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David Penny

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.8 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Concepts & Ideas

Phenomena

Molecular Evolution

Physiology

Evolution

Chemicals & Drugs

Anatomy

Activities & Behaviors

Computer Simulation

Genes & Molecular Sequences

Genome

Procedures

Living Beings

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Network (preview)

Co-Publications
Name
30
Hendy, Michael
15
Poole, Anthony
14
Roy, Scott William
10
Phillips, Matthew
9
Holland, Barbara
7
Collins, Lesley
6
Jeffares, Daniel
6
McLenachan, Patricia
6
Irimia, Manuel
5
Waddell, Peter
5
Moulton, Vincent
4
Slack, Kerryn
4
Harrison, Abby
3
Murray-McIntosh, RP
3
Ota, Rissa

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Publications

TOP 3
Penny David; Hoeppner Marc P; Poole Anthony M; Jeffares Daniel C
An overview of the introns-first theory.
Waddell Peter J; Ota Rissa; Penny David
Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests.
Collins Lesley J; Kurland Charles G; Biggs Patrick; Penny David
The modern RNP world of eukaryotes.

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All Publications

2009: Penny David; Hoeppner Marc P; Poole Anthony M; Jeffares Daniel C
An overview of the introns-first theory.
Journal of molecular evolution 2009;69(5):527-40.
2009: Waddell Peter J; Ota Rissa; Penny David
Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests.
Journal of molecular evolution 2009;69(4):289-99.
2009: Collins Lesley J; Kurland Charles G; Biggs Patrick; Penny David
The modern RNP world of eukaryotes.
The Journal of heredity 2009;100(5):597-604.
2009: Collins Lesley J; Penny David
The RNA infrastructure: dark matter of the eukaryotic cell?
Trends in genetics : TIG 2009;25(3):120-8.
2009: Pratt Renae C; Gibb Gillian C; Morgan-Richards Mary; Phillips Matthew J; Hendy Michael D; Penny David
Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors.
Molecular biology and evolution 2009;26(2):313-26.
2009: de Nooijer Silvester; Holland Barbara R; Penny David
The emergence of predators in early life: there was no Garden of Eden.
PloS one 2009;4(6):e5507.
2008: Irimia Manuel; Rukov Jakob Lewin; Penny David; Vinther Jeppe; Garcia-Fernandez Jordi; Roy Scott William
Origin of introns by 'intronization' of exonic sequences.
Trends in genetics : TIG 2008;24(8):378-81.
2008: Irimia Manuel; Rukov Jakob L; Penny David; Garcia-Fernandez Jordi; Vinther Jeppe; Roy Scott W
Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis.
Molecular biology and evolution 2008;25(2):375-82.
2008: Penny David; White W T; Hendy Mike D; Phillips Matthew J
A bias in ML estimates of branch lengths in the presence of multiple signals.
Molecular biology and evolution 2008;25(2):239-42.
2008: Shavit Grievink Liat; Penny David; Hendy Mike D; Holland Barbara R
LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.
BMC evolutionary biology 2008;8():317.
2008: Chen Xiaowei Sylvia; White W Timothy J; Collins Lesley J; Penny David
Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis.
PloS one 2008;3(8):e3106.
2008: Morgan-Richards Mary; Trewick Steve A; Bartosch-Härlid Anna; Kardailsky Olga; Phillips Matthew J; McLenachan Patricia A; Penny David
Bird evolution: testing the Metaves clade with six new mitochondrial genomes.
BMC evolutionary biology 2008;8():20.
2007: Shavit Liat; Penny David; Hendy Michael D; Holland Barbara R
The problem of rooting rapid radiations.
Molecular biology and evolution 2007;24(11):2400-11.
2007: White W T; Hills S F; Gaddam R; Holland B R; Penny David
Treeness triangles: visualizing the loss of phylogenetic signal.
Molecular biology and evolution 2007;24(9):2029-39.
2007: Roy Scott William; Penny David
Widespread intron loss suggests retrotransposon activity in ancient apicomplexans.
Molecular biology and evolution 2007;24(9):1926-33.
2007: Irimia Manuel; Maeso Ignacio; Penny David; Garcia-Fernàndez Jordi; Roy Scott William
Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata.
Molecular biology and evolution 2007;24(8):1604-7.
2007: Roy Scott William; Penny David
On the incidence of intron loss and gain in paralogous gene families.
Molecular biology and evolution 2007;24(8):1579-81.
2007: Irimia Manuel; Penny David; Roy Scott W
Coevolution of genomic intron number and splice sites.
Trends in genetics : TIG 2007;23(7):321-5.
2007: Roy Scott William; Penny David
A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain.
Molecular biology and evolution 2007;24(7):1447-57.
2007: Poole Anthony; Penny David
Eukaryote evolution: engulfed by speculation.
Nature 2007;447(7147):913.
2007: Poole Anthony M; Penny David
Response to Dagan and Martin.
BioEssays : news and reviews in molecular, cellular and developmental biology 2007;29(6):611-4.
2007: Roy Scott William; Penny David; Neafsey Daniel E
Evolutionary conservation of UTR intron boundaries in Cryptococcus.
Molecular biology and evolution 2007;24(5):1140-8.
2007: Poole Anthony M; Penny David
Evaluating hypotheses for the origin of eukaryotes.
BioEssays : news and reviews in molecular, cellular and developmental biology 2007;29(1):74-84.
2007: Roy Scott William; Penny David
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 2007;24(1):171-81.
2007: Gibb Gillian C; Kardailsky Olga; Kimball Rebecca T; Braun Edward L; Penny David
Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations.
Molecular biology and evolution 2007;24(1):269-80.
2007: Slack Kerryn E; Delsuc Frédéric; McLenachan Patricia A; Arnason Ulfur; Penny David
Resolving the root of the avian mitogenomic tree by breaking up long branches.
Molecular phylogenetics and evolution 2007;42(1):1-13.
2007: Irimia Manuel; Rukov Jakob Lewin; Penny David; Roy Scott William
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing.
BMC evolutionary biology 2007;7():188.
2007: Roy Scott William; Penny David
Intron length distributions and gene prediction.
Nucleic acids research 2007;35(14):4737-42.
2007: Chen Xiaowei Sylvia; Rozhdestvensky Timofey S; Collins Lesley J; Schmitz Jürgen; Penny David
Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis.
Nucleic acids research 2007;35(14):4619-28.
2007: Woodhams Michael D; Stadler Peter F; Penny David; Collins Lesley J
RNase MRP and the RNA processing cascade in the eukaryotic ancestor.
BMC evolutionary biology 2007;7 Suppl 1():S13.
2006: Roy Scott William; Penny David
Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses.
Molecular biology and evolution 2006;23(12):2259-62.
2006: Roy Scott William; Penny David
Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution.
Genome research 2006;16(10):1270-5.
2006: Matheson James W; Rich Fenella J; Cohet Catherine; Grimwood Keith; Huang Q Sue; Penny David; Hendy Michael D; Kirman Joanna R
Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years.
Journal of medical virology 2006;78(10):1354-64.
2006: Pierson Melanie J; Martinez-Arias Rosa; Holland Barbara R; Gemmell Neil J; Hurles Matthew E; Penny David
Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes.
Molecular biology and evolution 2006;23(10):1966-75.
2006: Roy Scott William; Irimia Manuel; Penny David
Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes.
Molecular biology and evolution 2006;23(10):1824-7.
2006: Slack Kerryn E; Jones Craig M; Ando Tatsuro; Harrison G L Abby; Fordyce R Ewan; Arnason Ulfur; Penny David
Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.
Molecular biology and evolution 2006;23(6):1144-55.
2006: Kurland C G; Collins L J; Penny D
Genomics and the irreducible nature of eukaryote cells.
Science (New York, N.Y.) 2006;312(5776):1011-4.
2006: Clarke Andrew C; Burtenshaw Michael K; McLenachan Patricia A; Erickson David L; Penny David;
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 2006;23(5):893-900.
2006: Collins Lesley; Penny David;
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes.
Molecular biology and evolution 2006;23(5):901-10.
2006: Phillips Matthew J; McLenachan Patricia A; Down Christin; Gibb Gillian C; Penny David
Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations.
Systematic biology 2006;55(1):122-37.
2006: Jeffares Daniel C; Mourier Tobias; Penny David
The biology of intron gain and loss.
Trends in genetics : TIG 2006;22(1):16-22.
2005: Collins Lesley; Penny David
Complex spliceosomal organization ancestral to extant eukaryotes.
Molecular biology and evolution 2005;22(4):1053-66.
2005: Holland B R; Huber K T; Penny D; Moulton V
The MinMax Squeeze: guaranteeing a minimal tree for population data.
Molecular biology and evolution 2005;22(2):235-42.
2004: Penny David; Phillips Matthew J
The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?
Trends in ecology & evolution (Personal edition) 2004;19(10):516-22.
2004: Phillips Matthew J; Delsuc Frédéric; Penny David
Genome-scale phylogeny and the detection of systematic biases.
Molecular biology and evolution 2004;21(7):1455-8.
2004: Harrison G L Abby; McLenachan P A; Phillips M J; Slack Kerryn E; Cooper Alan; Penny David
Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous.
Molecular biology and evolution 2004;21(6):974-83.
2003: Delsuc Frédéric; Phillips Matthew J; Penny David
Comment on "Hexapod origins: monophyletic or paraphyletic?".
Science (New York, N.Y.) 2003;301(5639):1482; author reply 1482.
2003: Phillips Matthew J; Penny David
The root of the mammalian tree inferred from whole mitochondrial genomes.
Molecular phylogenetics and evolution 2003;28(2):171-85.
2003: Penny David; Hendy Michael D; Poole Anthony M
Testing fundamental evolutionary hypotheses.
Journal of theoretical biology 2003;223(3):377-85.
2003: Gardner Paul P; Holland Barbara R; Moulton Vincent; Hendy Mike; Penny David
Optimal alphabets for an RNA world.
Proceedings. Biological sciences / The Royal Society 2003;270(1520):1177-82.
2003: Edvardsson Sverker; Gardner Paul P; Poole Anthony M; Hendy Michael D; Penny David; Moulton Vincent
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.
Bioinformatics (Oxford, England) 2003;19(7):865-73.
2003: Poole Anthony M; Phillips Matthew J; Penny David
Prokaryote and eukaryote evolvability.
Bio Systems 2003;69(2-3):163-85.
2003: Holland B R; Penny D; Hendy M D
Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.
Systematic biology 2003;52(2):229-38.
2003: Bromham Lindell; Penny David
The modern molecular clock.
Nature reviews. Genetics 2003;4(3):216-24.
2003: Slack Kerryn E; Janke Axel; Penny David; Arnason Ulfur
Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features.
Gene 2003;302(1-2):43-52.
2003: Collins Lesley J; Poole Anthony M; Penny David
Using ancestral sequences to uncover potential gene homologues.
Applied bioinformatics 2003;2(3 Suppl):S85-95.
2003: Ota Rissa; Penny David
Estimating changes in mutational mechanisms of evolution.
Journal of molecular evolution 2003;57 Suppl 1():S233-40.
2002: Lin Yu-Hsin; McLenachan Patricia A; Gore Alicia R; Phillips Matthew J; Ota Rissa; Hendy Michael D; Penny David
Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling.
Molecular biology and evolution 2002;19(12):2060-70.
2002: Lin Yu-Hsin; Waddell Peter J; Penny David
Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires.
Gene 2002;294(1-2):119-29.
2002: Huber Katharina T; Langton Michael; Penny David; Moulton Vincent; Hendy Michael
Spectronet: a package for computing spectra and median networks.
Applied bioinformatics 2002;1(3):159-61.
2001: Penny D; McComish B J; Charleston M A; Hendy M D
Mathematical elegance with biochemical realism: the covarion model of molecular evolution.
Journal of molecular evolution 2001;53(6):711-23.
2001: Poole A; Penny D
Does endo-symbiosis explain the origin of the nucleus?
Nature cell biology 2001;3(8):E173-4.
2001: Phillips M J; Lin Y H; Harrison G L; Penny D
Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials.
Proceedings. Biological sciences / The Royal Society 2001;268(1475):1533-8.
2001: Harrison G L; Murray-McIntosh R; Penny D
Hepatitis B virus genotypes: a South Pacific perspective.
Pacific health dialog 2001;8(1):188-92.
2000: Poole A; Penny D; Sjöberg B
Methyl-RNA: an evolutionary bridge between RNA and DNA?
Chemistry & biology 2000;7(12):R207-16.
2000: Moulton V; Gardner P P; Pointon R F; Creamer L K; Jameson G B; Penny D
RNA folding argues against a hot-start origin of life.
Journal of molecular evolution 2000;51(4):416-21.
2000: Chor B; Hendy M D; Holland B R; Penny D
Multiple maxima of likelihood in phylogenetic trees: an analytic approach.
Molecular biology and evolution 2000;17(10):1529-41.
2000: Collins L J; Moulton V; Penny D
Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP.
Journal of molecular evolution 2000;51(3):194-204.
2000: Bromham L; Penny D; Rambaut A; Hendy M D
The power of relative rates tests depends on the data.
Journal of molecular evolution 2000;50(3):296-301.
1999: Penny D; Poole A
The nature of the last universal common ancestor.
Current opinion in genetics & development 1999;9(6):672-7.
1999: Poole A; Jeffares D; Penny D
Early evolution: prokaryotes, the new kids on the block.
BioEssays : news and reviews in molecular, cellular and developmental biology 1999;21(10):880-9.
1999: Penny D; Hasegawa M; Waddell P J; Hendy M D
Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.
Systematic biology 1999;48(1):76-93.
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 1998;95(21):12386-9.
1998: Murray-McIntosh R P; Scrimshaw B J; Hatfield P J; 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 1998;95(15):9047-52.
1998: Penny D; Murray-McIntosh R P; Hendy M D
Estimating times of divergence with a change of rate: the orangutan/African ape divergence.
Molecular biology and evolution 1998;15(5):608-10.
1998: Jeffares D C; Poole A M; Penny D
Relics from the RNA world.
Journal of molecular evolution 1998;46(1):18-36.
1998: Poole A M; Jeffares D C; Penny D
The path from the RNA world.
Journal of molecular evolution 1998;46(1):1-17.
1997: Waddell P J; Penny D; Moore T
Hadamard conjugations and modeling sequence evolution with unequal rates across sites.
Molecular phylogenetics and evolution 1997;8(1):33-50.
1996: Lockhart P J; Larkum A W; Steel M; Waddell P J; 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 1996;93(5):1930-4.
1996: Hickson R E; Simon C; Cooper A; Spicer G S; Sullivan J; Penny D
Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA.
Molecular biology and evolution 1996;13(1):150-69.
1996: Hendy M D; 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 : a journal of computational molecular cell biology 1996;3(1):19-31.
1995: Penny D; Steel M; Waddell P J; Hendy M D
Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens.
Molecular biology and evolution 1995;12(5):863-82.
1995: Jeffares D C; Poole A M; Penny D
Pre-rRNA processing and the path from the RNA world.
Trends in biochemical sciences 1995;20(8):298-9.
1995: Steel M; Lockhart P J; Penny D
A frequency-dependent significance test for parsimony.
Molecular phylogenetics and evolution 1995;4(1):64-71.
1995: Lento G M; Hickson R E; Chambers G K; Penny D
Use of spectral analysis to test hypotheses on the origin of pinnipeds.
Molecular biology and evolution 1995;12(1):28-52.
1994: Lockhart P J; Steel M A; Hendy M D; Penny D
Recovering evolutionary trees under a more realistic model of sequence evolution.
Molecular biology and evolution 1994;11(4):605-12.
1994: Hendy M D; Penny D; Steel M A
A discrete Fourier analysis for evolutionary trees.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(8):3339-43.
1994: Charleston M A; Hendy M D; Penny D
The effects of sequence length, tree topology, and number of taxa on the performance of phylogenetic methods.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(2):133-51.
1993: Steel M A; Lockhart P J; Penny D
Confidence in evolutionary trees from biological sequence data.
Nature 1993;364(6436):440-2.
1993: Charleston M A; Hendy M D; Penny D
Neighbor-joining uses the optimal weight for net divergence.
Molecular phylogenetics and evolution 1993;2(1):6-12.
1990: Rinsma I; Hendy M; Penny D
Distribution of the number of matches between nucleotide sequences.
Bulletin of mathematical biology 1990;52(3):349-58.
1989: Henderson I M; Hendy M D; Penny D
Influenza viruses, comets and the science of evolutionary trees.
Journal of theoretical biology 1989;140(3):289-303.
1988: Steel M A; Hendy M D; Penny D
Loss of information in genetic distances.
Nature 1988;336(6195):118.
1987: Penny D; Hendy M D
TurboTree: a fast algorithm for minimal trees.
Computer applications in the biosciences : CABIOS 1987;3(3):183-7.
1987: Henderson I M; Penny D; Hendy M D
Models for the origin of influenza viruses.
Nature 1987;326(6108):22.
1987: Penny D; Hendy M D; Henderson I M
Reliability of evolutionary trees.
Cold Spring Harbor symposia on quantitative biology 1987;52():857-62.
1986: Penny D; Hendy M
Estimating the reliability of evolutionary trees.
Molecular biology and evolution 1986;3(5):403-17.
1982: Penny D; Foulds L R; Hendy M D
Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences.
Nature 1982;297(5863):197-200.

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