg CP, Duttke S, Whelan S, Kim M. Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves. Journal of Evolutionary Biology. 25: 115-29. PMID 22070353 DOI: 10.1111/j.1420-9101.2011.02410.x  1
2012 Ames RM, Money D, Ghatge VP, Whelan S, Lovell SC. Determining the evolutionary history of gene families Bioinformatics. 28: 48-55. PMID 22039210 DOI: 10.1093/bioinformatics/btr592  1
2011 Whelan S, Blackburne BP, Spencer M. Phylogenetic substitution models for detecting heterotachy during plastid evolution. Molecular Biology and Evolution. 28: 449-58. PMID 20724379 DOI: 10.1093/molbev/msq215  1
2010 Gorsi B, Whelan S, Stringer SE. Dynamic expression patterns of 6-O endosulfatases during zebrafish development suggest a subfunctionalisation event for sulf2. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 239: 3312-23. PMID 20981828 DOI: 10.1002/dvdy.22456  1
2010 Whelan S, Money D. The prevalence of multifurcations in tree-space and their implications for tree-search Molecular Biology and Evolution. 27: 2674-2677. PMID 20584772 DOI: 10.1093/molbev/msq163  1
2008 Whelan S. The genetic code can cause systematic bias in simple phylogenetic models. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 4003-11. PMID 18852102 DOI: 10.1098/rstb.2008.0171  1
2008 Whelan S. Inferring trees. Methods in Molecular Biology (Clifton, N.J.). 452: 287-309. PMID 18566770 DOI: 10.1007/978-1-60327-159-2_14  1
2008 Whelan S. Spatial and temporal heterogeneity in nucleotide sequence evolution. Molecular Biology and Evolution. 25: 1683-94. PMID 18502771 DOI: 10.1093/molbev/msn119  1
2008 Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/bioinformatics/btm547  1
2007 Whelan S. New approaches to phylogenetic tree search and their application to large numbers of protein alignments. Systematic Biology. 56: 727-40. PMID 17849327 DOI: 10.1080/10635150701611134  1
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Whelan S, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  1
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/gr.6034307  1
2006 Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Research. 34: D327-31. PMID 16381879 DOI: 10.1093/nar/gkj087  1
2006 Kosiol C, Bofkin L, Whelan S. Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome Journal of Biomedical Informatics. 39: 51-61. PMID 16226061 DOI: 10.1016/j.jbi.2005.08.003  1
2004 Whelan S, Goldman N. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics. 167: 2027-43. PMID 15342538 DOI: 10.1534/genetics.103.023226  1
2004 Bofkin L, Whelan S. Functional needles in a genomic haystack Heredity. 92: 363-364. PMID 15107806 DOI: 10.1038/sj.hdy.6800429  1
2003 Whelan S, de Bakker PI, Goldman N. Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics (Oxford, England). 19: 1556-63. PMID 12912837 DOI: 10.1093/bioinformatics/btg188  1
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, et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Research. 13: 13-26. PMID 12529302 DOI: 10.1101/gr.844103  1
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Whelan S, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/nature01262  1
2002 Goldman N, Whelan S. A novel use of equilibrium frequencies in models of sequence evolution. Molecular Biology and Evolution. 19: 1821-31. PMID 12411592  1
2001 Whelan S, Liò P, Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends in Genetics : Tig. 17: 262-72. PMID 11335036 DOI: 10.1016/S0168-9525(01)02272-7  1
2001 Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution. 18: 691-9. PMID 11319253  1
2000 Goldman N, Whelan S. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Molecular Biology and Evolution. 17: 975-8. PMID 10833204  1
2000 Hagelberg E, Goldman N, Lio P, Whelan S, Schiefenhovel W, Clegg JB, Bowden DK. Evidence for mitochondrial DNA recombination in a human population of island Melanesia: Correction Proceedings of the Royal Society B: Biological Sciences. 267: 1595-1596.  1
1999 Hagelberg E, Goldman N, Lió P, Whelan S, Schiefenhövel W, Clegg JB, Bowden DK. Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proceedings. Biological Sciences / the Royal Society. 266: 485-92. PMID 10189712 DOI: 10.1098/rspb.1999.0663  1
1999 Whelan S, Goldman N. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics Molecular Biology and Evolution. 16: 1292-1299.  1
1986 Muir CS, Wagner G, Démaret E, Nagy-Tiborcz A, Parkin DM, Schlaefer K, Villhauer-Lehr M, Whelan S. Directory of on-going research in cancer epidemiology. 1986 Iarc Scientific Publications. 1-805. PMID 3536739  1
1985 Muir CS, Wagner G, Démaret E, Nagy-Tiborcz A, Parkin DM, Schlaefer K, Villhauer-Lehr M, Whelan S. Directory of On-Going Research in Cancer Epidemiology. 1985 Iarc Scientific Publications. 1-756. PMID 3908310  1
1982 Muir CS, Wagner G, Demaret E, Nagy-Tiborcz A, Schlaefer K, Villhauer-Lehr M, Whelan S. Directory of on-going research in cancer epidemiology 1982 Iarc Scientific Publications. 1-715. PMID 6754598  1
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