Brian Golding, Ph.D.

Telephone: (905) 525-9140

Office: LSB-533 Ext 24829

Lab: LSB-522 Ext 27236

Email: golding@mcmaster.ca

Website: http://helix.biology.mcmaster.ca/

Interests & Activities

Molecular evolution, DNA sequence analysis, phylogenetics, population genetics, Bioinformatics.

Publications
  • Lenz, C., Haerty, W., Golding, G.B. 2014. Increased substitution rates surrounding low-complexity regions within primate proteins. Genome Biology and Evolution. In press.
  • Huang, Y.F., Golding, G.B. 2014. Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structure. PLoS Computational Biology. 10:e1003429.
  • Devault, A.M., Golding, G.B., Waglechner, N., Enk, J.M., Kuch, M., Tien, J.H., Shi, M., Fisman, D.N., Dhody, A.N., Forrest, S., Bos, K.I., Earn, D.J., Holmes, E.C., Poinar, H.N. 2014. Second-pandemic strain of Vibrio cholera from the Philadelphia cholera outbreak of 1849. New England Journal of Medicine. 370: 334-340.
  • Whelan, F.J., Yap, N.V., Surette, M.G., Golding, G.B., Bowdish, D.M. 2013. A guide to bioinformatics for immunologists. Frontiers in Immunology. 4:416.
  • Champigny, M.J., Sung, W.W., Catana, V., Salwan, R., Summers, P.S., Dudley, S.A., Provart, N.J., Cameron, R.K., Golding, G.B., Weretilnyk, E.A. (2013) RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. BMC Genomics 14:578.
  • Porter TM, Golding GB, King C, Froese D, Zazula G, Poinar HN. 2013. Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Molecular Ecology Resources. 13: 798-810.
  • Lenz, C., W. Haerty, G.B. Golding, 2014. Increased substitution rates surrounding low-complexity regions within primate proteins. Genome Biol Evol. 6:655-665.
  • Carviel, J.L., D.C. Wilson, M. Isaacs, P. Carella, V. Catana, B. Golding, E.A. Weretilnyk, R.K. Cameron, 2014. Investigation of Intercellular Salicylic Acid Accumulation during Compatible and Incompatible Arabidopsis- Pseudomonas syringae Interactions Using a Fast Neutron-Generated Mutant Allele of EDS5 Identified by Genetic Mapping and Whole-Genome Sequencing. PLoS ONE 9(3): e88608.
  • Porter, T., J. Gibson, S. Shokralla, D. Baird, G.B. Golding, M. Hajibabaei, 2014. Rapid and accurate taxonomic classification of insect (Class Insecta) +cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier. Mol. Ecol. Res. doi: 10.1111/1755-0998.12240
  • D. M. Wagner, J. Klunk, M. Harbeck, A. Devault, N. Waglechner, J.W. Sahl, J. Enk, D.N. Birdsell, M. Kuch, C. Lumibao, D. Poinar, T. Pearson, M. Fourment, B. Golding, J.M. Riehm, D.J.D. Earn, S. DeWitte, J-M. Rouillard, G. Grupe, I. Wiechmann, J.B. Bliska, P.S. Keim, H.C. Scholz, E.C. Holmes, H. Poinar, 2014 The Plague of Justinian was caused by a ‘dead-end’ emergence of Yersinia pestis. The Lancet Infectious Diseases 14:319-326
  • Y. Huang and G.B. Golding 2013. Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures. PLoS Computational Biology, 10(1):e1003429.
  • Whelan, F.J., N. Yap, M.G. Surette, G.B. Golding, D.M.E. Bowdish, 2013. A guide to bioinformatics for immunologists. Frontiers in Molecular Innate Immunity, 4:416.
  • Devault, A.M., G.B. Golding, N. Waglechner, J. Enk, M. Kuch, J.H. Tien, M. Shi, D.N. Fisman, A.N. Dhody, S. Forrest, K. Bos, D.J.D. Earn, E.C. Homes, and H.N. Poinar, 2013. Second-Pandemic Strain of Vibrio cholerae from the Philadelphia Cholera Outbreak of 1849. New England J. Medicine, 370: 334-340.
  • Champigny, M.J., W.L. Sung, V. Catana, R. Salwan, P.S. Summers, S.A. Dudley, N.J. Provart, R.K. Cameron, G.B. Golding, E.A. Weretilnyk, 2013. RNA-Seq effectively monitors gene expression in Thellungiella salsuginea plants growing in an extreme natural habitat and in controlled growth cabinet conditions. BMC Genomics, 14:578
  • Porter, T.M., G.B. Golding, C. King, D. Froese, G. Zazula, H.N. Poinar, 2013. Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Molecular Ecology Resources 13: 798-810
  • Ilie, L., Mohamadi, H., Golding, G.B., Smyth, W.F. 2013. BOND: Basic OligoNucleotide Design. BMC Bioinformatics 14: 69
  • Whelan, F.J., Meehan, C.J., Golding, G.B., McConkey, B.J., Bowdish, D.M. 2012. BMC Evol Biol 12:227. doi: 10.1186/1471-2148-12-227
  • Guevara, D.R., M.J. Champigny, A. Tattersal, J. Dedrick, C.E. Wong, Y. Li, A. Labbe, C.L. Ping, Y. Wang, P. Nuin, G.B. Golding, B.E. McCarry, P.S. Summers, B.A. Moffatt, E.A. Weretilnyk, 2012.Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity. BMC Plant Biology doi: 10.1186/1471-2229-12-175
  • Lou, M. and G.B. Golding 2012. The effect of sampling from subdivided populations population substructure on species identification with DNA barcodes using a Bayesian statistical approach. Molecular Phylogenetics and Evolution 65:765-73
  • Porter, T. and G.B. Golding 2012. Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method Primer Choice and Error. PLoS ONE 7(4): e35749.
  • Y. Huang and G.B. Golding 2012. Inferring Sequence Regions under Functional Divergence in Duplicate Genes. Bioinformatics 28:176-183.
  • K.I. Bos, V.J. Schuenemann, G.B. Golding, H. Burbano, N. Waglechner, B.K. Coombes, J.B. McPhee, S.N. DeWitte, M. Meyer, S. Schmedes, J. Wood, D.J.D. Earn, D.A. Herring, P. Bauer, H.N. Poinar, J. Krause 2011. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478:506-510. Errata 2011 480:278.
  • A.M. MacLean, W. Haerty,  G.B. Golding, T.M. Finan 2011. LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti Microbiology 157: 2522-2533.
  • Porter, T. and G.B. Golding 2011. Are similarity or phylogenetic-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? New Phytologist 192: 775-782.
  • V.M. DʼCosta, C.E. King, L. Kalan, M. Morar, W. Sung, C. Schwarz, D. Froese, G. Zazula, F. Calmels, R. Debruyne, G.B. Golding, H.N. Poinar, G.D. Wright 2011.  Antibiotic Resistance is Ancient. Nature 477: 457-461.
  • Haerty, W. and G.B. Golding 2011.  Increased polymorphism near low complexity sequences across the genomes of Plasmodium falciparum isolates.  Genome Biol. Evol. 3: 539-550.
  • Sun, S., B.J. Evans and G.B. Golding 2011. Patchy-tachy leads to false positives for recombination. Mol. Biol. Evol. 28: 2549-2459.
  • Lunzer, M., G.B. Golding and A.M. Dean 2011. Pervasive cryptic epsistasis in molecular evolution.  PLoS Genetics (in press August).
  • Haerty, W. and G.B. Golding 2010.  Low complexity sequences and single amino acid repeats: Not just “junk” peptide sequences.  Genome (in press July).
  • Hao, W. and G.B. Golding 2010. Inferring bacterial genome flux while considering truncated genes. Genetics (in press June 4). doi:10.1534/genetics.110.118448
  • Haerty, W. and G.B. Golding 2010.  Genome-wide evidence for selection acting on single amino acid repeats.  Genome Research 20: 755-760. doi:10.1101/gr.101246.109
  • Lou, M. and G.B. Golding 2010.  Assigning sequences to species in the absence of large interspecific differences.  Molecular Phylogenetics and Evolution 56:187-194. http://dx.doi.org/10.1016/j.ympev.2010.01.002
  • Albu, M., X.J. Min, G.B. Golding and D. Hickey 2009. Nucleotide substitution bias within the genus Drosophila affects the pattern of proteome evolution. Genome Biol Evol 2009:288-293.
  • Hao, W. and G.B. Golding 2009. Does gene translocation accelerate the evolution of laterally transferred genes? Genetics 182: 1365-1375. % (http://dx.doi.org/10.1534/genetics.109.104216)
  • Haerty, W. and G.B. Golding 2009. Similar selective factors affect both between gene and between exon divergence in Drosophila. Mol. Biol. Evol.  26: 859-66. % doi: 10.1093/molbev/msp006
  • Albu, M., X.J. Min, D. Hickey, and G.B. Golding 2008. Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selection. Mol. Biol. Evol. 25: 2521-2524.
  • Hao, W. and G.B. Golding 2008. High rates of lateral gene transfer are not due to false diagnosis of gene absence. Gene 421: 27-31 (http://dx.doi.org/10.1016/j.gene.2008.06.015).
  • Hao, W. and G.B. Golding 2008. Uncovering Rate Variation of Lateral Gene Transfer during Bacterial Genome Evolution. BMC Genomics 9:235 (doi:10.1186/1471-2164-9-235).
  • Hao, W. and G.B. Golding 2008. High rates of lateral gene transfer are not due to false diagnosis of gene absence. Gene (in press May 2008).
  • Hao, W. and G.B. Golding 2008. Uncovering Rate Variation of Lateral Gene Transfer during Bacterial Genome Evolution. BMC Genomics in press, (in press May 2 2008).
  • Marri, P.R. and G.B. Golding 2008. Gene Amelioration Demonstrated: The Journey of Nascent Genes in Bacteria. Genome 51:164-168.
  • Lou, M. and G.B. Golding 2007. Fingerprint: Visual depiction of variation in multiple sequence alignments. Molecular Ecology Notes 7:908-914.
  • Christodoulakis, M., G.B. Golding, C.S. Iliopoulos, Y.J. Ardila, W.F. Smyth 2007. Efficient algorithms for counting and reporting segregating sites in genomic sequences. J. Computational Biology 14:1001-1010.
  • Higgs, P., Hao, W. and G.B. Golding 2007. Identificalton of conflicting selective effects on highly expressed genes. Evolutionary Bioinformatics 2: 1-13.
  • Abdo, Z. and G.B. Golding 2007. A Step Toward Barcoding Life: A Model Based, Decision Theoretic Method to Assign Genes to Pre-existing Species Groups. Systematic Biology 56: 44-56.
  • Marri*, P.R. Hao*, W. and G.B. Golding 2007. Adaptive evolution: The role of laterally transferred genes. BMC Evolutionary Biology 7: s8. * joint first authors.
  • Cowie, A., Cheng, J., Sibley, C.D., Fong, Y., Zaheer, R., Patten, C.L., Morton, R.M., Golding, G.B., and T.M. Finan. 2006. An Integrated Approach to Functional Genomics: Construction of a Novel Reporter Gene Fusion Library of Sinorhizobium meliloti. Appl Environ Microbiology72:7156-7167.
  • Marri, P.R., J.P. Bannantine, and G.B. Golding, 2006. Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer. FEMS Microbiol. Rev. 30: 906-925.
  • Marri*, P.R. Hao*, W. and G.B. Golding 2006. Gene Gain and Gene Loss in Streptococcus: Is it Driven by Habitat? Mol. Biol. Evol. 23: 2379-2391, * joint first authors.
  • Huntley, M.A. and G.B. Golding 2006. Selection and slippage creating serine homopolymers. Mol. Biol. Evol. 23: 2017-2025.
  • Hao, W. and G.B. Golding 2006. The fate of laterally transferred genes: Life in the fast lane to adaptation or death. Genome Research 16: 636-643.
  • Wong, C.E., Y. Li, A. Labbe, D. Guevara, P. Nuin, B. Whitty, C. Diaz, G.B. Golding, G.R. Gray, E.A. Weretilnyk, M. Griffith, and B.A. Moffatt, 2006. Transcriptional Profiling Implicates Novel Interactions Between Abiotic Stress and Hormonal Responses in Thellungiella, a Close Relative of Arabidopsis.Plant Physiology, 140:1437-1450.
  • Marri, P.R., J.P. Bannantine, M.L. Paustian and G.B. Golding, 2006. Lateral Gene Transfer in Mycobacterium avium subspecies paratuberculosis. Canadian Journal of Microbiology, 52:560-569.
  • Hao, W. and G.B. Golding 2006. Asymmetrical Evolution of Cytochrome bd Subunits. J. Mol. Evol. 62:132-142.
  • C.E. Wong, Y. Li, B.R. Whitty, C. Dýaz-Camino, S.R. Akhter, J.E. Brandle,G.B. Golding, E.A. Weretilnyk, B.A. Moffatt and M. Griffith, 2005. Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. Plant Molecular Biology 58:561-574.
  • G. Zhu, G.B. Golding and A.M. Dean, 2005. Towards reconstructing an ancient adaptive event. Science 307:1279-1282.
  • Huntley, M., S. Mahmood and G.B. Golding, 2005. Simple sequence in proteins. Genome 48: 291-301.
  • Huntley, M. and G.B. Golding, 2004. Neurological proteins are not enriched for repetitive sequences. Genetics 166: 1141-1154.
  • Hao, W. and G.B. Golding, 2004. Patterns of bacterial gene movement.Mol. Biol. Evol. 21: 1294-1307.
  • Fellingham, J.S., T.A. Thing, N. Vythilingum, A. Keuroghlian, D. Bruno,G.B. Golding, and R.E. Pearlman, 2003. A non-LTR retrotransposon family is restricted to the germ-line micronucleus in the ciliated protozoan Tetrahymena thermophila. Eukaryotic Cell 3: 157-169.
  • Wong, K. and G.B. Golding, 2003. A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history. Can. J. of Microbiol. 49: 269-280.
  • Wong,K., T.M. Finan, and G.B. Golding, 2002. Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids. Functional and Integrative Genomics 2: 274-281.
  • Dean, A.M., C. Neuhauser, E. Grenier and G.B. Golding, 2002. The pattern of amino acid replacements in ./.-barrels. Mol. Biol. Evol. 19: 1846-1864.
  • Golding, G.B. 2002. Reconstructing the prior probabilities of allelic phylogenies. Genetics 161: 889-896.
  • Huntley, M.A. and G.B. Golding, 2002. Simple sequences are rare in the Protein Data Bank. Proteins: Structure, Function, and Genetics 48:134-140.
  • Finan, T.M., S.Weidner, K.Wong, J. Buhrmester, P. Chain, F.J. Vorh¨olter, I. Hernandez-Lucas, A. Becker, A. Cowie, J. Gouzy, B. Golding and A. P¨uhler, 2001. The complete sequence of the 1,683 kilobase pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc. Natl. Acad. Sci. USA 98: 9889-9894.
  • Galibert, F., T.M. Finan, S.R. Long, A. P¨uhler, P. Abola, F.Ampe, F. Barloy-Hubler, M.J. Barnett, A. Becker, P. Boistard, G. Bothe, M. Boutry, L. Bowser, J. Buhrmester, E. Cadieu, D. Capela, , P. Chain, A. Cowie, R.W. Davis, S. Dr´eano, N.A. Federspiel, R.F. Fisher, S. Gloux, T. Godrie, A. Goffeau, B. Golding, J. Gouzy, M. Gurjal, I. Hernandez-Lucas, A. Hong, L. Huizar, R.W. Hyman, T. Jones, D. Kahn, M.L. Kahn, S. Kalman, D.H. Keating, , E. Kiss, C. Komp, V. Lelaure, D.Masuy, C. Palm,M.C. Peck, T.MPohl, D. Portetelle, B. Purnelle, U. Ramsperger, R. Surzycki, P. Th´ebault, M. Vandenbol, F.-J. Vorh¨olter, S. Weidner, D.H. Wells, K. Wong, K.-C. Yeh, and J. Batut, 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668-672.
  • Koski, L.B. and G.B. Golding, 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52: 540-542.
  • Koski, L.B., R.A. Morton, and G.B. Golding, 2001. Codon bias and base composition are poor indicators of horizontally transferred genes.Mol.Biol.Evol.18: 404-412.
  • Chain, P., A. Cowrie, I. Hernandez-Lucas, G.B. Golding, and T.M. Finan, 2000. oriT-Directed Cloning of Defined Large Regions from Bacterial Genomes: Identification of the Sinorhizobium meliloti pExo Megaplasmid Replicator Region. Journal of Bacteriology 182: 5486-5495.
  • Huntley, M. and G.B. Golding, 2000. Evolution of simple sequence in proteins. J. Mol. Evol. 51: 131-140.
  • Dean, A.M. and G.B. Golding, 2000. Enzyme evolution explained (sort of). pp 6-17 in Pacific Symposia on Biocomputing in Protein Evolution and Structural Genomics. World Scientific Publ. Co.
  • Gray, M.W., G. Burger, R. Cedergren, G.B. Golding, C. Lemieux, D. Sankoff, M. Turmel, and B.F. Lang. 1999. A genomics approach to mitochondrial evolution. Biological Bulletin 196, 400-403.
  • Golding, G.B. 1999. Simple sequence is abundant in eukaryotic proteins. Protein Science 8: 1358-1361.
  • Riberio, S. and Golding, G.B. 1998. The mosaic nature of the eukaryotic nucleus. Mol. Biol. Evol. 15: 779-788.
  • Golding, G.B., and A.M. Dean, 1998. The structural basis of molecular adaptation. Mol. Biol. Evol. 15: 355-369.
  • Gray, M.W., B.F. Lang, R. Cedergren, G.B. Golding, C. Lemieux, D. Sankoff, M. Turmel, N. Brossard, E. Delage, T.G. Littlejohn, I. Plante, P. Rioux, D. Saint-Louis, Y. Zhu and G. Burger, 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Research 26: 865-878.
  • Hartmann, M., and G.B. Golding, 1998. Searching for substitution rate heterogeneity in sequences. Mol. Phylo. Evol. 9: 64-71.
    Other referred publications:

    1. Hao, W. and G.B. Golding 2010. Inferring bacterial genome flux while considering truncated genes. Genetics 186: 411-426.
    2. Haerty, W. and G.B. Golding 2010.  Genome-wide evidence for selection acting on single amino acid repeats.  Genome Research 20: 755-760.
    3. Lou, M. and G.B. Golding 2010.  Assigning sequences to species in the absence of large interspecific differences.  Molecular Phylogenetics and Evolution 56:187-194.
Research

Our research interests are in the area of bioinformatics, molecular evolution and DNA sequence analysis. Our research attempts to understand how the processes of evolution act to cause the changes actually observed between molecules, between genes and between genomes. The recent advances in molecular genetics are providing a storm of new data on DNA sequences, on gene structure and higher order genomic structure. However, the implications of these new data are not always clear. This area of scientific inquiry is called bioinformatics and is a relatively new inter-disciplinary field between biology, computer science and mathematics.
We make use of computer based analysis, statistical analysis and mathematical models to answer broad questions about the biology of all organisms. We are presently investigating …

  1. the frequency and properties of genes that have been horizontally transferred between bacterial species. We are developing meth ods to detect these unusual events and to measure their extent of transfer.
  2. we are uncovering the determinants of the rates of amino acid replacements as they relate to the three-dimensional structure of proteins. This has involved the development of new statistical methods to measure evolutionary signal across a potentially large phylogenetic history.
  3. we are determining the properties and determinants of simple repeats within individual proteins. This has included demonstrating that these repeats can form a significant pro- portion of the genomic protein sequence.
  4. we are involved in the creation of several genomic databases and are involved in several genomics projects including the Barcode of Life Project. Individual projects change over time but they are united by a consistent, broad interest in the fields of genomics, bioinformatics and molecular evolution.
    Click here to go to my web site.