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Joseph Bielawski

ASSOCIATE PROFESSOR

BSc (Southampton)
MA (Hofstra)
PhD (Texas A&M)
Post doctoral fellow: University College London, UK

  • Teaching & Research
  • Publications
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  • Teaching & Research
    adaptive evolution, molecular evolution, molecular phylogenetics, genomics

    bielawaskiam an associate professor cross-appointed in the Departments of Biology (75%) and Mathematics & Statistics (25%) at Dalhousie University (Halifax, NS). My PhD is in Genetics, from Texas A&M University, and I did my posdoctoral training at the University College London (UCL) under Dr. Ziheng Yang in the area of computational molecular evolution.

    I am broadly interested in statistical modeling of genes, genomes and metagenomes. My research group employs models to investigate the process of functional divergence from the gene level to the metagenome level. My current work involves novel Bayesian models dedicated to metagenome data.

    Research interests:

    Statistical modeling of molecular evolution: Research within this field is focused on (1) improving Markov models of codon and protein evolution, (2) assessment of model performance, and (3) combining such models with data mining methods for the purpose of genome-scale data analysis. The majority of the work has been with codon models, and my work in this area has had considerable influence on how statistical methods are used to detect adaptive molecular evolution.

    Microbial meta-genomics and eco-genomics: Research in this area utilizes statistical modeling to investigate the process of functional divergence in microbes. This research is driven by biological issues, and takes full advantage of both the power provided by the growing numbers of complete genomes from closely related prokaryotes and the large-scale datasets for uncultivable microorganisms that are being generated via environmental genomic methods. Current efforts are devoted to building novel Bayesian models for analyzing (1) microbial community structure and (2) the latent metabolic capacity of microbial communities. Model development is driven by pressing questions in the fields of human micorbiomics and marine microbial metagenomics.

    Simplex image
    This image portrays how the communities of microbes living in carnivores and herbivores differ in terms of their metabolic capacity.

    Modeling codon and amino acid evolution:

    This work involves extension and development of codon and protein models. One area of interest is developing realistic ways to model the effect of physiochemical properties on substitution probabilities among codons and amino acids. Empirical surveys are used to guide model development.
    Selected Publications

    Bay RA, Bielawski JP. (2013). Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary. J Mol Evol. 2013 Apr;76(4):205-15. doi: 10.1007/s00239-013-9549-0. Epub 2013 Feb 27. PubMed PMID: 23443835.

    Bielawski JP. (2013). Detecting the signatures of adaptive evolution in protein-coding genes. Curr Protoc Mol Biol. 2013 Jan; Chapter 19:Unit 19.1.. doi: 10.1002/0471142727.mb1901s101. PubMed PMID: 23288462.

    Dunn KA, Jiang W, Field C, Bielawski JP. (2013). Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices. PLoS One. 2013;8(1):e55816. doi: 10.1371/journal.pone.0055816. Epub 2013 Jan 31. PubMed PMID: 23383286; PubMed Central PMCID: PMC3561347.

    Bay RA, Bielawski JP. (2012). Recombination detection under evolutionary scenarios relevant to functional divergence. J Mol Evol. 2011 Dec;73(5-6):273-86. doi: 10.1007/s00239-011-9473-0. Epub 2012 Jan 1. PubMed PMID: 22210457.

    Garvin MR, Bielawski JP, Gharrett AJ. (2011). Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon. PLoS One. 2011;6(9):e24127. doi: 10.1371/journal.pone.0024127. Epub 2011 Sep 28. PubMed PMID: 21969854; PubMed Central PMCID: PMC3182164.

    Dunn KA, Bielawski JP, Ward TJ, Urquhart C, Gu H. (2009). Reconciling ecological and genomic divergence among lineages of listeria under an “extended mosaic genome concept”. Mol Biol Evol. 2009 Nov;26(11):2605-15. doi: 10.1093/molbev/msp176. Epub 2009 Aug 10. PubMed PMID: 19666992.

    Morine MJ, Gu H, Myers RA, Bielawski JP. (2009). Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth. J Mol Evol. 2009 May;68(5):506-15. doi: 10.1007/s00239-009-9226-5. Epub 2009 Apr 14. PubMed PMID: 19365645.

    Ward TJ, Ducey TF, Usgaard T, Dunn KA, Bielawski JP. (2008). Multilocus genotyping assays for single nucleotide polymorphism-based subtyping of Listeria monocytogenes isolates. Appl Environ Microbiol. 2008 Dec;74(24):7629-42. doi: 10.1128/AEM.01127-08. Epub 2008 Oct 17. PubMed PMID: 18931295; PubMed Central PMCID: PMC2607178.

    Sullivan MB, Coleman ML, Quinlivan V, Rosenkrantz JE, Defrancesco AS, Tan G, Fu R, Lee JA, Waterbury JB, Bielawski JP, Chisholm SW. (2008). Portal protein diversity and phage ecology. Environ Microbiol. 2008 Oct;10(10):2810-23. doi: 10.1111/j.1462-2920.2008.01702.x. Epub 2008 Jul 31. Erratum in: Environ Microbiol. 2011 Oct;13(10):2832. PubMed PMID: 18673386; PubMed Central PMCID: PMC2657995.

    Bao L, Gu H, Dunn KA, Bielawski JP. (2008). Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution. Mol Biol Evol. 2008 Sep;25(9):1995-2007. doi: 10.1093/molbev/msn145. Epub 2008 Jun 26. PubMed PMID: 18586695.

    Bao L, Gu H, Dunn KA, Bielawski JP. (2007). Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data. BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S5. PubMed PMID: 17288578; PubMed Central PMCID: PMC1796614.

    Aguileta G, Bielawski JP, Yang Z. (2006). Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes Genet Syst. 2006 Oct;81(5):367-71. PubMed PMID: 17159299.

    Aguileta G, Bielawski JP, Yang Z.(2006). Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene. 2006 Sep 15;380(1):21-9. Epub 2006 May 4. PubMed PMID: 16843621.

    Aris-Brosou S, Bielawski JP. (2006). Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation. Gene. 2006 Aug 15;378:58-64. Epub 2006 May 22. PubMed PMID: 16797879.

    Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. (2006). Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol. 2006 Jul;4(8):e234. PubMed PMID: 16802857; PubMed Central PMCID: PMC1484495.

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