Joseph P Bielawski

Summary

Affiliation: Dalhousie University
Country: Canada

Publications

  1. pmc Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data
    Le Bao
    Department of Mathematics and Statistics, Dalhousie University Halifax Nova Scotia, Canada
    BMC Evol Biol 7:S5. 2007
  2. pmc Phylogenomic analysis of natural selection pressure in Streptococcus genomes
    Maria Anisimova
    Department of Biology, University College London, London, UK
    BMC Evol Biol 7:154. 2007
  3. ncbi request reprint A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
  4. pmc Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment
    Joseph P Bielawski
    Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
    Proc Natl Acad Sci U S A 101:14824-9. 2004
  5. ncbi request reprint Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events
    Gabriela Aguileta
    University College London, Department of Biology, Darwin Building, Gower Street, London WC1E 6BT, England
    Gene 380:21-9. 2006
  6. ncbi request reprint Gene conversion and functional divergence in the beta-globin gene family
    Gabriela Aguileta
    Department of Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, England
    J Mol Evol 59:177-89. 2004
  7. ncbi request reprint Maximum likelihood methods for detecting adaptive evolution after gene duplication
    Joseph P Bielawski
    Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom
    J Struct Funct Genomics 3:201-12. 2003
  8. doi request reprint Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution
    Le Bao
    Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 25:1995-2007. 2008
  9. pmc Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices
    Katherine A Dunn
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    PLoS ONE 8:e55816. 2013
  10. doi request reprint Reconciling ecological and genomic divergence among lineages of listeria under an "extended mosaic genome concept"
    Katherine A Dunn
    Department of Biology, Dalhousie University, Halifax Nova Scotia, Canada
    Mol Biol Evol 26:2605-15. 2009

Collaborators

Detail Information

Publications26

  1. pmc Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data
    Le Bao
    Department of Mathematics and Statistics, Dalhousie University Halifax Nova Scotia, Canada
    BMC Evol Biol 7:S5. 2007
    ..Given a set of related fixed-effect models, the task of selecting the model that best fits the data is not trivial...
  2. pmc Phylogenomic analysis of natural selection pressure in Streptococcus genomes
    Maria Anisimova
    Department of Biology, University College London, London, UK
    BMC Evol Biol 7:154. 2007
    ..The genus Streptococcus is comprised of a wide variety of both pathogenic and commensal lineages, and we relate our findings to the pre-existing knowledge of Streptococcus virulence factors...
  3. ncbi request reprint A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
    ..Limitations of the new method are discussed...
  4. pmc Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment
    Joseph P Bielawski
    Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
    Proc Natl Acad Sci U S A 101:14824-9. 2004
    ..We suggest that spectral fine-tuning results from the combined effect of amino acids that directly interact with retinal and those that influence the confirmation of the retinal-binding pocket...
  5. ncbi request reprint Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events
    Gabriela Aguileta
    University College London, Department of Biology, Darwin Building, Gower Street, London WC1E 6BT, England
    Gene 380:21-9. 2006
    ..Lastly, phylogenetic analyses do not support a previous report that avian globins are members of a relic lineage of omega globins...
  6. ncbi request reprint Gene conversion and functional divergence in the beta-globin gene family
    Gabriela Aguileta
    Department of Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, England
    J Mol Evol 59:177-89. 2004
    ..Overall, our results suggest that following gene duplications, paralogous copies of beta-globin genes evolved under a nonepisodic process of functional divergence...
  7. ncbi request reprint Maximum likelihood methods for detecting adaptive evolution after gene duplication
    Joseph P Bielawski
    Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom
    J Struct Funct Genomics 3:201-12. 2003
    ..We also comment on the limitations of these methods and discuss directions for further improvements...
  8. doi request reprint Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution
    Le Bao
    Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 25:1995-2007. 2008
    ..In these cases, LiBaC-based methods offer an important addition to a "toolbox" of methods thereby helping to uncover robust evidence for the action of positive selection...
  9. pmc Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices
    Katherine A Dunn
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    PLoS ONE 8:e55816. 2013
    ..We also discuss how the general approach might be employed to improve a variety of mitogenomic-based research activities...
  10. doi request reprint Reconciling ecological and genomic divergence among lineages of listeria under an "extended mosaic genome concept"
    Katherine A Dunn
    Department of Biology, Dalhousie University, Halifax Nova Scotia, Canada
    Mol Biol Evol 26:2605-15. 2009
    ..Based on these findings, we propose an expanded role for natural selection in core-genome evolution under the MGC...
  11. ncbi request reprint Proposed standard nomenclature for the alpha- and beta-globin gene families
    Gabriela Aguileta
    Department of Biology, University College London, London, England
    Genes Genet Syst 81:367-71. 2006
    ....
  12. ncbi request reprint Widespread adaptive evolution in the human immunodeficiency virus type 1 genome
    Wa Yang
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    J Mol Evol 57:212-21. 2003
    ..Furthermore, amino acid residues at exposed positive selection sites were more physiochemically diverse than at buried positive selection sites. Our results demonstrate genomewide diversifying selection acting on the HIV-1...
  13. doi request reprint Detecting the signatures of adaptive evolution in protein-coding genes
    Joseph P Bielawski
    Department of Biology, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
    Curr Protoc Mol Biol . 2013
    ..Each activity includes an explicit analytical protocol based on programs provided by the Phylogenetic Analysis by Maximum Likelihood (PAML) package...
  14. ncbi request reprint Accuracy and power of bayes prediction of amino acid sites under positive selection
    Maria Anisimova
    Department of Biology, Galton Laboratory, University College London, United Kingdom
    Mol Biol Evol 19:950-8. 2002
    ....
  15. doi request reprint Recombination detection under evolutionary scenarios relevant to functional divergence
    Rachael A Bay
    Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
    J Mol Evol 73:273-86. 2011
    ..Based on analysis of both real and simulated datasets we present some guidelines for the investigation of recombination in genes that may have experienced functional divergence...
  16. doi request reprint Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth
    Melissa J Morine
    Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
    J Mol Evol 68:506-15. 2009
    ..These results highlight the biologic relevance of variation in network structure and the potential role of niche breadth in shaping metabolic strategies of efficiency and robustness...
  17. doi request reprint Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary
    Rachael A Bay
    Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
    J Mol Evol 76:205-15. 2013
    ..Although computationally costly, simulations motivated by data in hand are warranted when several aspects of the substitution process are either misspecified or not included in the models upon which the statistical tests were built...
  18. pmc Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium
    Todd J Ward
    Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, U S Department of Agriculture, Agricultural Research Service, 1815 North University Street, Peoria, IL 61604, USA
    Proc Natl Acad Sci U S A 99:9278-83. 2002
    ..Chemotype-specific differences in selective constraint and evidence of adaptive evolution within trichothecene genes are also reported...
  19. ncbi request reprint Adaptive diversification of vomeronasal receptor 1 genes in rodents
    Peng Shi
    Laboratory of Molecular Biology of Domestic Animals and Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology Chinese Academy of Sciences
    J Mol Evol 60:566-76. 2005
    ....
  20. ncbi request reprint Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates
    Gil Zeidner
    Biology Sciences Faculties, Technion Israel Institute of Technology, Haifa 32000, Israel
    Environ Microbiol 7:1505-13. 2005
    ..Overall, these observations raise the possibility that marine viruses serve as a potential genetic pool in shaping the evolution of cyanobacterial photosynthesis...
  21. ncbi request reprint Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation
    Stephane Aris-Brosou
    Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada K1N 6N5
    Gene 378:58-64. 2006
    ..We reanalyze three large data sets to demonstrate the relevance of our results to empirical data analysis...
  22. pmc Portal protein diversity and phage ecology
    Matthew B Sullivan
    Departments of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
    Environ Microbiol 10:2810-23. 2008
    ....
  23. ncbi request reprint Adaptive evolution of multicolored fluorescent proteins in reef-building corals
    Steven F Field
    Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, 32080, USA
    J Mol Evol 62:332-9. 2006
    ..Evolution of such a mechanism would explain both the adaptive diversification of colors and the coevolutionary chase at the putative algae-protein binding interface in coral fluorescent proteins...
  24. ncbi request reprint Novel Proteorhodopsin variants from the Mediterranean and Red Seas
    Gazalah Sabehi
    Department of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
    Environ Microbiol 5:842-9. 2003
    ..These variants could represent functionally divergent paralogous genes, derived from the same or similar species, or orthologous proteorhodopsins that are distributed amongst divergent planktonic microbial taxa...
  25. pmc Mutation patterns of mitochondrial H- and L-strand DNA in closely related Cyprinid fishes
    Joseph P Bielawski
    Center for Biosystematics and Biodiversity, Texas A and M University, College Station, Texas 77843 2258, USA
    Genetics 161:1589-97. 2002
    ..The problem occurs because the rate of any single class of substitution inferred from one strand is actually a sum of rates on two strands. The validity of the likelihood-ratio test is not affected by this problem...
  26. pmc Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
    Matthew B Sullivan
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 4:e234. 2006
    ..This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution...