Gavin C Conant

Summary

Affiliation: Trinity College
Country: Ireland

Publications

  1. pmc Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
    Amy J Powell
    Department of Computational Systems Biology, Sandia National Laboratories, Albuquerque, NM, USA
    BMC Genomics 9:147. 2008
  2. ncbi request reprint Modeling amino acid substitution patterns in orthologous and paralogous genes
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
    Mol Phylogenet Evol 42:298-307. 2007
  3. doi request reprint GenomeVx: simple web-based creation of editable circular chromosome maps
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
    Bioinformatics 24:861-2. 2008
  4. pmc Increased glycolytic flux as an outcome of whole-genome duplication in yeast
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
    Mol Syst Biol 3:129. 2007
  5. pmc The rarity of gene shuffling in conserved genes
    Gavin C Conant
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Biol 6:R50. 2005
  6. pmc Functional partitioning of yeast co-expression networks after genome duplication
    Gavin C Conant
    Department of Genetics, Trinity College, University of Dublin, Dublin, Ireland
    PLoS Biol 4:e109. 2006
  7. pmc Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
    Genetics 179:1681-92. 2008
  8. pmc Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
    Devin R Scannell
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
    Proc Natl Acad Sci U S A 104:8397-402. 2007
  9. pmc A conserved mammalian protein interaction network
    Asa Pérez-Bercoff
    Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
    PLoS ONE 8:e52581. 2013
  10. pmc The T box regulatory element controlling expression of the class I lysyl-tRNA synthetase of Bacillus cereus strain 14579 is functional and can be partially induced by reduced charging of asparaginyl-tRNAAsn
    Niall Foy
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
    BMC Microbiol 10:196. 2010

Detail Information

Publications17

  1. pmc Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
    Amy J Powell
    Department of Computational Systems Biology, Sandia National Laboratories, Albuquerque, NM, USA
    BMC Genomics 9:147. 2008
    ..To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, despite this phenomenon's known importance in virulence in bacteria and viruses...
  2. ncbi request reprint Modeling amino acid substitution patterns in orthologous and paralogous genes
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
    Mol Phylogenet Evol 42:298-307. 2007
    ..Improved understanding of such gene-specific variation in substitution patterns may have implications for applications such as sequence alignment and phylogenetic inference...
  3. doi request reprint GenomeVx: simple web-based creation of editable circular chromosome maps
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland
    Bioinformatics 24:861-2. 2008
    ..In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator...
  4. pmc Increased glycolytic flux as an outcome of whole-genome duplication in yeast
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
    Mol Syst Biol 3:129. 2007
    ..We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD...
  5. pmc The rarity of gene shuffling in conserved genes
    Gavin C Conant
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Biol 6:R50. 2005
    ..However, surprisingly little is known about its incidence on a genome-wide scale...
  6. pmc Functional partitioning of yeast co-expression networks after genome duplication
    Gavin C Conant
    Department of Genetics, Trinity College, University of Dublin, Dublin, Ireland
    PLoS Biol 4:e109. 2006
    ....
  7. pmc Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast
    Gavin C Conant
    Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
    Genetics 179:1681-92. 2008
    ..We suggest that while duplicate copies of some genes may be lost neutrally after WGD, another set of genes may be initially preserved in duplicate by natural selection for reasons including dosage...
  8. pmc Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
    Devin R Scannell
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
    Proc Natl Acad Sci U S A 104:8397-402. 2007
    ..The apparent low initial sequence divergence of the gene pairs leads us to propose that the yeast WGD was probably an autopolyploidization...
  9. pmc A conserved mammalian protein interaction network
    Asa Pérez-Bercoff
    Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
    PLoS ONE 8:e52581. 2013
    ..Collectively, the results suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles...
  10. pmc The T box regulatory element controlling expression of the class I lysyl-tRNA synthetase of Bacillus cereus strain 14579 is functional and can be partially induced by reduced charging of asparaginyl-tRNAAsn
    Niall Foy
    Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
    BMC Microbiol 10:196. 2010
    ..The lysK gene (encoding LysRS1) of B. cereus strain 14579 has an associated T box element, the first reported instance of potential T box control of LysRS expression...
  11. doi request reprint Patterns of indirect protein interactions suggest a spatial organization to metabolism
    Asa Pérez-Bercoff
    Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
    Mol Biosyst 7:3056-64. 2011
    ....
  12. pmc Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans
    Gavin C Conant
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA
    Proc Biol Sci 271:89-96. 2004
    ..We discuss the different causes of mutational robustness in single-copy and duplicate genes, as well as its evolutionary origin...
  13. pmc Asymmetric sequence divergence of duplicate genes
    Gavin C Conant
    Department of Biology, The University of New Mexico, Albuquerque, New Mexico 87131, USA
    Genome Res 13:2052-8. 2003
    ..The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise gene comparisons...
  14. ncbi request reprint Convergent evolution of gene circuits
    Gavin C Conant
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, New Mexico 87131, USA
    Nat Genet 34:264-6. 2003
    ..Specifically, we show that multiple types of transcriptional regulation circuitry in Escherichia coli and the yeast Saccharomyces cerevisiae have evolved independently and not by duplication of one or a few ancestral circuits...
  15. pmc GenomeHistory: a software tool and its application to fully sequenced genomes
    Gavin C Conant
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA
    Nucleic Acids Res 30:3378-86. 2002
    ..In contrast, a weakly negative such correlation is seen in multicellular eukaryotes...
  16. pmc A fast algorithm for determining the best combination of local alignments to a query sequence
    Gavin C Conant
    Department of Biology, The University of New Mexico, Albuquerque, NM, USA
    BMC Bioinformatics 5:62. 2004
    ..Recombination perturbs this order. An algorithm that can reconstruct sequence similarity despite rearrangement would be helpful for reconstructing the evolutionary history of recombined sequences...
  17. ncbi request reprint Molecular evolution in large genetic networks: does connectivity equal constraint?
    Matthew W Hahn
    Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA mwhahn ucdavis edu
    J Mol Evol 58:203-11. 2004
    ..The finding that highly connected proteins can tolerate just as many amino acid substitutions as other proteins leads us to conclude that power-laws in cellular networks do not reflect selection for mutational robustness...