Joe Bielawski

Assistant Professor

Cross-appointed in the Department of Mathematics & Statistics

Email: j.bielawski@dal.ca


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Recent Submissions

  • Detecting the signatures of adaptive evolution in protein-coding genes. 

    Bielawski, JP. 2013. "Detecting the signatures of adaptive evolution in protein-coding genes.." In Current protocols in molecular biology, .
    The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the processes responsible for generating this variation. Many DNA ...
  • Detecting the signatures of adaptive evolution in protein-coding genes. 

    Bielawski JP, . 2013. "Detecting the signatures of adaptive evolution in protein-coding genes.." Current protocols in molecular biology / edited by Frederick M.Ausubel ...[et al.] Chapter.
    The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the processes responsible for generating this variation. Many DNA ...
  • Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of Listeria monocytogenes Isolates 

    Ward, Todd J., Thomas F. Ducey, Thomas Usgaard, Katherine A. Dunn, et al. 2008. "Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of Listeria monocytogenes Isolates." Applied and Environmental Microbiology 74(24): 7629-7642.
    Listeria monocytogenes is responsible for serious invasive illness associated with consumption of contaminated food and places a significant burden on public health and the agricultural economy. We recently developed a ...
  • Phylogenomic analysis of natural selection pressure in Streptococcus genomes 

    Anisimova, Maria, Joseph Bielawski, Katherine Dunn, and Ziheng Yang. 2007. "Phylogenomic analysis of natural selection pressure in Streptococcus genomes." Bmc Evolutionary Biology 7: 154-154.
    Background: In comparative analyses of bacterial pathogens, it has been common practice to discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic relatives (core genes), and (ii) ...
  • Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts 

    Sullivan, Matthew B., Debbie Lindell, Jessica A. Lee, Luke R. Thompson, et al. 2006. "Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts." Plos Biology 4(8): 1344-1357.
    Cyanophages ( cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express ...
  • Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates 

    Zeidner, G., JP Bielawski, M. Shmoish, DJ Scanlan, et al. 2005. "Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates." Environmental microbiology 7(10): 1505-1513.
    Genes (psbA and psbD) encoding for photosynthetically important proteins were recently found in a number of cultured cyanophage genomes. This phenomenon may be a beneficial trait to the viruses or their photosynthetic ...
  • Proposed standard nomenclature for the alpha- and beta-globin gene families 

    Aguileta, Gabriela, Joseph P. Bielawski, and Ziheng Yang. 2006. "Proposed standard nomenclature for the alpha- and beta-globin gene families." Genes & genetic systems 81(5): 367-371.
    The globin family of genes and proteins has been a recurrent object of study for many decades. This interest has generated a vast amount of knowledge. However it has also created an inconsistent and confusing nomenclature, ...
  • Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation 

    Aris-Brosou, Stephane, and Joseph P. Bielawski. 2006. "Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation." Gene 378: 58-64.
  • Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution 

    Bao, Le, Hong Gu, Katherine A. Dunn, and Joseph P. Bielawski. 2008. "Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution." Molecular biology and evolution 25(9): 1995-2007.
    Models of codon evolution are useful for investigating the strength and direction of natural selection via a parameter for the nonsynonymous/synonymous rate ratio (omega = d(N)/d(S)). Different codon models are available ...
  • Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data 

    Bao, Le, Hong Gu, Katherine A. Dunn, and Joseph P. Bielawski. 2007. "Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data." Bmc Evolutionary Biology 7: 5-S5.
    Background: Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous ...
  • Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary 

    Bay, Rachael A., and Joseph P. Bielawski. 2013. "Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary." Journal of Molecular Evolution 76(4): 205-215.
    Functional shifts during protein evolution are expected to yield shifts in substitution rate, and statistical methods can test for this at both codon and amino acid levels. Although methods based on models of sequence ...
  • Recombination Detection Under Evolutionary Scenarios Relevant to Functional Divergence 

    Bay, Rachael A., and Joseph P. Bielawski. 2011. "Recombination Detection Under Evolutionary Scenarios Relevant to Functional Divergence." Journal of Molecular Evolution 73(5-6): 273-286.
    Recombination can negatively impact methods designed to detect divergent gene function that rely on explicit knowledge of a gene tree. However, we know little about how recombination detection methods perform under ...
  • A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution 

    Bielawski, JP, and ZH Yang. 2004. "A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution." Journal of Molecular Evolution 59(1): 121-132.
    The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One ...
  • Reconciling Ecological and Genomic Divergence among Lineages of Listeria under an "Extended Mosaic Genome Concept" 

    Dunn, Katherine A., Joseph P. Bielawski, Todd J. Ward, Caroline Urquhart, et al. 2009. "Reconciling Ecological and Genomic Divergence among Lineages of Listeria under an "Extended Mosaic Genome Concept"." Molecular biology and evolution 26(11): 2605-2615.
    There is growing evidence for a discontinuity between genomic and ecological divergence in several groups of bacteria. This evidence is difficult to reconcile with the traditional concept that ecologically divergent species ...
  • Randomly amplified polymorphic DNA (RAPD) analysis of Atlantic coast striped bass 

    Bielawski, J. P., and DE Pumo. 1997. "Randomly amplified polymorphic DNA (RAPD) analysis of Atlantic coast striped bass." Heredity 78(1): 32-40.
    Atlantic Coast striped bass exhibit exceptionally low levels of genetic variation. The ability of the randomly amplified polymorphic DNA (RAPD) method to uncover genetic variation in this highly conserved species was ...
  • Adaptive evolution of multicolored fluorescent proteins in reef-building corals 

    Field, SF, MY Bulina, IV Kelmanson, JP Bielawski, et al. 2006. "Adaptive evolution of multicolored fluorescent proteins in reef-building corals." Journal of Molecular Evolution 62(3): 332-U15.
    Here we investigate the evolutionary scenarios that led to the appearance of fluorescent color diversity in reef-building corals. We show that the mutations that have been responsible for the generation of new cyan and ...
  • Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment 

    Bielawski, JP, KA Dunn, G. Sabehi, and O. Beja. 2004. "Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment." Proceedings of the National Academy of Sciences of the United States of America 101(41): 14824-14829.
    Proteorhodopsin, a retinal-binding protein, represents a potentially significant source of light-driven energy production in the world's oceans. The distribution of photochemically divergent proteorhodopsins is stratified ...
  • Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices 

    Dunn, Katherine A., Wenyi Jiang, Christopher Field, and Joseph P. Bielawski. 2013. "Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices." Plos One 8(1): 55816-e55816.
    Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of ...
  • Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon 

    Garvin, Michael R., Joseph P. Bielawski, and Anthony J. Gharrett. 2011. "Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon." Plos One 6(9): 24127-e24127.
    The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial ...
  • Evolutionary rate variation among vertebrate beta globin genes: Implications for dating gene family duplication events 

    Aguileta, Gabriela, Joseph P. Bielawski, and Ziheng Yang. 2006. "Evolutionary rate variation among vertebrate beta globin genes: Implications for dating gene family duplication events." Gene 380(1): 21-29.
    A comprehensive dataset of 62 globin gene sequences from various vertebrates was compiled to test the molecular clock, and to estimate dates of gene duplications. We found that evolution of the globin family of genes is ...

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