L D Hurst

Summary

Affiliation: University of Bath
Country: UK

Publications

  1. pmc Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
    Claudia C Weber
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Genome Biol 12:R23. 2011
  2. pmc Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals
    Shanye Yin
    Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai JiaoTong University School of Medicine, South Chongqing Road, Shanghai 200025, PR China
    Genome Biol 10:R74. 2009
  3. pmc Do Alu repeats drive the evolution of the primate transcriptome?
    Araxi O Urrutia
    Department of Biology and Biochemistry, University of Bath, Bath, BA4 7AY, UK
    Genome Biol 9:R25. 2008
  4. pmc Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    J V Chamary
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Biol 6:R75. 2005
  5. pmc The determinants of gene order conservation in yeasts
    Juan F Poyatos
    Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre, Centro Superior de Investigaciones Científicas CSIC, Darwin 3, Campus de Cantoblanco, Madrid 28049, Spain
    Genome Biol 8:R233. 2007
  6. pmc Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Genome Biol 9:R29. 2008
  7. pmc Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes
    Ping Wang
    Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, 225 South Chong Qing Road, Shanghai 200025, PR China
    Genome Biol 9:R169. 2008
  8. pmc How biologically relevant are interaction-based modules in protein networks?
    Juan F Poyatos
    Evolutionary Systems Biology Initiative, Structural and Computational Biology Program, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Genome Biol 5:R93. 2004
  9. pmc Does negative auto-regulation increase gene duplicability?
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, UK
    BMC Evol Biol 9:193. 2009
  10. pmc Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay
    Zhenguo Zhang
    Institute of Health Sciences, Shanghai Institutes for Biological Sciences SIBS, Chinese Academy of Sciences CAS and Shanghai Jiao Tong University School of Medicine SJTUSM, Shanghai, PR China
    BMC Biol 7:23. 2009

Collaborators

Detail Information

Publications90

  1. pmc Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
    Claudia C Weber
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Genome Biol 12:R23. 2011
    ..Whether similar clusters show gene order conservation in other lineages is, however, undecided. Here, we examine this issue in Drosophila melanogaster using high-resolution chromosome rearrangement data...
  2. pmc Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals
    Shanye Yin
    Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai JiaoTong University School of Medicine, South Chongqing Road, Shanghai 200025, PR China
    Genome Biol 10:R74. 2009
    ....
  3. pmc Do Alu repeats drive the evolution of the primate transcriptome?
    Araxi O Urrutia
    Department of Biology and Biochemistry, University of Bath, Bath, BA4 7AY, UK
    Genome Biol 9:R25. 2008
    ..Here we consider whether Alus have increased expression breadth of genes in their vicinity...
  4. pmc Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    J V Chamary
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Biol 6:R75. 2005
    ..Here we test whether synonymous mutations might be under selection owing to their effects on the thermodynamic stability of mRNA, mediated by changes in secondary structure...
  5. pmc The determinants of gene order conservation in yeasts
    Juan F Poyatos
    Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre, Centro Superior de Investigaciones Científicas CSIC, Darwin 3, Campus de Cantoblanco, Madrid 28049, Spain
    Genome Biol 8:R233. 2007
    ....
  6. pmc Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Genome Biol 9:R29. 2008
    ....
  7. pmc Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes
    Ping Wang
    Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, 225 South Chong Qing Road, Shanghai 200025, PR China
    Genome Biol 9:R169. 2008
    ....
  8. pmc How biologically relevant are interaction-based modules in protein networks?
    Juan F Poyatos
    Evolutionary Systems Biology Initiative, Structural and Computational Biology Program, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Genome Biol 5:R93. 2004
    ..These constituents correlate only weakly with other levels of organization. We also discuss how such structures could be used for finding targets for antimicrobial drugs...
  9. pmc Does negative auto-regulation increase gene duplicability?
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, UK
    BMC Evol Biol 9:193. 2009
    ..Using data from the transcriptional networks of E. coli and S. cerevisiae, we test the hypothesis that genes under negative auto-regulation show enhanced duplicability...
  10. pmc Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay
    Zhenguo Zhang
    Institute of Health Sciences, Shanghai Institutes for Biological Sciences SIBS, Chinese Academy of Sciences CAS and Shanghai Jiao Tong University School of Medicine SJTUSM, Shanghai, PR China
    BMC Biol 7:23. 2009
    ..Alternatively, nonsense-mediated decay can be regulated under certain conditions so the presence of a premature termination codon can be a means to up-regulate transcripts needed when nonsense-mediated decay is suppressed...
  11. ncbi request reprint Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
    J Mol Evol 63:174-82. 2006
    ..The pairing sites also have low Ka values and the selection on the synonymous sites is unlikely to lead to misleading reports of localized high Ka/Ks ratios...
  12. pmc Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
    BMC Evol Biol 5:62. 2005
    ..Here we ask whether ligands are more closely linked to their receptors than expected by chance...
  13. doi request reprint Fundamental concepts in genetics: genetics and the understanding of selection
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Somerset, BA2 7AY, UK
    Nat Rev Genet 10:83-93. 2009
    ..Understanding how and why selection acts has important potential applications, from understanding the mechanisms of disease and microbial resistance, to improving the design of transgenes and drugs...
  14. pmc Bioinformatics with a French accent
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Biol 6:349. 2005
  15. pmc Evolutionary genomics and the reach of selection
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Somerset, UK
    J Biol 8:12. 2009
    ..Unexpected findings in evolutionary genomics both question the role of selection in genome evolution and clarify how genomes work...
  16. ncbi request reprint Evidence for purifying selection acting on silent sites in BRCA1
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, Claverton Down, BA27AY, Bath, UK
    Trends Genet 17:62-5. 2001
    ..Unusually, this peak is caused by a plummet in the silent-site rate of evolution. The most parsimonious interpretation of these data is that purifying selection is acting on silent sites...
  17. ncbi request reprint The evolutionary dynamics of eukaryotic gene order
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Nat Rev Genet 5:299-310. 2004
  18. ncbi request reprint Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
    Gene 261:107-14. 2000
    ..If the positive correlation is real then, we argue, this is hard to reconcile with the biased gene conversion model for isochore formation as this predicts a negative correlation...
  19. ncbi request reprint Growth effects of uniparental disomies and the conflict theory of genomic imprinting
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, UK
    Trends Genet 13:436-43. 1997
    ..Perhaps surprisingly, we find that much of the data do not support the hypothesis...
  20. pmc High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, UK
    Proc Biol Sci 268:493-7. 2001
    ..Against the expectations of the thermal adaptation hypothesis, within prokaryotes GC content in protein-coding genies, even at relatively freely evolving sites, cannot be considered an adaptation to the thermal environment...
  21. ncbi request reprint Do essential genes evolve slowly?
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
    Curr Biol 9:747-50. 1999
    ....
  22. ncbi request reprint Do we understand the evolution of genomic imprinting?
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 4SD, UK
    Curr Opin Genet Dev 8:701-8. 1998
    ..The status of theory remains undecided, however, as post-hoc explanations can be provided as to why these predictions are not borne out...
  23. pmc The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?
    N G Smith
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genetics 152:661-73. 1999
    ..This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of alpha, obtained using this method, need to be treated with caution...
  24. pmc Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
    Genome Res 14:1002-13. 2004
    ..As regards K4, our results appear consistent with the notion that local similarity is due to processes associated with meiotic recombination...
  25. pmc The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents
    N G Smith
    Department of Biology and Biochemistry, University of Bath, Bath B42 7AY, United Kingdom
    Genetics 153:1395-402. 1999
    ..Finally, we find that K(S) is reduced at the start of genes, which suggests that selection for RNA structure may affect silent sites in mammalian protein-coding genes...
  26. ncbi request reprint Vertebrate genome evolution: a slow shuffle or a big bang?
    N G Smith
    Department of Biology and Biochemistry, University of Bath, Bath, UK
    Bioessays 21:697-703. 1999
    ..However, with more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters...
  27. ncbi request reprint The evolutionary dynamics of male-killers and their hosts
    J P Randerson
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
    Heredity (Edinb) 84:152-60. 2000
    ..The presence of a resistance gene can allow a less efficient male-killer to outcompete its rival and hence reverse the trend towards more efficient transmission and reduced metabolic load on the host...
  28. ncbi request reprint Evolution of chromosome organization driven by selection for reduced gene expression noise
    Nizar N Batada
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Nat Genet 39:945-9. 2007
    ..We conclude that different noise characteristics of different genomic domains favors nonrandom gene positioning. This has implications for gene therapy and understanding transgenic phenotypes...
  29. pmc Splicing and the evolution of proteins in mammals
    Joanna L Parmley
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    PLoS Biol 5:e14. 2007
    ..Thus there exists a strong force operating on protein evolution in mammals that is not explained directly in terms of the biology of the protein...
  30. pmc Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor
    N G Smith
    Centre for Mathematical Biology, School of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genetics 150:823-33. 1998
    ..These results suggest that, in contrast to previous studies of intragenic variation, Ks patterns are not simply caused by the same forces responsible for Ka/Ks correlations...
  31. ncbi request reprint Sex biases in the mutation rate
    L D Hurst
    Department of Biology and Biochemistry, University of Bath, UK
    Trends Genet 14:446-52. 1998
    ..While the number of germ-line cell divisions might contribute to differences, this by no means accounts for all of the data...
  32. ncbi request reprint Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias
    M J Lercher
    Department of Biology and Biochemistry, University of Bath, Claverton Downs, Bath, England
    Mol Biol Evol 18:2032-9. 2001
    ..As autosomal heterogeneity cannot be owing to different times spent in the germ line, this demonstrates that the dominant determiner of synonymous rates of evolution is not, as has been conjectured, the time spent in the male germ line...
  33. ncbi request reprint Evidence for co-evolution of gene order and recombination rate
    Csaba Pal
    Department of Biology and Biochemistry, University of Bath, BA2 7AY, Bath, Somerset, UK
    Nat Genet 33:392-5. 2003
    ..These results suggest that selection acts to modify both the fine-scale intragenomic variation in the recombination rate and the distribution of genes and provide evidence for co-evolution of gene order and recombination rate...
  34. pmc The signature of selection mediated by expression on human genes
    Araxi O Urrutia
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Res 13:2260-4. 2003
    ..We conclude that, contrary to the usual supposition, human genes show signatures consistent with selection mediated by expression level...
  35. ncbi request reprint Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
    Balazs Papp
    Department of Biology and Biochemistry, University of Bath, BA2 7AY Bath, Somerset, UK
    Nature 429:661-4. 2004
    ..Instead their presence is better explained by selection for high enzymatic flux...
  36. ncbi request reprint Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
    Joanna L Parmley
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    Mol Biol Evol 23:301-9. 2006
    ..Additionally, selection on ESEs appears to affect nonsynonymous sites and may explain why amino acid usage near intron-exon junctions is nonrandom...
  37. ncbi request reprint Protein evolution: causes of trends in amino-acid gain and loss
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
    Nature 442:E11-2; discussion E12. 2006
    ..This reinforces the need for caution in the interpretation of results derived from closely related taxa...
  38. ncbi request reprint Co-expressed yeast genes cluster over a long range but are not regularly spaced
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    J Mol Biol 359:825-31. 2006
    ..Further, analysis of yeast transcription factor binding data sets suggests that there is currently no statistical evidence for chromosomal periodicity of co-regulation...
  39. ncbi request reprint Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
    Joanna L Parmley
    Department of Biology and Biochemistry, University of Bath, Bath, UK
    Mol Biol Evol 24:1600-3. 2007
    ..Similar results are observed in mouse exons. We conclude that splice regulation impacts on the choice of synonymous codons in mammals, but the magnitude of this effect is less than might at first have been supposed...
  40. pmc GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Bath, UK
    Mol Syst Biol 6:340. 2010
    ..These findings provide independent evidence for a role of misfolding in shaping gene evolution and highlight the need to co-characterize adaptations in cis and trans to unravel the workings of integrated molecular systems...
  41. ncbi request reprint Chromatin remodelling is a major source of coexpression of linked genes in yeast
    Nizar N Batada
    Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
    Trends Genet 23:480-4. 2007
    ..These results have implications for gene therapy and for understanding gene order evolution, suggesting that chromosomal proximity alone is adequate to achieve some level of coexpression...
  42. doi request reprint Timing of replication is a determinant of neutral substitution rates but does not explain slow Y chromosome evolution in rodents
    Catherine J Pink
    Department of Biology and Biochemistry, University of Bath, Somerset, United Kingdom
    Mol Biol Evol 27:1077-86. 2010
    ..These results support the hypothesis that replication timing is an important source of substitution rate heterogeneity...
  43. ncbi request reprint Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?
    Jean Vincent Chamary
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Trends Genet 21:256-9. 2005
    ..Evidence for selection between synonymous codons that are associated with splicing enhancers remains after controlling for this bias, whereas support for cryptic splice-site avoidance is diminished...
  44. pmc Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Res 13:238-43. 2003
    ..The central importance of tandem duplicate genes in these patterns renders the worm genome different from both yeast and human...
  45. ncbi request reprint A unification of mosaic structures in the human genome
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, UK
    Hum Mol Genet 12:2411-5. 2003
    ..This is not only a confirmation of the adaptive hypothesis, but is also the first direct systematic evidence of a general interdependence of expression patterns with base composition and chromosome structure...
  46. ncbi request reprint Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage
    Jean Vincent Chamary
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    Mol Biol Evol 21:1014-23. 2004
    ..Therefore, by elimination, we propose this to be strong evidence for selectively driven codon usage in mammals...
  47. ncbi request reprint Dosage sensitivity and the evolution of gene families in yeast
    Balazs Papp
    Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK
    Nature 424:194-7. 2003
    ..The balance hypothesis therefore provides a single theoretical framework for understanding components both of dominance and of gene family size...
  48. pmc The evolution of isochores: evidence from SNP frequency distributions
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genetics 162:1805-10. 2002
    ..The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions...
  49. ncbi request reprint Can mutation or fixation biases explain the allele frequency distribution of human single nucleotide polymorphisms (SNPs)?
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, Somerset BA2 7AY, UK
    Gene 300:53-8. 2002
    ..Together these results demonstrate that mutation bias fails to explain the evolution of isochores, and suggest that either selection or biased gene conversion are involved...
  50. ncbi request reprint The Ka/Ks ratio: diagnosing the form of sequence evolution
    Laurence D Hurst
    Department of Biology and Biochemistry, University of Bath, Bath, UK BA2 7AY
    Trends Genet 18:486. 2002
  51. ncbi request reprint How common are intragene windows with KA > KS owing to purifying selection on synonymous mutations?
    Joanna L Parmley
    Department of Biology and Biochemistry, University of Bath, Bath, UK
    J Mol Evol 64:646-55. 2007
    ..As so few K (A)/K (S) peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone...
  52. pmc The impact of the nucleosome code on protein-coding sequence evolution in yeast
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    PLoS Genet 4:e1000250. 2008
    ..As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread...
  53. ncbi request reprint Human SNP variability and mutation rate are higher in regions of high recombination
    Martin J Lercher
    Dept of Biology and Biochemistry, University of Bath, BA2 7AY, Bath, UK
    Trends Genet 18:337-40. 2002
    ..One possible explanation for this is that recombination is mutagenic...
  54. ncbi request reprint Natural selection promotes the conservation of linkage of co-expressed genes
    Laurence D Hurst
    Dept of Biology and Biochemistry, University of Bath, Claverton Down, BA2 7AY, Bath, UK
    Trends Genet 18:604-6. 2002
    ..This physical proximity, however, only accounts for a small proportion of the enhanced degree of conservation of co-expressed gene pairs. These results demonstrate that purely neutralist models of gene order evolution are not realistic...
  55. ncbi request reprint Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
    Mol Biol Evol 24:2755-62. 2007
    ..These results have implications for inferring aspects of the mechanism of splicing given nothing more than a well-annotated genome...
  56. pmc A comparative test of a theory for the evolution of anisogamy
    J P Randerson
    Department of Biology and Biochemistry, Bath University, Claverton Down, UK
    Proc Biol Sci 268:879-84. 2001
    ..The predictions that larger organisms should (i) have a greater degree of gamete dimorphism and (ii) have larger eggs are broadly upheld. However, the results are highly sensitive to the phylogeny and the mode of analysis used...
  57. ncbi request reprint Evolution of cis-regulatory elements in duplicated genes of yeast
    Balazs Papp
    Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK
    Trends Genet 19:417-22. 2003
    ..These results suggest that the evolution of functional novelty has a substantial role in yeast duplicate gene evolution...
  58. pmc Leukocyte tyrosine kinase functions in pigment cell development
    Susana S Lopes
    Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
    PLoS Genet 4:e1000026. 2008
    ..In summary, we have discovered a novel signalling pathway in NCC development and demonstrate fate specification of iridophores as the first identified role for Ltk...
  59. ncbi request reprint Genomic function: Rate of evolution and gene dispensability
    Csaba Pal
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Nature 421:496-7; discussion 497-8. 2003
  60. doi request reprint Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Biochem Soc Trans 37:756-61. 2009
    ..These results indicate that there is substantially more to protein evolution than protein functional constraints...
  61. ncbi request reprint Clustering of tissue-specific genes underlies much of the similarity in rates of protein evolution of linked genes
    Elizabeth J B Williams
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
    J Mol Evol 54:511-8. 2002
    ..The distribution of placentally expressed genes, in contrast, does have an effect...
  62. pmc Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
    A O Urrutia
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genetics 159:1191-9. 2001
    ..The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans...
  63. pmc Male killing can select for male mate choice: a novel solution to the paradox of the lek
    J P Randerson
    Department of Biology and Biochemistry, University of Bath, Claverton Down, UK
    Proc Biol Sci 267:867-74. 2000
    ..This is the first model to allow this result, and may explain the long-term persistence of a male killer in Hypolimnas bolina...
  64. pmc Unique cost dynamics elucidate the role of frameshifting errors in promoting translational robustness
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    Genome Biol Evol 2:636-45. 2010
    ..We therefore propose that selection on tRNA repertoires may operate to reduce frameshifting errors...
  65. ncbi request reprint Clustering of housekeeping genes provides a unified model of gene order in the human genome
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Nat Genet 31:180-3. 2002
    ..In addition, we show that the apparent clustering of genes with high expression rates is a consequence of the clustering of housekeeping genes...
  66. ncbi request reprint Evidence that the human X chromosome is enriched for male-specific but not female-specific genes
    Martin J Lercher
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    Mol Biol Evol 20:1113-6. 2003
    ..This we propose is consistent with Rice's model of the evolution of sexually antagonistic alleles...
  67. doi request reprint Maternally-inherited Grb10 reduces placental size and efficiency
    Marika Charalambous
    Department of Biology and Biochemistry, University of Bath, Building 4 South, Bath BA27AY, UK
    Dev Biol 337:1-8. 2010
    ..This grandparental effect suggests Grb10 can influence reproductive strategy through the allocation of maternal resources such that offspring number is offset against size...
  68. pmc Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts
    Miao Sun
    Department of Medicine, Section of Hematology Oncology, University of Chicago, 5841 S Maryland Avenue, MC2115, Chicago, IL 60637, USA
    Nucleic Acids Res 33:5533-43. 2005
    ..These findings underscore the preference for, and conservation of, 3'-UTR-targeted antisense regulation, and the importance of 3'-UTRs in gene regulation...
  69. ncbi request reprint Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts
    Jianjun Chen
    Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC2115, Chicago, IL 60637, USA
    Trends Genet 21:326-9. 2005
    ..Moreover, co-expressed and inversely expressed SA pairs exhibit a striking pattern of evolutionary conservation. These findings suggest that antisense regulation is a common and important mechanism of gene regulation in the human genome...
  70. ncbi request reprint Identification of a new pebp2alphaA2 isoform from zebrafish runx2 capable of inducing osteocalcin gene expression in vitro
    Jorge P Pinto
    CCMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
    J Bone Miner Res 20:1440-53. 2005
    ..The runx2b pebp2alphaA2 isoform induces osteocalcin gene expression by binding to a specific region of the promoter and seems to have been selectively conserved in the teleost lineage...
  71. ncbi request reprint Is the synonymous substitution rate in mammals gene-specific?
    Elizabeth J B Williams
    Mol Biol Evol 19:1395-8. 2002
  72. ncbi request reprint Comparative evolutionary analysis of VPS33 homologues: genetic and functional insights
    Paul Gissen
    Section of Medical and Molecular Genetic, University of Birmingham, UK
    Hum Mol Genet 14:1261-70. 2005
    ..These investigations are consistent with the hypothesis that there are two functional classes of Vps33p homologues in all multicellular organisms and that the two classes reflect the evolution of organelle/tissue-specific functions...
  73. pmc The small introns of antisense genes are better explained by selection for rapid transcription than by "genomic design"
    Jianjun Chen
    Genetics 171:2151-5. 2005
    ..We show that the effects are not specific to noncoding RNAs and that the predictions of the "genomic design" model for the most part are not upheld...
  74. ncbi request reprint Human antisense genes have unusually short introns: evidence for selection for rapid transcription
    Jianjun Chen
    Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC2115, Chicago, IL 60637, USA
    Trends Genet 21:203-7. 2005
    ....
  75. ncbi request reprint Is optimal gene order impossible?
    Juan F Poyatos
    Evolutionary Systems Biology Initiative, Structural and Computational Biology Programme, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Trends Genet 22:420-3. 2006
    ..Under such a model an "optimal" gene order is never stable...
  76. doi request reprint A test of the null model for 5' UTR evolution based on GC content
    Max Reuter
    Mol Biol Evol 25:801-4. 2008
    ..We conclude that UTR length may be shaped to some degree by the forces considered in the null model but that the model fails to provide a complete explanation for UTR length evolution...
  77. ncbi request reprint Comparisons of dN/dS are time dependent for closely related bacterial genomes
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Paris VI, 75005 Paris, France
    J Theor Biol 239:226-35. 2006
    ..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...
  78. pmc Stratus not altocumulus: a new view of the yeast protein interaction network
    Nizar N Batada
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    PLoS Biol 4:e317. 2006
    ..In turn, control of the activity of the most highly connected proteins may be vital. Indeed, we find that a fluctuation in steady-state levels of the most connected proteins is minimized...
  79. pmc Imprinted chromosomal regions of the human genome have unusually high recombination rates
    Martin J Lercher
    Genetics 165:1629-32. 2003
  80. ncbi request reprint Chance and necessity in the evolution of minimal metabolic networks
    Csaba Pal
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
    Nature 440:667-70. 2006
    ..We conclude that, at least for the particular cases considered here, gene content of an organism can be predicted with knowledge of its distant ancestors and its current lifestyle...
  81. ncbi request reprint Hearing silence: non-neutral evolution at synonymous sites in mammals
    J V Chamary
    Center for Integrative Genomics, University of Lausanne, Switzerland
    Nat Rev Genet 7:98-108. 2006
    ..This has implications for understanding disease, optimizing transgene design, detecting positive selection and estimating the mutation rate...
  82. ncbi request reprint Evolution encoded
    Stephen J Freeland
    University of Maryland, Baltimore County, USA
    Sci Am 290:84-91. 2004
  83. pmc Evolutionary and physiological importance of hub proteins
    Nizar N Batada
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    PLoS Comput Biol 2:e88. 2006
    ..We conclude that hub proteins are more important for cellular growth rate and under tight regulation but are not slow evolving...
  84. ncbi request reprint Evidence against the selfish operon theory
    Csaba Pal
    MTA, Theoretical Biology Research Group, Eotvos Lorand University, Budapest, Hungary
    Trends Genet 20:232-4. 2004
    ..Contrary to expectations, essential genes with related functions have an especially strong tendency to cluster, even if they are not in operons. Moreover, essential genes are particularly abundant in operons...
  85. pmc Still stratus not altocumulus: further evidence against the date/party hub distinction
    Nizar N Batada
    PLoS Biol 5:e154. 2007
  86. ncbi request reprint Dissecting dispensability
    Laurence D Hurst
    Nat Genet 37:214-5. 2005
  87. pmc Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
    Cathal Seoighe
    Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
    PLoS Genet 1:e13. 2005
    ..These observations thus support the view that selection for efficiency contributes to the reduction in intron length and provide the first report of a molecular signature of strong gametophytic selection...
  88. pmc Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity
    Miao Sun
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 16:922-33. 2006
    ..Instead, our results suggest that antisense transcription might be prevalent in almost all metazoan genomes, nematodes being an unexplained exception...
  89. ncbi request reprint Parasitic sex puppeteers
    Laurence D Hurst
    Sci Am 286:56-61. 2002
  90. doi request reprint Understanding the limits to generalizability of experimental evolutionary models
    Samantha E Forde
    Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA
    Nature 455:220-3. 2008
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