| Year |
Citation |
Score |
| 2018 |
Fang L, Leliaert F, Novis PM, Zhang Z, Zhu H, Liu G, Penny D, Zhong B. Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models. Molecular Phylogenetics and Evolution. PMID 29885933 DOI: 10.1016/J.Ympev.2018.06.006 |
0.418 |
|
| 2017 |
Penny D. Phylogenetics: Tertiary protein structures needed. Nature Ecology & Evolution. 1: 80. PMID 28812725 DOI: 10.1038/S41559-017-0080 |
0.313 |
|
| 2017 |
Fang L, Leliaert F, Zhang Z, Penny D, Zhong B. Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses Journal of Systematics and Evolution. 55: 322-332. DOI: 10.1111/Jse.12248 |
0.423 |
|
| 2016 |
Sun L, Fang L, Zhang Z, Chang X, Penny D, Zhong B. Chloroplast Phylogenomic Inference of Green Algae Relationships. Scientific Reports. 6: 20528. PMID 26846729 DOI: 10.1038/Srep20528 |
0.371 |
|
| 2016 |
Poole AM, Jeffares DC, Hoeppner MP, Penny D. Does the Ribosome Challenge our Understanding of the RNA World? Journal of Molecular Evolution. 82: 1-4. PMID 26582049 DOI: 10.1007/S00239-015-9720-X |
0.309 |
|
| 2015 |
Gibb GC, England R, Hartig G, McLenachan PA, Taylor Smith BL, McComish BJ, Cooper A, Penny D. New Zealand Passerines Help Clarify the Diversification of Major Songbird Lineages During the Oligocene. Genome Biology and Evolution. PMID 26475316 DOI: 10.1093/Gbe/Evv196 |
0.366 |
|
| 2015 |
Penny D, Zhong B. Two fundamental questions about protein evolution. Biochimie. 119: 278-83. PMID 25447137 DOI: 10.1016/J.Biochi.2014.10.020 |
0.349 |
|
| 2015 |
Carr LM, Trish Mclenachan PA, Waddell PJ, Gemmell NJ, Penny D. Analyses of the mitochondrial genome of Leiopelma hochstetteri argues against the full drowning of New Zealand Journal of Biogeography. 42: 1066-1076. DOI: 10.1111/Jbi.12482 |
0.368 |
|
| 2014 |
Penny D, Collins LJ, Daly TK, Cox SJ. The relative ages of eukaryotes and akaryotes. Journal of Molecular Evolution. 79: 228-39. PMID 25179144 DOI: 10.1007/S00239-014-9643-Y |
0.346 |
|
| 2014 |
Dodt WG, McComish BJ, Nilsson MA, Gibb GC, Penny D, Phillips MJ. The complete mitochondrial genome of the eastern grey kangaroo (Macropus giganteus). Mitochondrial Dna. 1-2. PMID 25103427 DOI: 10.3109/19401736.2014.947583 |
0.59 |
|
| 2014 |
Robins JH, Tintinger V, Aplin KP, Hingston M, Matisoo-Smith E, Penny D, Lavery SD. Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species. Plos One. 9: e98002. PMID 24865350 DOI: 10.1371/Journal.Pone.0098002 |
0.349 |
|
| 2014 |
Zhong B, Fong R, Collins LJ, McLenachan PA, Penny D. Two new fern chloroplasts and decelerated evolution linked to the long generation time in tree ferns. Genome Biology and Evolution. 6: 1166-73. PMID 24787621 DOI: 10.1093/Gbe/Evu087 |
0.348 |
|
| 2014 |
Mahmood MT, McLenachan PA, Gibb GC, Penny D. Phylogenetic position of avian nocturnal and diurnal raptors. Genome Biology and Evolution. 6: 326-32. PMID 24448983 DOI: 10.1093/Gbe/Evu016 |
0.395 |
|
| 2014 |
Zhong B, Xi Z, Goremykin VV, Fong R, McLenachan PA, Novis PM, Davis CC, Penny D. Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes. Molecular Biology and Evolution. 31: 177-83. PMID 24136916 DOI: 10.1093/Molbev/Mst200 |
0.341 |
|
| 2014 |
Lockhart PJ, Larkum AWD, Becker M, Penny D. We are Still Learning About the Nature of Species and Their Evolutionary Relationships1 Annals of the Missouri Botanical Garden. 100: 6-13. DOI: 10.3417/2012084 |
0.355 |
|
| 2013 |
Lockhart PJ, Penny D, Hendy MD, Larkum AD. IsProchlorothrix hollandica the best choice as a prokaryotic model for higher plant Chla/b photosynthesis? Photosynthesis Research. 37: 61-8. PMID 24317654 DOI: 10.1007/Bf02185439 |
0.373 |
|
| 2013 |
White WT, Zhong B, Penny D. Beyond reasonable doubt: evolution from DNA sequences. Plos One. 8: e69924. PMID 23950906 DOI: 10.1371/Journal.Pone.0069924 |
0.413 |
|
| 2013 |
Daly TK, Sutherland-Smith AJ, Penny D. In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes Genome Biology and Evolution. 5: 1567-1583. PMID 23887922 DOI: 10.1093/Gbe/Evt113 |
0.346 |
|
| 2013 |
Zhong B, Liu L, Yan Z, Penny D. Origin of land plants using the multispecies coalescent model. Trends in Plant Science. 18: 492-5. PMID 23707196 DOI: 10.1016/J.Tplants.2013.04.009 |
0.34 |
|
| 2013 |
Gibb GC, Kennedy M, Penny D. Beyond phylogeny: pelecaniform and ciconiiform birds, and long-term niche stability. Molecular Phylogenetics and Evolution. 68: 229-38. PMID 23562800 DOI: 10.1016/J.Ympev.2013.03.021 |
0.403 |
|
| 2013 |
Shavit Grievink L, Penny D, Holland BR. Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice. Genome Biology and Evolution. 5: 681-7. PMID 23471508 DOI: 10.1093/Gbe/Evt032 |
0.356 |
|
| 2013 |
Daly TK, Sutherland-Smith AJ, Penny D. Beyond BLASTing: Tertiary and quaternary structure analysis helps identify major vault proteins Genome Biology and Evolution. 5: 217-232. PMID 23275487 DOI: 10.1093/Gbe/Evs135 |
0.312 |
|
| 2012 |
Corser CA, McLenachan PA, Pierson MJ, Harrison GL, Penny D. The Q2 mitochondrial haplogroup in Oceania. Plos One. 7: e52022. PMID 23284859 DOI: 10.1371/Journal.Pone.0052022 |
0.32 |
|
| 2012 |
Saurabh K, Holland BR, Gibb GC, Penny D. Gaps: An Elusive Source of Phylogenetic Information Systematic Biology. 61: 1075-1082. PMID 22438330 DOI: 10.1093/Sysbio/Sys043 |
0.35 |
|
| 2011 |
Chen XS, Penny D, Collins LJ. Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis. Bmc Genomics. 12: 550. PMID 22053856 DOI: 10.1186/1471-2164-12-550 |
0.301 |
|
| 2011 |
Zhong B, Deusch O, Goremykin VV, Penny D, Biggs PJ, Atherton RA, Nikiforova SV, Lockhart PJ. Systematic error in seed plant phylogenomics. Genome Biology and Evolution. 3: 1340-8. PMID 22016337 DOI: 10.1093/Gbe/Evr105 |
0.418 |
|
| 2011 |
Harrison A, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Supuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A, Shapiro B. Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses. 3: 83-101. PMID 21765983 DOI: 10.3390/V3020083 |
0.329 |
|
| 2010 |
McComish BJ, Hills SF, Biggs PJ, Penny D. Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biology and Evolution. 2: 410-24. PMID 20624744 DOI: 10.1093/Gbe/Evq029 |
0.404 |
|
| 2010 |
Shavit Grievink L, Penny D, Hendy MD, Holland BR. Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree. Systematic Biology. 59: 288-97. PMID 20525636 DOI: 10.1093/Sysbio/Syq003 |
0.365 |
|
| 2010 |
Phillips MJ, Gibb GC, Crimp EA, Penny D. Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Systematic Biology. 59: 90-107. PMID 20525622 DOI: 10.1093/Sysbio/Syp079 |
0.629 |
|
| 2010 |
Steel M, Penny D. Origins of life: Common ancestry put to the test. Nature. 465: 168-9. PMID 20463725 DOI: 10.1038/465168A |
0.334 |
|
| 2010 |
Gibb GC, Penny D. Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves. Molecular Phylogenetics and Evolution. 56: 698-706. PMID 20399870 DOI: 10.1016/J.Ympev.2010.04.016 |
0.393 |
|
| 2009 |
Chen XS, Collins LJ, Biggs PJ, Penny D. High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biology and Evolution. 1: 165-75. PMID 20333187 DOI: 10.1093/Gbe/Evp017 |
0.308 |
|
| 2009 |
Waddell PJ, Ota R, Penny D. Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests. Journal of Molecular Evolution. 69: 289-99. PMID 19851702 DOI: 10.1007/S00239-009-9268-8 |
0.387 |
|
| 2009 |
Penny D, Hoeppner MP, Poole AM, Jeffares DC. An overview of the introns-first theory. Journal of Molecular Evolution. 69: 527-40. PMID 19777149 DOI: 10.1007/S00239-009-9279-5 |
0.304 |
|
| 2009 |
Collins LJ, Kurland CG, Biggs P, Penny D. The modern RNP world of eukaryotes. The Journal of Heredity. 100: 597-604. PMID 19643816 DOI: 10.1093/Jhered/Esp064 |
0.333 |
|
| 2009 |
Pratt RC, Gibb GC, Morgan-Richards M, Phillips MJ, Hendy MD, Penny D. Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Molecular Biology and Evolution. 26: 313-26. PMID 18981298 DOI: 10.1093/Molbev/Msn248 |
0.625 |
|
| 2008 |
Shavit Grievink L, Penny D, Hendy MD, Holland BR. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. Bmc Evolutionary Biology. 8: 317. PMID 19021917 DOI: 10.1186/1471-2148-8-317 |
0.333 |
|
| 2008 |
Chen XS, White WT, Collins LJ, Penny D. Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. Plos One. 3: e3106. PMID 18769729 DOI: 10.1371/Journal.Pone.0003106 |
0.319 |
|
| 2008 |
Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW. Origin of introns by 'intronization' of exonic sequences. Trends in Genetics : Tig. 24: 378-81. PMID 18597887 DOI: 10.1016/J.Tig.2008.05.007 |
0.365 |
|
| 2008 |
Morgan-Richards M, Trewick SA, Bartosch-Härlid A, Kardailsky O, Phillips MJ, McLenachan PA, Penny D. Bird evolution: testing the Metaves clade with six new mitochondrial genomes. Bmc Evolutionary Biology. 8: 20. PMID 18215323 DOI: 10.1186/1471-2148-8-20 |
0.644 |
|
| 2008 |
Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, Roy SW. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Molecular Biology and Evolution. 25: 375-82. PMID 18048400 DOI: 10.1093/Molbev/Msm262 |
0.329 |
|
| 2008 |
Penny D, White WT, Hendy MD, Phillips MJ. A bias in ML estimates of branch lengths in the presence of multiple signals. Molecular Biology and Evolution. 25: 239-42. PMID 18048399 DOI: 10.1093/Molbev/Msm263 |
0.578 |
|
| 2007 |
Irimia M, Rukov JL, Penny D, Roy SW. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. Bmc Evolutionary Biology. 7: 188. PMID 17916237 DOI: 10.1186/1471-2148-7-188 |
0.348 |
|
| 2007 |
Shavit L, Penny D, Hendy MD, Holland BR. The problem of rooting rapid radiations. Molecular Biology and Evolution. 24: 2400-11. PMID 17720690 DOI: 10.1093/Molbev/Msm178 |
0.382 |
|
| 2007 |
White WT, Hills SF, Gaddam R, Holland BR, Penny D. Treeness triangles: visualizing the loss of phylogenetic signal. Molecular Biology and Evolution. 24: 2029-39. PMID 17630280 DOI: 10.1093/Molbev/Msm139 |
0.393 |
|
| 2007 |
Chen XS, Rozhdestvensky TS, Collins LJ, Schmitz J, Penny D. Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Research. 35: 4619-28. PMID 17586815 DOI: 10.1093/Nar/Gkm474 |
0.306 |
|
| 2007 |
Irimia M, Maeso I, Penny D, Garcia-Fernàndez J, Roy SW. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Molecular Biology and Evolution. 24: 1604-7. PMID 17525471 DOI: 10.1093/Molbev/Msm105 |
0.391 |
|
| 2007 |
Irimia M, Penny D, Roy SW. Coevolution of genomic intron number and splice sites. Trends in Genetics : Tig. 23: 321-5. PMID 17442445 DOI: 10.1016/J.Tig.2007.04.001 |
0.394 |
|
| 2007 |
Penny D, Phillips MJ. Evolutionary biology: mass survivals. Nature. 446: 501-2. PMID 17392773 DOI: 10.1038/446501A |
0.521 |
|
| 2007 |
Roy SW, Penny D, Neafsey DE. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Molecular Biology and Evolution. 24: 1140-8. PMID 17374879 DOI: 10.1093/Molbev/Msm045 |
0.357 |
|
| 2007 |
Roy SW, Penny D. A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Molecular Biology and Evolution. 24: 1447-57. PMID 17350938 DOI: 10.1093/Molbev/Msm048 |
0.399 |
|
| 2007 |
Woodhams MD, Stadler PF, Penny D, Collins LJ. RNase MRP and the RNA processing cascade in the eukaryotic ancestor. Bmc Evolutionary Biology. 7: S13. PMID 17288571 DOI: 10.1186/1471-2148-7-S1-S13 |
0.307 |
|
| 2007 |
Poole AM, Penny D. Evaluating hypotheses for the origin of eukaryotes. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 29: 74-84. PMID 17187354 DOI: 10.1002/Bies.20516 |
0.353 |
|
| 2007 |
Roy SW, Penny D. Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Molecular Biology and Evolution. 24: 171-81. PMID 17065597 DOI: 10.1093/Molbev/Msl159 |
0.336 |
|
| 2007 |
Gibb GC, Kardailsky O, Kimball RT, Braun EL, Penny D. Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Molecular Biology and Evolution. 24: 269-80. PMID 17062634 DOI: 10.1093/Molbev/Msl158 |
0.381 |
|
| 2007 |
Slack KE, Delsuc F, McLenachan PA, Arnason U, Penny D. Resolving the root of the avian mitogenomic tree by breaking up long branches. Molecular Phylogenetics and Evolution. 42: 1-13. PMID 16854605 DOI: 10.1016/J.Ympev.2006.06.002 |
0.426 |
|
| 2006 |
Roy SW, Penny D. Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Research. 16: 1270-5. PMID 16963708 DOI: 10.1101/Gr.5410606 |
0.309 |
|
| 2006 |
Roy SW, Penny D. Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses. Molecular Biology and Evolution. 23: 2259-62. PMID 16943250 DOI: 10.1093/Molbev/Msl098 |
0.341 |
|
| 2006 |
Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, Penny D. Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Molecular Biology and Evolution. 23: 1966-75. PMID 16855009 DOI: 10.1093/Molbev/Msl063 |
0.443 |
|
| 2006 |
Roy SW, Irimia M, Penny D. Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. Molecular Biology and Evolution. 23: 1824-7. PMID 16847043 DOI: 10.1093/Molbev/Msl061 |
0.326 |
|
| 2006 |
Kurland CG, Collins LJ, Penny D. Genomics and the irreducible nature of eukaryote cells. Science (New York, N.Y.). 312: 1011-4. PMID 16709776 DOI: 10.1126/Science.1121674 |
0.389 |
|
| 2006 |
Slack KE, Jones CM, Ando T, Harrison GL, Fordyce RE, Arnason U, Penny D. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Molecular Biology and Evolution. 23: 1144-55. PMID 16533822 DOI: 10.1093/Molbev/Msj124 |
0.427 |
|
| 2006 |
Phillips MJ, McLenachan PA, Down C, Gibb GC, Penny D. Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Systematic Biology. 55: 122-37. PMID 16507529 DOI: 10.1080/10635150500481614 |
0.651 |
|
| 2006 |
Clarke AC, Burtenshaw MK, McLenachan PA, Erickson DL, Penny D. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). Molecular Biology and Evolution. 23: 893-900. PMID 16401685 DOI: 10.1093/Molbev/Msj092 |
0.339 |
|
| 2006 |
Collins L, Penny D. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes. Molecular Biology and Evolution. 23: 901-10. PMID 16371412 DOI: 10.1093/Molbev/Msj084 |
0.368 |
|
| 2006 |
Jeffares DC, Mourier T, Penny D. The biology of intron gain and loss. Trends in Genetics : Tig. 22: 16-22. PMID 16290250 DOI: 10.1016/J.Tig.2005.10.006 |
0.366 |
|
| 2005 |
Penny D. Evolutionary biology: relativity for molecular clocks. Nature. 436: 183-4. PMID 16015312 DOI: 10.1038/436183A |
0.328 |
|
| 2005 |
Lockhart PJ, Penny D. The place of Amborella within the radiation of angiosperms. Trends in Plant Science. 10: 201-2. PMID 15882650 DOI: 10.1016/J.Tplants.2005.03.006 |
0.368 |
|
| 2005 |
Collins L, Penny D. Complex spliceosomal organization ancestral to extant eukaryotes. Molecular Biology and Evolution. 22: 1053-66. PMID 15659557 DOI: 10.1093/Molbev/Msi091 |
0.319 |
|
| 2005 |
Penny D. An interpretive review of the origin of life research Biology and Philosophy. 20: 633-671. DOI: 10.1007/S10539-004-7342-6 |
0.308 |
|
| 2004 |
Penny D, Phillips MJ. The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution? Trends in Ecology & Evolution. 19: 516-22. PMID 16701316 DOI: 10.1016/J.Tree.2004.07.015 |
0.535 |
|
| 2004 |
Holland BR, Huber KT, Penny D, Moulton V. The MinMax Squeeze: Guaranteeing a Minimal Tree for Population Data Molecular Biology and Evolution. 22: 235-242. PMID 15483326 DOI: 10.1093/Molbev/Msi010 |
0.412 |
|
| 2004 |
Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, Henze K, Kretschmann E, Richly E, Leister D, Bryant D, Steel MA, Lockhart PJ, Penny D, Martin W. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Molecular Biology and Evolution. 21: 1643-60. PMID 15155797 DOI: 10.1093/Molbev/Msh160 |
0.413 |
|
| 2004 |
Phillips MJ, Delsuc F, Penny D. Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution. 21: 1455-8. PMID 15084674 DOI: 10.1093/Molbev/Msh137 |
0.612 |
|
| 2004 |
Harrison GL, McLenachan PA, Phillips MJ, Slack KE, Cooper A, Penny D. Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Molecular Biology and Evolution. 21: 974-83. PMID 14739240 DOI: 10.1093/Molbev/Msh065 |
0.641 |
|
| 2004 |
Penny D. Evolutionary biology: our relative genetics. Nature. 427: 208. PMID 14724623 DOI: 10.1038/427208A |
0.34 |
|
| 2004 |
Collins LJ, Macke TJ, Penny D. Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif Journal of Integrative Bioinformatics. 1. DOI: 10.1515/Jib-2004-6 |
0.381 |
|
| 2004 |
Penny D. Evolutionary trees for all Trends in Ecology and Evolution. 19: 273. DOI: 10.1016/J.Tree.2004.04.007 |
0.458 |
|
| 2004 |
Steel MA, Penny D. Two further links between MP and ML under the Poisson model Applied Mathematics Letters. 17: 785-790. DOI: 10.1016/J.Aml.2004.06.006 |
0.399 |
|
| 2003 |
Ota R, Penny D. Estimating changes in mutational mechanisms of evolution. Journal of Molecular Evolution. 57: S233-40. PMID 15008420 DOI: 10.1007/S00239-003-0032-1 |
0.372 |
|
| 2003 |
Delsuc F, Phillips MJ, Penny D. Comment on "Hexapod origins: monophyletic or paraphyletic?". Science (New York, N.Y.). 301: 1482; author reply 1. PMID 12970547 DOI: 10.1126/Science.1086558 |
0.548 |
|
| 2003 |
Phillips MJ, Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Molecular Phylogenetics and Evolution. 28: 171-85. PMID 12878457 DOI: 10.1016/S1055-7903(03)00057-5 |
0.629 |
|
| 2003 |
Penny D, Hendy MD, Poole AM. Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology. 223: 377-85. PMID 12850457 DOI: 10.1016/S0022-5193(03)00099-7 |
0.359 |
|
| 2003 |
Holland BR, Penny D, Hendy MD. Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study. Systematic Biology. 52: 229-238. PMID 12746148 DOI: 10.1080/10635150390192771 |
0.396 |
|
| 2003 |
Poole AM, Phillips MJ, Penny D. Prokaryote and eukaryote evolvability. Bio Systems. 69: 163-85. PMID 12689728 DOI: 10.1016/S0303-2647(02)00131-4 |
0.597 |
|
| 2003 |
Bromham L, Penny D. The modern molecular clock Nature Reviews Genetics. 4: 216-224. PMID 12610526 DOI: 10.1038/Nrg1020 |
0.327 |
|
| 2003 |
Slack KE, Janke A, Penny D, Arnason U. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene. 302: 43-52. PMID 12527195 DOI: 10.1016/S0378111902010533 |
0.422 |
|
| 2003 |
Hurles ME, Matisoo-Smith E, Gray RD, Penny D. Untangling Oceanic settlement: The edge of the knowable Trends in Ecology and Evolution. 18: 531-540. DOI: 10.1016/S0169-5347(03)00245-3 |
0.302 |
|
| 2002 |
Lin YH, McLenachan PA, Gore AR, Phillips MJ, Ota R, Hendy MD, Penny D. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology and Evolution. 19: 2060-70. PMID 12446798 DOI: 10.1093/Oxfordjournals.Molbev.A004031 |
0.654 |
|
| 2002 |
Lin YH, Waddell PJ, Penny D. Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene. 294: 119-29. PMID 12234673 DOI: 10.1016/S0378-1119(02)00695-9 |
0.41 |
|
| 2002 |
Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proceedings of the National Academy of Sciences of the United States of America. 99: 12246-51. PMID 12218172 DOI: 10.1073/Pnas.182432999 |
0.391 |
|
| 2001 |
Penny D, McComish BJ, Charleston MA, Hendy MD. Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution Journal of Molecular Evolution. 53: 711-723. PMID 11677631 DOI: 10.1007/S002390010258 |
0.349 |
|
| 2001 |
Phillips MJ, Lin Y, Harrison G, Penny D. Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials. Proceedings of the Royal Society B: Biological Sciences. 268: 1533-1538. PMID 11454299 DOI: 10.1098/Rspb.2001.1677 |
0.626 |
|
| 2001 |
Lin Y, Penny D. Implications for Bat Evolution from Two New Complete Mitochondrial Genomes Molecular Biology and Evolution. 18: 684-688. PMID 11264422 DOI: 10.1093/Oxfordjournals.Molbev.A003850 |
0.428 |
|
| 2000 |
Poole A, Penny D, Sjöberg B. Methyl-RNA: an evolutionary bridge between RNA and DNA? Chemistry & Biology. 7. PMID 11137821 DOI: 10.1016/S1074-5521(00)00042-9 |
0.307 |
|
| 2000 |
Collins LJ, Moulton V, Penny D. Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. Journal of Molecular Evolution. 51: 194-204. PMID 11029064 DOI: 10.1007/S002390010081 |
0.35 |
|
| 2000 |
Steel M, Penny D. Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics Molecular Biology and Evolution. 17: 839-850. PMID 10833190 DOI: 10.1093/Oxfordjournals.Molbev.A026364 |
0.372 |
|
| 2000 |
Bromham L, Penny D, Rambaut A, Hendy MD. The power of relative rates tests depends on the data Journal of Molecular Evolution. 50: 296-301. PMID 10754073 DOI: 10.1007/S002399910034 |
0.363 |
|
| 1999 |
Penny D, Hasegawa M, Waddell PJ, Hendy MD. Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition. Systematic Biology. 48: 76-93. PMID 12078647 DOI: 10.1080/106351599260454 |
0.409 |
|
| 1999 |
Penny D, Poole A. The nature of the last universal common ancestor. Current Opinion in Genetics & Development. 9: 672-677. PMID 10607605 DOI: 10.1016/S0959-437X(99)00020-9 |
0.328 |
|
| 1999 |
Poole A, Jeffares D, Penny D. Early evolution: prokaryotes, the new kids on the block Bioessays. 21: 880-889. PMID 10497339 DOI: 10.1002/(Sici)1521-1878(199910)21:10<880::Aid-Bies11>3.0.Co;2-P |
0.322 |
|
| 1999 |
Bromham L, Penny D, Phillips M. Reply from L. Bromham, D. Penny and M.J. Phillips. Trends in Ecology & Evolution. 14: 278. PMID 10370264 DOI: 10.1016/S0169-5347(99)01651-1 |
0.495 |
|
| 1999 |
Bromham L, Phillips MJ, Penny D. Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends in Ecology & Evolution. 14: 113-118. PMID 10322512 DOI: 10.1016/S0169-5347(98)01507-9 |
0.56 |
|
| 1999 |
Hurr KA, Lockhart PJ, Heenan PB, Penny D. Evidence for the recent dispersal of Sophora (Leguminosae) around the Southern Oceans: molecular data Journal of Biogeography. 26: 565-577. DOI: 10.1046/J.1365-2699.1999.00302.X |
0.377 |
|
| 1998 |
Matisoo-Smith E, Roberts RM, Irwin GJ, Allen JS, Penny D, Lambert DM. Patterns of prehistoric human mobility in Polynesia indicated by mtDNA from the Pacific rat Proceedings of the National Academy of Sciences of the United States of America. 95: 15145-15150. PMID 9844030 DOI: 10.1073/Pnas.95.25.15145 |
0.31 |
|
| 1998 |
Bromham L, Rambaut A, Fortey R, Cooper A, Penny D. Testing the Cambrian explosion hypothesis by using a molecular dating technique Proceedings of the National Academy of Sciences of the United States of America. 95: 12386-12389. PMID 9770496 DOI: 10.1073/Pnas.95.21.12386 |
0.346 |
|
| 1998 |
Murray-McIntosh RP, Scrimshaw BJ, Hatfield PJ, Penny D. Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences Proceedings of the National Academy of Sciences of the United States of America. 95: 9047-9052. PMID 9671802 DOI: 10.1073/Pnas.95.15.9047 |
0.342 |
|
| 1998 |
Jeffares DC, Poole AM, Penny D. Relics from the RNA world. Journal of Molecular Evolution. 46: 18-36. PMID 9419222 DOI: 10.1007/Pl00006280 |
0.324 |
|
| 1998 |
Poole AM, Jeffares DC, Penny D. The Path from the RNA World Journal of Molecular Evolution. 46: 1-17. PMID 9419221 DOI: 10.1007/Pl00006275 |
0.366 |
|
| 1998 |
Steel M, Hendy MD, Penny D. Reconstructing phylogenies from nucleotide pattern probabilities: a survey and some new results Discrete Applied Mathematics. 88: 367-396. DOI: 10.1016/S0166-218X(98)00080-8 |
0.411 |
|
| 1997 |
Waddell PJ, Penny D, Moore T. Hadamard Conjugations and Modeling Sequence Evolution with Unequal Rates across Sites Molecular Phylogenetics and Evolution. 8: 33-50. PMID 9242594 DOI: 10.1006/Mpev.1997.0405 |
0.328 |
|
| 1997 |
Penny D, Hasegawa M. Molecular systematics: The platypus put in its place Nature. 387: 549-550. PMID 9177333 DOI: 10.1038/42352 |
0.408 |
|
| 1997 |
Cooper A, Penny D. Mass Survival of Birds Across the Cretaceous- Tertiary Boundary: Molecular Evidence Science. 275: 1109-1113. PMID 9027308 DOI: 10.1126/Science.275.5303.1109 |
0.314 |
|
| 1996 |
Lockhart PJ, Larkum AW, Steel M, Waddell PJ, Penny D. 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. 93: 1930-4. PMID 8700861 DOI: 10.1073/Pnas.93.5.1930 |
0.372 |
|
| 1996 |
Hendy MD, Penny D. Complete families of linear invariants for some stochastic models of sequence evolution, with and without the molecular clock assumption. Journal of Computational Biology. 3: 19-31. PMID 8697236 DOI: 10.1089/Cmb.1996.3.19 |
0.344 |
|
| 1996 |
Hickson RE, Simon C, Cooper A, Spicer GS, Sullivan J, Penny D. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Molecular Biology and Evolution. 13: 150-69. PMID 8583888 DOI: 10.1093/Oxfordjournals.Molbev.A025552 |
0.4 |
|
| 1996 |
Penny D, Hendy MD, Lockhart PJ, Steel MA. Corrected Parsimony, Minimum Evolution, and Hadamard Conjugations Systematic Biology. 45: 596-606. DOI: 10.1093/Sysbio/45.4.596 |
0.329 |
|
| 1996 |
Steel MA, Cooper ANC, Penny D. Confidence Intervals for the Divergence Time of Two Clades Systematic Biology. 45: 127-134. DOI: 10.1093/Sysbio/45.2.127 |
0.372 |
|
| 1995 |
Steel M, Lockhart PJ, Penny D. A frequency-dependent significance test for parsimony. Molecular Phylogenetics and Evolution. 4: 64-71. PMID 7620636 DOI: 10.1006/Mpev.1995.1006 |
0.369 |
|
| 1995 |
Penny D, Steel M, Waddell PJ, Hendy MD. Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens. Molecular Biology and Evolution. 12: 863-882. PMID 7476132 DOI: 10.1093/Oxfordjournals.Molbev.A040263 |
0.442 |
|
| 1995 |
Lockhart P, Penny D, Meyer A. Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis Journal of Molecular Evolution. 41. DOI: 10.1007/Bf00175825 |
0.39 |
|
| 1994 |
Lockhart PJ, Steel MA, Hendy MD, Penny D. Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution. 11: 605-612. PMID 19391266 DOI: 10.1093/Oxfordjournals.Molbev.A040136 |
0.407 |
|
| 1994 |
Charleston MA, Hendy MD, Penny D. The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods Journal of Computational Biology. 1: 133-151. PMID 8790460 DOI: 10.1089/Cmb.1994.1.133 |
0.394 |
|
| 1994 |
Hendy MD, Penny D, Steel MA. A discrete Fourier analysis for evolutionary trees. Proceedings of the National Academy of Sciences of the United States of America. 91: 3339-3343. PMID 8159749 DOI: 10.1073/Pnas.91.8.3339 |
0.384 |
|
| 1993 |
Steel MA, Lockhart PJ, Penny D. Confidence in evolutionary trees from biological sequence data Nature. 364: 440-442. PMID 8332213 DOI: 10.1038/364440A0 |
0.403 |
|
| 1993 |
Charleston MA, Hendy MD, Penny D. Neighbor-Joining Uses the Optimal Weight for Net Divergence Molecular Phylogenetics and Evolution. 2: 6-12. PMID 8081548 DOI: 10.1006/Mpev.1993.1002 |
0.327 |
|
| 1993 |
Steel MA, Hendy MD, Penny D. Parsimony Can Be Consistent Systematic Biology. 42: 581-587. DOI: 10.1093/Sysbio/42.4.581 |
0.31 |
|
| 1993 |
Steel MA, Penny D. Distributions of Tree Comparison Metrics—Some New Results Systematic Biology. 42: 126-141. DOI: 10.1093/Sysbio/42.2.126 |
0.327 |
|
| 1993 |
Penny D, Watson EE, Hickson RE, Lockhart PJ. Some recent progress with methods for evolutionary trees New Zealand Journal of Botany. 31: 275-288. DOI: 10.1080/0028825X.1993.10419505 |
0.373 |
|
| 1993 |
Székely LA, Erdős P, Steel MA, Penny D. A Fourier Inversion Formula For Evolutionary Trees Applied Mathematics Letters. 6: 13-16. DOI: 10.1016/0893-9659(93)90004-7 |
0.332 |
|
| 1993 |
Hendy MD, Penny D. Spectral Analysis of Phylogenetic Data Journal of Classification. 10: 5-24. DOI: 10.1007/Bf02638451 |
0.392 |
|
| 1992 |
Penny D, Hendy MD, Steel MA. Progress with methods for constructing evolutionary trees Trends in Ecology and Evolution. 7: 73-79. PMID 21235960 DOI: 10.1016/0169-5347(92)90244-6 |
0.386 |
|
| 1992 |
Lockhart PJ, Penny D, Hendy MD, Howe CJ, Beanland TJ, Larkum AW. Controversy on chloroplast origins. Febs Letters. 301: 127-31. PMID 1568469 DOI: 10.1016/0014-5793(92)81231-A |
0.409 |
|
| 1992 |
Hickson RE, Penny D, Scott DB. Molecular systematics and evolution in New Zealand: Applications to cryptic skink species New Zealand Journal of Zoology. 19: 33-44. DOI: 10.1080/03014223.1992.10423249 |
0.386 |
|
| 1992 |
Steel MA, Hendy MD, Penny D. Significance of the length of the shortest tree Journal of Classification. 9: 71-90. DOI: 10.1007/Bf02618469 |
0.379 |
|
| 1990 |
Rinsma I, Hendy M, Penny D. Distribution of the number of matches between nucleotide sequences. Bulletin of Mathematical Biology. 52: 349-358. PMID 2379020 DOI: 10.1007/Bf02458576 |
0.322 |
|
| 1989 |
Henderson IM, Hendy MD, Penny D. Influenza viruses, comets and the science of evolutionary trees. Journal of Theoretical Biology. 140: 289-303. PMID 2615399 DOI: 10.1016/S0022-5193(89)80087-6 |
0.375 |
|
| 1989 |
Hendy MD, Penny D. A Framework for the Quantitative Study of Evolutionary Trees Systematic Biology. 38: 297-309. DOI: 10.2307/2992396 |
0.341 |
|
| 1987 |
Penny D, Hendy MD, Henderson IM. Reliability of evolutionary trees. Cold Spring Harbor Symposia On Quantitative Biology. 52: 857-862. PMID 3454294 DOI: 10.1101/Sqb.1987.052.01.093 |
0.312 |
|
| 1987 |
Hendy MD, Penny D. Edge lengths of trees from sequence data Bellman Prize in Mathematical Biosciences. 83: 157-165. DOI: 10.1016/0025-5564(87)90108-8 |
0.367 |
|
| 1986 |
Penny D, Hendy M. Estimating the reliability of evolutionary trees. Molecular Biology and Evolution. 3: 403-417. PMID 2832694 DOI: 10.1093/Oxfordjournals.Molbev.A040407 |
0.402 |
|
| 1985 |
Penny D, Hendy MD. Testing Methods Of Evolutionary Tree Construction Cladistics. 1: 266-278. DOI: 10.1111/J.1096-0031.1985.Tb00427.X |
0.379 |
|
| 1985 |
Penny D. The evolution of meiosis and sexual reproduction Biological Journal of the Linnean Society. 25: 209-220. DOI: 10.1111/J.1095-8312.1985.Tb00393.X |
0.349 |
|
| 1982 |
Penny D. Towards a basis for classification: the incompleteness of distance measures, incompatibility analysis and phenetic classification Journal of Theoretical Biology. 96: 129-142. PMID 7121024 DOI: 10.1016/0022-5193(82)90216-8 |
0.322 |
|
| 1982 |
Penny D, Foulds LR, Hendy MD. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences Nature. 297: 197-200. PMID 7078635 DOI: 10.1038/297197A0 |
0.368 |
|
| 1982 |
Hendy MD, Penny D. Branch and bound algorithms to determine minimal evolutionary trees Bellman Prize in Mathematical Biosciences. 59: 277-290. DOI: 10.1016/0025-5564(82)90027-X |
0.323 |
|
| 1980 |
Hendy MD, Foulds LR, Penny D. Proving phylogenetic trees minimal with l-clustering and set partitioning Bellman Prize in Mathematical Biosciences. 51: 71-88. DOI: 10.1016/0025-5564(80)90091-7 |
0.341 |
|
| 1979 |
Foulds LR, Hendy MD, Penny D. A graph theoretic approach to the development of minimal phylogenetic trees Journal of Molecular Evolution. 13: 127-149. PMID 480370 DOI: 10.1007/Bf01732868 |
0.334 |
|
| 1979 |
Foulds LR, Penny D, Hendy MD. A general approach to proving the minimality of phylogenetic trees illustrated by an example with a set of 23 vertebrates. Journal of Molecular Evolution. 13: 151-166. PMID 225499 DOI: 10.1007/Bf01732869 |
0.368 |
|
| 1978 |
Hendy MD, Penny D, Foulds LR. Identification of phylogenetic trees of minimal length. Journal of Theoretical Biology. 71: 441-452. PMID 205733 DOI: 10.1016/0022-5193(78)90171-6 |
0.361 |
|
| 1976 |
Penny D. Criteria for optimising phylogenetic trees and the problem of determining the root of a tree. Journal of Molecular Evolution. 8: 95-116. PMID 966292 DOI: 10.1007/Bf01739097 |
0.359 |
|
| 1974 |
Penny D. Evolutionary clock: The rate of evolution of rattlesnake cytochromec Journal of Molecular Evolution. 3: 179-188. PMID 4368708 DOI: 10.1007/Bf01797452 |
0.332 |
|
| Show low-probability matches. |