New methods for understanding the functional significance of noncoding DNA

Research output

Research output per year 2004 2004 2005 2006 2007 2009

• 23 Article
• 1 Comment/debate
• 1 Letter

Research output per year

Research output per year

Search results

• 2009

  Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

  Keightley, P. D., Trivedi, U., Thomson, M., Oliver, F., Kumar, S. & Blaxter, M. L., 2009, In: Genome Research. 19, 7, p. 1195-1201 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Drosophila Melanogaster 100%
  • Mutation Rate 100%
  • Mutation Accumulation 100%
  • Transversion 40%
  • Indel 20%
• 2008

  Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

  Daniel J, G. & Keightley, P., Sept 2008, In: BMC Evolutionary Biology. 8, 7 p., 265.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • CpG Site 100%
  • DNA Sequence 50%

• Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster

  Haag-Liautard, C., Coffey, N., Houle, D., Lynch, M., Charlesworth, B. & Keightley, P. D., Aug 2008, In: PLoS Biology. 6, 8, p. 1706-1714 9 p., e204.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • DNA Mutation 100%
  • Drosophila Melanogaster 100%
  • Mutation Rate 100%
  • Mitochondrial DNA 100%
  • Indel 42%
• 2007

  Evolution of genes and genomes on the Drosophila phylogeny

  Drosophila 12 Genomes Consortium, Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M. & Akashi, H. & 31 others, Anderson, W. W., Aquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo de Carvalho, A., Caspi, A., Castrezana, S., Halligan, D. L., Keightley, P. D., Kumar, S., Ponting, C. P., Barry, A. & Matthews, C., 8 Nov 2007, In: Nature. 450, 7167, p. 203-218 16 p.

  Research output: Contribution to journal › Article › peer-review

  • Genetics 100%
  • Cladistics 100%
  • Regulatory Region 100%
  • Cell Maturation 100%
  • Taxon 100%

• Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites.

  Wang, J., Keightley, P. & Halligan, D., 2007, In: Journal of molecular evolution. 65, p. 627-639

  Research output: Contribution to journal › Article › peer-review

• Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies

  Keightley, P. & Eyre-Walker, A., 2007, In: Genetics. 177, 4, p. 2251–2261

  Research output: Contribution to journal › Article › peer-review

  • Gene Frequency 100%
  • Allele Frequency 100%
  • Genetics 50%
  • Amino Acids 50%
  • Population Size 50%

• Patterns of selective constraints in noncoding DNA of rice

  Keightley, P., Guo, X., Wang, Y. & Fan, L., 2007, In: BMC Evolutionary Biology. 7, 208, 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Noncoding DNA 100%
  • Intron 100%
  • Intergenic Region 100%
  • Negative Selection (Natural Selection) 30%
  • GC-content 20%

• The distribution of fitness effects of new mutations.

  Eyre-Walker, A. & Keightley, P., 2007, In: Nature Reviews Genetics. 450, p. 610-618

  Research output: Contribution to journal › Article › peer-review

• 2006

  Genomic Selective Constraints in Murid Noncoding DNA

  Gaffney, D. & Keightley, P., 2006, In: PLoS Genetics. 2, 11, 12 p., e204.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Noncoding DNA 100%
  • Genomics 100%
  • Intergenic Region 100%
  • Intron 50%
  • Mutation Rate 25%

• Interference among deleterious mutations favours sex and recombination in finite populations.

  Keightley, P. & Otto, S., 2006, In: Nature. 443, p. 89-92

  Research output: Contribution to journal › Article › peer-review

• MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution

  Wang, J., Johnson, T. & Keightley, P., 2006, In: BMC Bioinformatics. 7, 292, 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Indel 100%
  • DNA Sequence 100%
  • Noncoding DNA 100%
  • Intergenic Region 100%
  • Hidden Markov Model 50%

• Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison

  Halligan, D. & Keightley, P., 2006, In: Genome Research. 16, 7, p. 875-88

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Drosophila simulans 100%
• 2005

  Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes

  Keightley, P., Lercher, M. & Eyre-Walker, A., 2005, In: PLoS Biology. 3, 2, p. 282-288 e42.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Regulatory Element 100%
  • Gene Control 100%
  • Gene Expression 100%
  • Effective Population Size 50%
  • Natural Selection 50%

• Evolutionary constraints in conserved nongenic sequences of mammals.

  Keightley, P., Kryukov, G., Sunyaev, S., Halligan, D. & Gaffney, D., 2005, In: Genome Research. 15, 10, p. 1373-1378

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Negative Selection (Natural Selection) 100%
  • Mutation Rate 100%
  • Taxon 100%
  • Autosome 50%
  • Effective Population Size 50%

• Genetic instability of C. elegans comes naturally.

  Keightley, P. & Charlesworth, B., 2005, In: Trends in Genetics. 21, p. 67-70

  Research output: Contribution to journal › Article › peer-review

• Intron Size and Exon Evolution in Drosophila

  Marais, G., Nouvellet, P., Keightley, P. & Charlesworth, B., 2005, In: Genetics. 170, 1, p. 481-485

  Research output: Contribution to journal › Article › peer-review

  • Exon 100%
  • Intron 100%
  • Regulatory Sequence 20%
  • Evolutionary Rate 20%

• The scale of mutational variability in the murid genome.

  Keightley, P. & Gaffney, D., 2005, In: Genome Research. 15, 8, p. 1086-1094

  Research output: Contribution to journal › Article › peer-review

  File

  • Mutation Rate 100%
  • Autosome 33%
  • X Chromosome 16%
  • Comparative Genomics 16%
  • Transposable Element 16%
• 2004

  Comparing analysis methods for mutation-accumulation data.

  Keightley, P., 2004, In: Genetics. 167, p. 551-553

  Research output: Contribution to journal › Article › peer-review

• DNA sequence error rates in Genbank records estimated using the mouse genome as a reference.

  Wesche, P., Gaffney, D. & Keightley, P., 2004, In: DNA Sequence. 15, p. 362-364

  Research output: Contribution to journal › Article › peer-review

• MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution

  Keightley, P. & Johnson, T., 2004, In: Genome Research. 14, p. 442-450

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Noncoding DNA 100%
  • Intergenic Region 100%
  • Indel 66%

• Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila

  Halligan, D., Eyre-Walker, A., Andolfatto, P. & Keightley, P., 2004, In: Genome Research. 14, p. 273-279

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Intergenic Region 100%
  • Spacer DNA 100%
  • Intron 60%
  • Noncoding DNA 40%
  • Amino Acids 20%

• Rates of molecular evolution in nuclear genes of East Mediterranean scorpions.

  Keightley, P. & Gantenbein, B., 2004, In: Evolution: International Journal of Organic Evolution. 58, p. 2486-2497

  Research output: Contribution to journal › Article › peer-review

• Unexpected conserved noncoding DNA blocks in mammals.

  Keightley, P. & Gaffney, D., 2004, In: Trends in Genetics. 20, p. 332-337

  Research output: Contribution to journal › Article › peer-review