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Education
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Research Interests
My current research focuses on understanding how the human microbiome and its metabolites impacts health and disease. My current specific areas of research include: Examining the impact of the microbiome and their metabolites on treatment and side effects in oncology. Investigating if we can use the microbiomes to predict remission in Crohn's disease. Role of Bacterial heat shock genes in Crohn's disease. Examine how the development of the preterm microbiome is impacted by early diet and the NICU environment.
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. submitted to Leukemia and Lymphoma
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
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;14(3):702-713. * co-first author
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;157(2):440-450.e8. doi: 10.1053/j.gastro.2019.04.021
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/s12862-018-1326-7.
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's disease. Microbiome 6(1):13.
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. 22(12):2853-2862.
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. Inflammatory Bowel Disease. 22(11):2607-2618.
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):905-922.
Moore-Connors J.M., Dunn K.A., Bielawski J.P., Van Limbergen J. 2016. Novel strategies for applied metagenomics. Inflammatory Bowel Disease. 22(3):709-718.
Xu X, Dunn KA, Field C. 2015. A Robust ANOVA approach to estimating a phylogeny from multiple genes. Molecular Biology Evolution. 32(8):2186-2194.
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: Bacterial diversity in Bedford Basin. Environmental Microbiology. 17(10):3642-3661.
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):e1003918
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. 37:305-324.
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. Molecular Biology and Evolution. 26: 2605-2615.
Ward TJ, Ducey TF, Usgaard T, Dunn KA, Bielawski JP. 2008. A multilocus genotyping assay for SNP-based subtyping of Listeria monocytogenes. Applied and Enviromental Microbiology. 74: 7570-7577.
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. Molecular Biology and Evolution. 25: 1995-2007.
Anisimova M, Bielawski JP, Dunn KA, Yang Z. 2007. Phylogenomic analysis of natural selection pressure in Streptococcus. BMC Evolutionary Biology. 7:154.
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. 274:489-498. #Authors contributed equally
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. 101:14824-14829.
Dunn KA, McEachran JD, Honeycutt RL. 2003. Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood. Molecular Phylogenetics and Evolution. 27:259-270.
Dunn KA, Bielawski JP, Yang Z. 2001. Rates and patterns of synonymous substitutions in Drosophila: implications for translational selection. Genetics. 157:295-305.
Bielawski JP, Dunn KA, Yang Z. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics. 156:1299-1308.
McEachran JD, Dunn KA. 1998. Phylogenetic analysis of skates, a morphologically conservative clade of elasmobranchs (Chondrichthyes: Rajidae). Copeia. 2:271-290.
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.
McEachran JD, Dunn KA, Miyake T. 1996. Interrelationships within the batoid fishes (Chondrichthyes:Batoidea). Pages 63-84 in Interrelationship of fishes (MLJ Stiassney MLR, Parenti LR, Johnson GD, eds.). Academic Press, New York.
Dunn KA, Morrissey JF. 1995. Molecular phylogeny of elasmobranchs. Copeia. 3:526-531.
Conference Publications
Ghiboub M, Charlotte Verburgt CM, 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 in pediatric Crohn’s disease is associated with a marked decrease of Kynurenine, a tryptophan metabolite associated with inflammation. United European Gastroenterology week UEGW Oct 11-13 2020 Oral presentation
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
Dunn KA, Connors J, Van Limbergen J, Langille MGI, Fernandez CV, MacDonald T, Kulkarni K. (2020) Significant association of gut microbiome with serum asparaginase levels in pediatric patients with acute lymphoblastic leukemia. International Society of Paediatric Oncology SIOP Oct 14-27, 2020 Oral presentation
Walters I, Connors J, Dunn KA, Van Limbergen J, West M, Dyack S. (2020) A Comparison of the Gut Microbiome in Children Affected by Fabry Disease and their Unaffected Siblings: A Pilot Project WORLDSymposium poster presentation
Levine A, Dunn KA, Gerasimidis K, Bielawski JP, Sigall-Boneh R, Wine E, Van Limbergen J. (2019) Fecal SCFA measurement and microbiome metabotype shifts in nutritional therapy of pediatric Crohn’s disease. UEGW oral presentation
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. UEGW oral presentation
Levine A, Dunn KA, Gerasimidis K, Bielawski JP, Sigall-Boneh R, Wine E, Van Limbergen J. (2019) Fecal SCFA measurement and microbiome metabotype shifts in nutritional therapy of pediatric Crohn’s disease. PIBD poster of destinction
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
Dunn KA, Bielawski JP, Turner D, Sigall-Boneh R, Shamir R, Wine E, Van Limbergen J, Levine A. (2019) EEN and CDED produce broadly similar taxonomic changes during the induction of remission, but many taxa rebound upon the transition from EEN back to free diet. European Crohn’s and Colitis Organization.
Allott J, Dunn K, Connors J, Bandsma R, Whitehouse S, MacIntyre B, Noble A, Rashid M, Otley A, Bielawski J, Van Limbergen J. (2018) Identification of a Bile Acid profile and Gut Microbiome Community Structure associated with early flare after nutritional therapy in Paediatric Crohn’s Disease UEGW
Dunn KA, Sigall-Boneh R, Bielawski JP, Turner D, Van Limbergen J, Levine A. (2017) Crohn's disease exclusion diet and partial enteral nutrition (CDED+PEN) vs exclusive enteral nutrition (EEN). Microbiome changes of a randomized clinical trial (RCT) in pediatric CD: remission is associated with similar structural + functional profiles. Journal of Crohn’s and Colitis 11(suppl_1):S29-S29.
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, Hepatology and Nutrition
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, Hepatology and Nutrition
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's Disease is Associated with Microbiome Metabolic changes toward increased Xenobiotic Biodegradation and Metabolism. Digestive Disease Week Gastroenterology
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
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's disease from healthy siblings. United European Gastroenterology Week