Resolving the root of the avian mitogenomic tree by breaking up long branches. (2008)
Slack, Kerryn E, Delsuc, Frédéric, McLenachan, Patricia A, Arnason, Ulfur, Penny, David
Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey...
Resolving the root of the avian mitogenomic tree by breaking up long branches. (2008)
Slack, Kerryn E, Delsuc, Frédéric, McLenachan, Patricia A, Arnason, Ulfur, Penny, David
Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey...
Bird evolution: testing the Metaves clade with six new mitochondrial genomes (2008)
Morgan-Richards, Mary, Trewick, Steve A, Bartosch-Härlid, Anna, Kardailsky, Olga, Phillips, Matthew J, McLenachan, Patricia A, ...
Abstract Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their...
Genome-scale phylogeny and the detection of systematic biases. (2007)
Phillips, Matthew J, Delsuc, Frédéric, Penny, David
Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study...
Comment on "Hexapod origins: monophyletic or paraphyletic?". (2007)
Delsuc, Frédéric, Phillips, Matthew J, Penny, David
Nardi et al. (Science, 21 March 2003, 1887) suggested that extant hexapods might be diphyletic based on the analysis of amino acids sequences of mitochondrial genes. However, improved phylogenetic...
Comment on "Hexapod origins: monophyletic or paraphyletic?". (2007)
Delsuc, Frédéric, Phillips, Matthew J, Penny, David
Nardi et al. (Science, 21 March 2003, 1887) suggested that extant hexapods might be diphyletic based on the analysis of amino acids sequences of mitochondrial genes. However, improved phylogenetic...
Genome-scale phylogeny and the detection of systematic biases. (2007)
Phillips, Matthew J, Delsuc, Frédéric, Penny, David
Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study...
Irimia, Manuel, Rukov, Jakob, Penny, David, Roy, Scott
Abstract Background Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative...
RNase MRP and the RNA processing cascade in the eukaryotic ancestor (2007)
Woodhams, Michael D, Stadler, Peter F, Penny, David, Collins, Lesley J
Abstract Background Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing...
Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif (2004)
Collins, Lesley J., Macke, Thomas J., Penny, David
Non-coding RNAs (ncRNAs) contain both characteristic secondary-structure and short sequence motifs. However, "complex" ncRNAs (RNA bound to proteins in ribonucleoprotein complexes) can be hard to...
Spectronet: A package for computing spectra and median networks (2003)
Katharina T. Huber, Michael Langton, David Penny, Vincent Moulton, Michael Hendy
Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by...
Spectronet: A package for computing spectra and median networks (2002)
Katharina T. Huber, Michael Langton, David Penny, Vincent Moulton, Michael Hendy
Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by...
Growing up with dinosaurs: Molecular dates and the mammalian radiation (1999)
Bromham, Lindell, Phillips, Matthew J., Penny, David
Dates of divergence derived from molecular data have been used to place the beginning of the radiation of modern mammalian orders in the Cretaceous, long before the final extinction of the dinosaurs....
The redemption of nature in Romans 8 /--by David Penny. (1970)
Thesis (Th. M.)--Dallas Theological Seminary, 1970.
Murray-McIntosh, Rosalind P., Scrimshaw, Brian J., Hatfield, Peter J., Penny, David
The hypervariable 1 region of human mtDNA shows markedly reduced variability in Polynesians, and this variability decreases from western to eastern Polynesia. Fifty-four sequences from New Zealand...
Testing the Cambrian explosion hypothesis by using a molecular dating technique
Bromham, Lindell, Rambaut, Andrew, Fortey, Richard, Cooper, Alan, Penny, David
Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account...
Martin, William, Rujan, Tamas, Richly, Erik, Hansen, Andrea, Cornelsen, Sabine, Lins, Thomas, ...
Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only ≈5–10% as many genes as those of their free-living cousins,...
Relationship of Lipid Metabolism to the Respiration and Growth of Pea Stem Sections 1
Biologically active lipids increase the growth of pea stem sections within 3 hours at the same time their respiration is increased and their growth rate is more than that of the intact plant. The...
Murray-McIntosh, Rosalind P., Scrimshaw, Brian J., Hatfield, Peter J., Penny, David
The hypervariable 1 region of human mtDNA shows markedly reduced variability in Polynesians, and this variability decreases from western to eastern Polynesia. Fifty-four sequences from New Zealand...
Testing the Cambrian explosion hypothesis by using a molecular dating technique
Bromham, Lindell, Rambaut, Andrew, Fortey, Richard, Cooper, Alan, Penny, David
Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account...
Martin, William, Rujan, Tamas, Richly, Erik, Hansen, Andrea, Cornelsen, Sabine, Lins, Thomas, ...
Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only ≈5–10% as many genes as those of their free-living cousins,...
Relationship of Lipid Metabolism to the Respiration and Growth of Pea Stem Sections 1
Biologically active lipids increase the growth of pea stem sections within 3 hours at the same time their respiration is increased and their growth rate is more than that of the intact plant. The...
RNase MRP and the RNA processing cascade in the eukaryotic ancestor
Woodhams, Michael D, Stadler, Peter F, Penny, David, Collins, Lesley J
Optimal alphabets for an RNA world.
Gardner, Paul P, Holland, Barbara R, Moulton, Vincent, Hendy, Mike, Penny, David
Experiments have shown that the canonical AUCG genetic alphabet is not the only possible nucleotide alphabet. In this work we address the question 'is the canonical alphabet optimal?' We make the...
Roy, Scott William, Penny, David
The age of modern introns and the evolutionary forces controlling intron loss and gain remain matters of much debate. In the case of the apicomplexan malaria parasite Plasmodium falciparum, previous...
Intron length distributions and gene prediction
Roy, Scott William, Penny, David
Accurate gene prediction in eukaryotes is a difficult and subtle problem. Here we point out a useful feature of expected distributions of spliceosomal intron lengths. Since introns are removed from...
Chen, Xiaowei (Sylvia), Rozhdestvensky, Timofey S., Collins, Lesley J., Schmitz, Jürgen, Penny, David
Non-protein-coding RNAs represent a large proportion of transcribed sequences in eukaryotes. These RNAs often function in large RNA–protein complexes, which are catalysts in various RNA-processing...
Bird evolution: testing the Metaves clade with six new mitochondrial genomes
Morgan-Richards, Mary, Trewick, Steve A, Bartosch-Härlid, Anna, Kardailsky, Olga, Phillips, Matthew J, McLenachan, Patricia A, ...
Regional economic indicators, February 2008, with a focus on regional productivity
Sumit Dey-Chowdhury, David Penny, Birgit Wosnitza, Martin Walker
Compiles information covering the nine English Government Office Regions, Northern Ireland, Scotland and Wales for the aboveThis quarter, the regional economic indicators article starts by presenting...
Chen, Xiaowei Sylvia, White, W. Timothy J., Collins, Lesley J., Penny, David
RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing...
Significance of the length of the shortest tree
Michael Steel, Michael Hendy, David Penny
Binary trees, Parsimony, Minimum-length tree, Fitch's algorithm, Distributions,
Spectral analysis of phylogenetic data
Phylogenetic trees, Bipartition, Hadamard transform, Hadamard conjugation, Spectrum, Nucleotide sequences, Distance data, Fast Hadamard Transform,