| Year |
Citation |
Score |
| 2021 |
Irisarri I, Burki F, Whelan S. Automated Removal of Non-homologous Sequence Stretches with PREQUAL. Methods in Molecular Biology (Clifton, N.J.). 2231: 147-162. PMID 33289892 DOI: 10.1007/978-1-0716-1036-7_10 |
0.392 |
|
| 2020 |
Varón-González C, Whelan S, Klingenberg CP. Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable. Systematic Biology. PMID 31985800 DOI: 10.1093/Sysbio/Syaa003 |
0.364 |
|
| 2018 |
Whelan S, Irisarri I, Burki F. PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics (Oxford, England). PMID 29868763 DOI: 10.1093/bioinformatics/bty448 |
0.395 |
|
| 2017 |
Whelan S, Morrison DA. Inferring Trees. Methods in Molecular Biology (Clifton, N.J.). 1525: 349-377. PMID 27896728 DOI: 10.1007/978-1-4939-6622-6_14 |
0.357 |
|
| 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 |
0.401 |
|
| 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 |
0.393 |
|
| 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 |
0.605 |
|
| 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 |
0.604 |
|
| 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 |
0.51 |
|
| 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 |
0.489 |
|
| 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 |
0.579 |
|
| 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 |
0.689 |
|
| 2012 |
Blackburne BP, Whelan S. Measuring the distance between multiple sequence alignments Bioinformatics. 28: 495-502. PMID 22199391 DOI: 10.1093/Bioinformatics/Btr701 |
0.444 |
|
| 2012 |
Money D, Whelan S. Characterizing the phylogenetic tree-search problem Systematic Biology. 61: 228-239. PMID 22076302 DOI: 10.1093/Sysbio/Syr097 |
0.585 |
|
| 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 |
0.31 |
|
| 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 |
0.612 |
|
| 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 |
0.421 |
|
| 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 |
0.309 |
|
| 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 |
0.53 |
|
| 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 |
0.489 |
|
| 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 |
0.336 |
|
| 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 |
0.392 |
|
| 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 |
0.718 |
|
| 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 |
0.395 |
|
| 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 |
0.747 |
|
| 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 |
0.758 |
|
| 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 |
0.632 |
|
| 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 |
0.739 |
|
| 2005 |
Whelan S, Nielsen R. Statistical Methods in Molecular Evolution Systematic Biology. 55: 698-700. DOI: 10.1080/10635150600899780 |
0.492 |
|
| 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 |
0.607 |
|
| 2004 |
Bofkin L, Whelan S. Functional needles in a genomic haystack Heredity. 92: 363-364. PMID 15107806 DOI: 10.1038/sj.hdy.6800429 |
0.739 |
|
| 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 |
0.654 |
|
| 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 |
0.629 |
|
| 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 |
0.695 |
|
| 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 DOI: 10.1093/Oxfordjournals.Molbev.A004007 |
0.617 |
|
| 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 |
0.631 |
|
| 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 DOI: 10.1093/Oxfordjournals.Molbev.A003851 |
0.655 |
|
| 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 DOI: 10.1093/Oxfordjournals.Molbev.A026378 |
0.542 |
|
| 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. DOI: 10.1098/Rspb.2000.1183 |
0.528 |
|
| 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 |
0.544 |
|
| 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. DOI: 10.1093/Oxfordjournals.Molbev.A026219 |
0.622 |
|
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