G B Golding

Summary

Affiliation: McMaster University
Country: Canada

Publications

  1. pmc RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions
    Marc J Champigny
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    BMC Genomics 14:578. 2013
  2. pmc Increased substitution rates surrounding low-complexity regions within primate proteins
    Carolyn Lenz
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Genome Biol Evol 6:655-65. 2014
  3. pmc Increased polymorphism near low-complexity sequences across the genomes of Plasmodium falciparum isolates
    Wilfried Haerty
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Genome Biol Evol 3:539-50. 2011
  4. pmc Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures
    Yi Fei Huang
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    PLoS Comput Biol 10:e1003429. 2014
  5. pmc Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity
    David R Guevara
    Department of Biology, McMaster University, Hamilton, ON, Canada
    BMC Plant Biol 12:175. 2012
  6. pmc The evolution of the class A scavenger receptors
    Fiona J Whelan
    Department of Pathology and Molecular Medicine, McMaster University, 1200 Main Street West, Hamilton, L8N 3Z5 Ontario, Canada
    BMC Evol Biol 12:227. 2012
  7. pmc BOND: Basic OligoNucleotide Design
    Lucian Ilie
    Department of Computer Science, University of Western Ontario, London, ON, Canada
    BMC Bioinformatics 14:69. 2013
  8. pmc Uncovering rate variation of lateral gene transfer during bacterial genome evolution
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    BMC Genomics 9:235. 2008
  9. pmc The role of laterally transferred genes in adaptive evolution
    Pradeep Reddy Marri
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    BMC Evol Biol 7:S8. 2007
  10. pmc Reconstructing the prior probabilities of allelic phylogenies
    G Brian Golding
    Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
    Genetics 161:889-96. 2002

Collaborators

Detail Information

Publications38

  1. pmc RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions
    Marc J Champigny
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    BMC Genomics 14:578. 2013
    ....
  2. pmc Increased substitution rates surrounding low-complexity regions within primate proteins
    Carolyn Lenz
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Genome Biol Evol 6:655-65. 2014
    ..Along with substitution rates, dN/dS ratios were also determined for each site, and the proportion of sites undergoing negative selection was found to have a negative relationship with distance from the LCR. ..
  3. pmc Increased polymorphism near low-complexity sequences across the genomes of Plasmodium falciparum isolates
    Wilfried Haerty
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Genome Biol Evol 3:539-50. 2011
    ..This observation strongly suggests the joint effects of lowered selective constraints on low-complexity sequences and a mutagenic effect of these simple sequences...
  4. pmc Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures
    Yi Fei Huang
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    PLoS Comput Biol 10:e1003429. 2014
    ..GP4Rate may be a useful tool for the in silico prediction of functionally important regions in the proteins with known structures. ..
  5. pmc Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity
    David R Guevara
    Department of Biology, McMaster University, Hamilton, ON, Canada
    BMC Plant Biol 12:175. 2012
    ..However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm...
  6. pmc The evolution of the class A scavenger receptors
    Fiona J Whelan
    Department of Pathology and Molecular Medicine, McMaster University, 1200 Main Street West, Hamilton, L8N 3Z5 Ontario, Canada
    BMC Evol Biol 12:227. 2012
    ..The 5 members of this family are strikingly variable in their protein structure and function, raising the question as to whether it is appropriate to group them as a family based on their ligand binding abilities...
  7. pmc BOND: Basic OligoNucleotide Design
    Lucian Ilie
    Department of Computer Science, University of Western Ontario, London, ON, Canada
    BMC Bioinformatics 14:69. 2013
    ..None of the existing programs meet all these criteria...
  8. pmc Uncovering rate variation of lateral gene transfer during bacterial genome evolution
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    BMC Genomics 9:235. 2008
    ..This makes it possible to address whether a difference between informational genes and non-informational genes is the main contributor to rate variation of lateral gene transfers...
  9. pmc The role of laterally transferred genes in adaptive evolution
    Pradeep Reddy Marri
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    BMC Evol Biol 7:S8. 2007
    ..Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches...
  10. pmc Reconstructing the prior probabilities of allelic phylogenies
    G Brian Golding
    Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
    Genetics 161:889-96. 2002
    ..Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions...
  11. pmc Simple sequence is abundant in eukaryotic proteins
    G B Golding
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Protein Sci 8:1358-61. 1999
    ..Although they are the most common shared feature of yeast proteins, their ubiquity and simplicity argue that their probable function may be to simply serve as spacers between other protein motifs...
  12. ncbi request reprint DNA and the revolutions of molecular evolution, computational biology, and bioinformatics
    G Brian Golding
    Department of Biology, McMaster University, Hamilton, ON, Canada
    Genome 46:930-5. 2003
    ..The analysis of these data has lead to new fields of science and to amazing advances in our understanding of evolution...
  13. ncbi request reprint Gene gain and gene loss in streptococcus: is it driven by habitat?
    Pradeep Reddy Marri
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 23:2379-91. 2006
    ..We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation...
  14. pmc The fate of laterally transferred genes: life in the fast lane to adaptation or death
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
    Genome Res 16:636-43. 2006
    ..Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific...
  15. ncbi request reprint Evolution of allosteric control in glycogen phosphorylase
    J W Hudson
    Department of Biology, York University, Ontario, Canada
    J Mol Biol 234:700-21. 1993
    ....
  16. ncbi request reprint The mosaic nature of the eukaryotic nucleus
    S Ribeiro
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 15:779-88. 1998
    ..A chimeric origin of eukaryotes or an ancient, massive horizontal transfer of genes from Gram-negative bacteria to eucarya can explain many of the observed phylogenies...
  17. ncbi request reprint A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history
    Kim Wong
    McMaster University, Department of Biology, Hamilton, ON L8S 4K1, Canada
    Can J Microbiol 49:269-80. 2003
    ..These data show that 13% of pSymB genes have nearest neighbors in species that are not members of the Rhizobiaceae family (including two archaea), and that these likely represent genes that have been involved in horizontal transfer...
  18. doi request reprint High rates of lateral gene transfer are not due to false diagnosis of gene absence
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
    Gene 421:27-31. 2008
    ..All of these factors need to be considered...
  19. ncbi request reprint Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap
    C E Wong
    Department of Biology, University of Waterloo, N2L 3G1, Waterloo ON, Canada
    Plant Mol Biol 58:561-74. 2005
    ..Moreover, Thellungiella is a closer relative of agriculturally important Brassica spp. than Arabidopsis, which may prove valuable in transferring information to crop improvement programs...
  20. ncbi request reprint Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis
    Pradeep Reddy Marri
    Department of Biology, McMaster University, Hamilton, ON, Canada
    Can J Microbiol 52:560-9. 2006
    ..The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges...
  21. ncbi request reprint Codon bias and base composition are poor indicators of horizontally transferred genes
    L B Koski
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 18:404-12. 2001
    ..Hence, atypical nucleotide composition alone is not a reliable indicator of horizontal transmission...
  22. pmc Does gene translocation accelerate the evolution of laterally transferred genes?
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    Genetics 182:1365-75. 2009
    ..Furthermore, more recently acquired genes have a higher proportion of genes on the leading strand, suggesting a strong strand bias of lateral gene transfer...
  23. doi request reprint Assigning sequences to species in the absence of large interspecific differences
    Melanie Lou
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Phylogenet Evol 56:187-94. 2010
    ....
  24. pmc A non-long terminal repeat retrotransposon family is restricted to the germ line micronucleus of the ciliated protozoan Tetrahymena thermophila
    Jeffrey S Fillingham
    Department of Biology, York University, Toronto M3J 1P3, Ontario, Canada
    Eukaryot Cell 3:157-69. 2004
    ..The presence of a repeated transposable element in the genome is consistent with the model that programmed DNA deletion in T. thermophila evolved as a method of eliminating deleterious transposons from the somatic macronucleus...
  25. ncbi request reprint Asymmetrical evolution of cytochrome bd subunits
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
    J Mol Evol 62:132-42. 2006
    ..coli due to their large divergence. Together, the two subunits of cytochrome bd reveal an interesting example of an asymmetric pattern of evolutionary change...
  26. ncbi request reprint Selection and slippage creating serine homopolymers
    Melanie A Huntley
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 23:2017-25. 2006
    ..The polyserine tract within the phosphatidylserine receptor protein is used as an excellent example of one such case...
  27. ncbi request reprint Patterns of bacterial gene movement
    Weilong Hao
    Department of Biology, McMaster University, Hamilton, Ontario, Canada
    Mol Biol Evol 21:1294-307. 2004
    ..This indicates that many of the insertions are specific to each organism and are lost before related species can evolve. Simulations of the process of insertion and deletion, tailored to each phylogeny, support this conclusion...
  28. pmc Evidence for intron capture: an unusual path for the evolution of proteins
    G B Golding
    Department of Biology, McMaster University, Hamilton, ON, Canada
    Proc Natl Acad Sci U S A 91:7506-9. 1994
    ..Via this path a truly unique sequence can be incorporated into an existing protein, leading in time to the evolution of a new, functionally distinct protein...
  29. doi request reprint Gene amelioration demonstrated: the journey of nascent genes in bacteria
    Pradeep Reddy Marri
    Department of Biology, McMaster University, Hamilton, Canada
    Genome 51:164-8. 2008
    ..We use 7 sequenced genomes of Streptococcus pyogenes and 6 sequenced genomes of Staphylococcus aureus to illustrate the action of amelioration on these genomes...
  30. ncbi request reprint Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids
    Kim Wong
    Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
    Funct Integr Genomics 2:274-81. 2002
    ..meliloti chromosome, while the pSymA signature is typical of other alpha-proteobacterial plasmids...
  31. pmc Neurological proteins are not enriched for repetitive sequences
    Melanie A Huntley
    Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    Genetics 166:1141-54. 2004
    ..Codon type homogeneity tends to be favored, suggesting replicative slippage instead of selection as the main force responsible for producing these homopolymers...
  32. pmc An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti
    Alison Cowie
    Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    Appl Environ Microbiol 72:7156-67. 2006
    ..A database containing all the gene expression activities together with a web interface showing the precise locations of reporter fusion junctions has been constructed (www.sinorhizobium.org)...
  33. ncbi request reprint Simple sequence in brain and nervous system specific proteins
    Melanie A Huntley
    Department of Biology, McMaster University, Hamilton, ON, Canada
    Genome 48:291-301. 2005
    ..Determining the function of these histidine-rich regions within brain-specific proteins requires more experimental data...
  34. ncbi request reprint The pattern of amino acid replacements in alpha/beta-barrels
    Antony M Dean
    The Biological Process Technology Institute, University of Minnesota, St Paul, 55108, USA
    Mol Biol Evol 19:1846-64. 2002
    ..A statistical analysis shows that, in all cases, much of the remaining unexplained variation is not attributable to chance and that other, as yet unidentified, causal relations must exist...
  35. ncbi request reprint The selective cause of an ancient adaptation
    Guoping Zhu
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Science 307:1279-82. 2005
    ..Those with only an NAD-dependent IDH never have isocitrate lyase. Hence, the NADP dependence of prokaryotic IDH is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate...
  36. ncbi request reprint A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups
    Zaid Abdo
    Department of Mathematics, University of Idaho, Moscow, Idaho 83844, USA
    Syst Biol 56:44-56. 2007
    ..We believe that this approach makes efficient use of the available information in the data. Our preliminary results indicated that this approach is more accurate than using a simple measure of distance for assignment...
  37. ncbi request reprint Efficient algorithms for counting and reporting segregating sites in genomic sequences
    Manolis Christodoulakis
    Department of Computer Science, King s College London, London, United Kingdom
    J Comput Biol 14:1001-10. 2007
    ....