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group:kathy:home [2020/09/09 10:59] (current) kathy |
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- | **Research associate - Bielawski Research Group** | + | **Education |
- | * Ph.D. Wildlife and Fisheries Sciences, | + | * Ph.D. 2001 Texas A&M University |
- | * M.A. Biology, | + | * M.A. 1994 Hofstra University |
- | * B.S. Biology, | + | * B.S. 1990 Long Island University Southampton |
+ | **Training ** | ||
+ | * Research Associate, Division of Oncology and Haematology, | ||
+ | * Research Associate, Department of Pediatrics, Dalhousie University, 2019; Supervisor: Ketan Kulkarni & Johan Van Limbergen | ||
+ | * Research Associate, Department of Biology, Dalhousie University, 2017-2019; Supervisor: Joseph Bielawski & Johan Van Limbergen | ||
+ | * Research Associate, Department of Biology, Dalhousie University, 2013-2017; Supervisor: Joseph Bielawski | ||
+ | * Tula foundation Post-Doctoral Research Fellow, Department of Biology, Dalhousie University, 2007-2013 | ||
+ | * NSERC Post-Doctoral Research Fellow, Department of Biology, Dalhousie University, 2006-2007 | ||
+ | * Genome Atlantic Post-Doctoral Research Fellow, Department of Biology, Dalhousie University, 2003-2006 | ||
+ | * Post-Doctoral Research Fellow, Department of Biology, University College London, UK, 1999-2003 | ||
**Research Interests** | **Research Interests** | ||
- | My current research | + | My current research |
+ | **Publications** | ||
+ | Dunn KA, Connors J, Bielawski JP, Nearing JT, Langille MGI, Van Limbergen J, Fernandez CV, Mac Donald T, Kulkarni K. The relationship between the gut microbiome and changes in serum asparaginase levels in children undergoing treatment for acute lymphoblastic leukemia. | ||
+ | Cui TT, Dawson T, McLatchie S, Dunn KA, Bielawski JP, Walsh D. Modelling free-living and particle-associated bacterial assemblages across the deep and hypoxic Lower St. Lawrence Estuary 2020 accepted mSphere | ||
+ | Jones CMA, Moore-Connors J, Dunn KA, Bielawski JP, Comeau AM, Langille MGI, Van Limbergen J. Bacterial taxa and functions are predictive of sustained remission following exclusive enteral nutrition in pediatric Crohn’s disease Inflammatory Bowel Disease 2020 izaa001 | ||
- | **Publications** | + | Connors J*, Dunn KA*, Allott J, BandsmaR, NobleA, Rashid M, Otley AR, Bielawski JP, Van Limbergen J. The Relationship Between Bile Acids and Gut Community Structure in Pediatric Crohn’s Disease ISME 2020 Mar; |
+ | |||
+ | Levine A, Wine E, Assa A, Sigall Boneh R, Shaoul R, Kori M, Cohen S, Peleg S, Shamali H, On A, Millman P, Abramas L, Ziv-Baran T, Grant S, Abitbol G, Dunn KA, Bielawski JP, Turner D, Van Limbergen. Crohn’s Disease Exclusion Diet Plus Partial Enteral Nutrition Induces Sustained Remission in a Randomized Controlled Trial Gastroenterology 2019 Aug; | ||
+ | |||
+ | Dunn KA, Kenney T, Gu H, Bielawski J. 2019. Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates. BMC Evolutionary Biology 19(1):22. DOI: 10.1186/ | ||
+ | |||
+ | Dunn KA, Andrews K, Bashwih R, Bielawski J. 2018. Bayesian Inference of Microbial Community Structure from Metagenomic data using BioMiCo. In: Beiko R, Hsiao W, Parkinson J, editors. Microbiome Analysis: Methods and Protocols. 1st In Pr. Totowa, NJ: Humana Press. | ||
+ | Douglas GM, Hansen R, Jones C, Dunn KA, Comeau AM, Bielawski JP, El-Omar EM, Russell RK, Hold G, Langille MGI, Van Limbergen J. 2018 Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn' | ||
+ | |||
+ | Dunn KA, Moore-Connors J, MacIntyre B, Stadnyk A, Thomas NA, Noble A, Mahdi G, Rashid M, Otley A, Bielawski JP, Van Limbergen J. 2016. Early changes in microbial community structure are associated with sustained remission after nutritional treatment of pediatric Crohn’s disease. Inflammatory Bowel Disease. | ||
+ | |||
+ | Dunn KA, Moore-Connors J, MacIntyre B, Stadnyk A, Thomas NA, Noble A, Mahdi G, Rashid M, Otley A, Bielawski JP, Van Limbergen J. 2016. The gut microbiome of pediatric Crohn’s disease differs from healthy controls in genes that can influence the balance between a healthy and dysregulated immune response. | ||
+ | |||
+ | Baker JL, Dunn KA, Mingrone J, Wood BA, Karpinshi BA, Sherwood CC, Wildman DE, Maynard TM, Bielawski JP. 2016. Functional divergence of the Nuclear receptor NR2C1 as a modulator of pluripotentiality during Hominid evolution. Genetics. 203(2): | ||
+ | |||
+ | Moore-Connors J.M., Dunn K.A., Bielawski J.P., Van Limbergen J. 2016. Novel strategies for applied metagenomics. Inflammatory Bowel Disease. 22(3): | ||
+ | |||
+ | Xu X, Dunn KA, Field C. 2015. A Robust ANOVA approach to estimating a phylogeny from multiple genes. Molecular Biology Evolution. 32(8): | ||
+ | |||
+ | Shafiei M, Dunn KA, Boon E, MacDonald SM, Walsh DA, Gu H, Bielawski J.P., 2015. BioMiCo: a supervised Bayesian model for inference of microbial community structure. Microbiome. 3:3:8. | ||
+ | |||
+ | El-Swais H, Dunn KA, Bielawski JP, Li WWK, Walsh D. 2014. Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton: | ||
+ | |||
+ | Shafiei M, Dunn KA, Chipman H, Gu H, Bielawski JP. 2014. BiomeNet: A Bayesian model for inference of metabolic divergence among microbial communities. PLoS Computational Biology. 10(11): | ||
+ | |||
+ | Dunn KA, Jiang W, Field C, Bielawski JP. 2013. Improving evolutionary models in mitochondrial protein data with site-class specific amino acid exchangeability matrices. PLoS ONE 8(1): e55816 | ||
+ | |||
+ | Gu, H, Dunn KA, Bielawski JP. 2011. Likelihood based clustering (LiBaC) for codon models. in Codon Evolution (Cannarozzi GM, Schneider A, eds.). Oxford University Press. | ||
+ | |||
+ | Rowe DL, Dunn KA, Adkins RM, Honeycutt RL. 2010. Molecular clock keeps dispersal hypothesis afloat: evidence for trans-Atlantic rafting by rodents. Journal of biogeography. 37: | ||
+ | |||
+ | 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. | ||
+ | |||
+ | Ward TJ, Ducey TF, Usgaard T, Dunn KA, Bielawski JP. 2008. A multilocus genotyping assay for SNP-based subtyping of Listeria monocytogenes. | ||
+ | |||
+ | 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 molecular evolution. | ||
+ | |||
+ | Anisimova M, Bielawski JP, Dunn KA, Yang Z. 2007. Phylogenomic analysis of natural selection pressure in Streptococcus. | ||
+ | |||
+ | Hurley# IA, Lockridge Mueller# R, Dunn# KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG, Coates MI. 2007. A new time-scale for ray-finned fish evolution. Proceedings Royal Soceity B. 274: | ||
+ | |||
+ | 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 Evolutionary Biology. 7:S5 | ||
+ | |||
+ | Bielawski JP, Dunn KA, Sabehi G, Béjà O. 2004. Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proceedings of the National Academy of Science. 101: | ||
+ | |||
+ | Dunn KA, McEachran JD, Honeycutt RL. 2003. Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: | ||
- | Dunn, K.A., W. Jiang, C. Field, | + | Dunn KA, Bielawski JP, Yang Z. 2001. Rates and patterns of synonymous substitutions in Drosophila: implications for translational selection. Genetics. 157:295-305. |
- | Gu, H., K.A. Dunn, and J.P. Bielawski. 2011. Likelihood based clustering (LiBaC) for codon models. in Codon Evolution (G.M. Cannarozzi | + | Bielawski JP, Dunn KA, Yang Z. 2000. Rates of nucleotide substitution |
- | Rowe, D.L., K.A. Dunn, R.M. Adkins, and R.L. Honeycutt. 2010. Molecular clock keeps dispersal hypothesis afloat: evidence for trans-Atlantic rafting by rodents. Journal of biogeography. 37:305-324. | + | McEachran JD, Dunn KA. 1998. Phylogenetic analysis of skates, a morphologically conservative clade of elasmobranchs (Chondrichthyes: Rajidae). Copeia. 2:271-290. |
- | Dunn, K.A., J.P. Bielawski, T.J. Ward, C. Urquhart and H. Gu. 2009. Reconciling ecological and genomic divergence among lineages of Listeria under an extended mosaic genome concept. | + | Morrissey JF, Dunn KA, Mulé F. 1997. The phylogenetic position of Megachasma pelagios inferred from mtDNA sequence data. Pages 33-37 in Biology of the megamouth shark (Yano K, Morrissey JF, Yabumoto Y, Nakaya K, eds.). Tokai University Press, Tokyo, Japan. |
- | Ward, T.J., T.F. Ducey, T. Usgaard, K.A. Dunn, and J.P. Bielawski. | + | McEachran JD, Dunn KA, Miyake |
- | Bao, L., H. Gu, K.A. Dunn, and J.P. Bielawski. | + | Dunn KA, Morrissey JF. 1995. Molecular phylogeny |
- | Anisimova, M., J.P. Bielawski, K.A. Dunn, and Z. Yang. 2007. Phylogenomic analysis of natural selection pressure in Streptococcus. | + | **Conference Publications** |
- | Hurley, I.A., R.L. Lockridge Mueller, K.A. Dunn, E.J. Schmidt, M. Friedman, R.K. Ho, V.E. Prince, Z. Yang, M.G. Thomas, and M.I. Coates. 2007. A new time-scale for ray-finned fish evolution. Proc. R. Soc. B. 274: | + | Ghiboub M, Charlotte Verburgt CM, Penny S, Sigall Boneh R, Wine E, Cohen A, Dunn KA, Pinto D, Benninga |
- | Bao, L., H. Gu, K.A. Dunn, and J.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:S5 | + | Verburgt CM, Ghiboub M, Penny S, Sigall Boneh R, Wine E, Cohen A, Dunn KA, Pinto D, Benninga M, Levine A, de Jonge WJ, van Limbergen JE. (2020) Diet-induced remission is not driven by bile acid modification. United European Gastroenterology week UEGW Oct 11-13 2020 Poster presentation |
- | Bielawski, J.P., K.A. Dunn, G. Sabehi, and O. Béjà. 2004. Darwinian adaptation | + | Dunn KA, Connors |
- | Dunn, K.A., J.D. McEachran, and R.L. Honeycutt. 2003. Molecular phylogenetics of myliobatiform fishes | + | Walters I, Connors J, Dunn KA, Van Limbergen |
- | Dunn, K.A., J.P. Bielawski, | + | Levine A, Dunn KA, Gerasimidis |
- | Bielawski, | + | Dunn KA, Bielawski |
- | McEachran, J.D., and K.A. Dunn. 1998. Phylogenetic analysis of skates, a morphologically conservative clade of elasmobranchs | + | Levine A, Dunn KA, Gerasimidis |
- | Morrissey, J.F., K.A. Dunn, and F. Mulé. 1997. The phylogenetic position of Megachasma pelagios inferred from mtDNA sequence data. Pages 33-37 in Biology of the megamouth shark (K. Yano, J. F. Morrissey, Y. Yabumoto, and K. Nakaya, eds.). Tokai University Press, Tokyo, Japan. | + | Dunn KA, Bielawski JP, Sigall-Boneh R, Shamir R, Wine E, Levine A, Van Limbergen J. (2019) Shifts in bacterial community function are associated with short chain fatty acid pathways during nutritional therapy in Pediatric Crohn’s disease patients. PIBD oral presentation |
- | McEachran, J.D., K.A. Dunn, and T. Miyake. 1996. Interrelationships within the batoid fishes | + | Dunn KA, Bielawski JP, Turner |
+ | |||
+ | Allott | ||
- | Dunn, K.A., and J.F. Morrissey. 1995. Molecular phylogeny | + | Dunn KA, Sigall-Boneh R, Bielawski JP, Turner D, Van Limbergen J, Levine |
+ | Dunn KA, Moore-Connors J, MacIntyre B, Stadnyk A, Thomas NA, Noble A, Mahdi G, Rashid M, Otley AR, Bielawski JP, Van Limbergen J. (2016) Early changes in microbial community structure areassociated with sustained remission following nutritional treatment ofPediatric Crohn’s Disease. World Congress of Pediatric Gastroenterology, | ||
+ | Dunn KA, Connors-Moore J, MacIntyre B, Mahdi G, Noble A, Rashid M, Thomas N, Stadnyk A, Otley AR, Bielawski JP, Van Limbergen J. (2016) EEN induces significant changes in the metabolic capacity of gut microbiomes in pediatric CD patients. World Congress of Pediatric Gastroenterology, | ||
+ | Connors J, Dunn KA, Bielawski JP, Stadnyk A, Thomas NA, Otley AR, Van Limbergen J. (2015). Clinical Remission Induced by Exclusive Enteral Nutrition (EEN) in Pediatric Crohn' | ||
+ | Dunn KA, Connors J, MacIntyre B, Stadnyk A, Bielawski JP, Thomas N, Otley AR, Van Limbergen J. (2015). Clinical remission induced by exclusive enteral nutrition (een) in pediatric Crohn’s disease is associated with microbiome metabolic changes toward increased xenobiotic biodegradation and metabolism. United European Gastroenterology Week
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+ | Connors J, Hansen R, Dunn KA, Langille MG, Russell R, Otley AR, MacIntyre B, El-Omar E, Bielawski JP, Hold GL, Van Limbergen J. (2015). Assessment of community structure and predictive functional profiling of the mucosa-associated microbiome implicates alterations in benzoate metabolism in ‘de novo’ IBD after pouch-surgery and in treatment-naïve pediatric IBD. Digestive Disease Week Gastroenterology | ||
+ | Dunn KA, Connors J, MacIntyre B, Stadnyk A, Bielawski JP, Thomas N, Otley AR, Van Limbergen J. (2015). The dysbiosis index does not distinguish children with Crohn' | ||