The group's publications are simply ordered by date
(sorry, no links to PDFs at this time) and divided into
two broad groups. The first
is simply a list of all our journal articles and book
chapters. The second
is a list of the clinical conference presentations that
were competitive, and are published as an abstract.
1. Journal Articles & Book Chapters
Jones, C.T., Susko, E., Bielawski, J.P.
2022.
Evolution of the connectivity and indispensability
of a transferable gene: the simplicity hypothesis.
BMC
Ecology and Evolution. In Press.
Lean, C.H., Doolittle, W.F. and Bielawski, J.P., 2022.
Community-level
evolutionary processes: Linking community genetics with
replicator-interactor theory. Proceedings of the
National Academy of Sciences,
119(46),
p.e2202538119
Verburgt, C.M., Dunn, K.A., Ghiboub, M., Lewis, J.D., Wine,
E., Sigall Boneh, R., Gerasimidis, K., Shamir, R., Penny, S.,
Pinto, D.M. and Cohen, A., 2022.
Successful dietary
therapy in paediatric Crohn’s disease is associated with
shifts in bacterial dysbiosis and inflammatory metabotype
towards healthy controls.
Journal of Crohn's and
Colitis.
Dunn, K.A., MacDonald, T., Rodrigues, G.J., Forbrigger, Z.,
Bielawski, J.P., Langille, M.G., Van Limbergen, J. and
Kulkarni, K., 2022.
Antibiotic and antifungal use in
pediatric leukemia and lymphoma patients are associated with
increasing opportunistic pathogens and decreasing bacteria
responsible for activities that enhance colonic defense.
Frontiers in cellular and infection microbiology,
p.1085.
Bjorndahl, P., Bielawski, J.P., Liu, L., Zhou, W. and Gu, H.,
2022.
Novel Application of Survival Models for Predicting
Microbial Community Transitions with Variable Selection for
Environmental DNA.
Applied and Environmental
Microbiology, 88(6), pp.e02146-21.
Youssef N., Susko E., Roger A.J., Bielawski J.P. 2022.
Evolution
of Amino Acid Propensities under Stability-Mediated
Epistasis. Mol Biol Evol. 2022 Mar 2;39(3):msac030. doi:
10.1093/molbev/msac030.
Massey, M.D.B., Arif, S., Embuldeniya, S., Nanglu, K. and
Bielawski, J., 2022.
Ten simple rules for succeeding as an
underrepresented STEM undergraduate.
PLOS
Computational Biology, 18(6), p.e1010101.
Dunn K.A., Forbrigger Z., Connors J., Rahman M,. Cohen A., Van
Limbergen J,. Langille M.G.I., Stadnyk A.W., Bielawski J.P.,
Penny S.L., MacDonald T,. Kulkarni K. 2021.
Gut
bacterial gene changes following pegaspargase treatment in
pediatric patients with acute lymphoblastic leukemia.
Leuk
Lymphoma. 2021 Dec;62(13):3244-3255. doi:
10.1080/10428194.2021.1953006. 76.
Youssef N., Susko E., Roger, A., Bielawski J.P. 2021.
Shifts
in amino acid preferences as proteins evolve: a synthesis of
experimental and theoretical work.
Protein Science.
Protein Sci. 2021 Oct;30(10):2009-2028. doi: 10.1002/pro.4161.
Doolittle W.F., Brunet T.D.P., Bielawski JP.. 2021.
The
role of purifying selection in the origin and maintenance of
Complex Function.
Studies In History and Philosophy
of Science Part A 87(33):125-135 doi:
10.1016/j.shpsa.2021.03.005
Dunn K.A. ,Connors J., Bielawski J.P., Nearing J.T., Langille
M.G.I., VanLimbergen J., Fernandez C.V., MacDonald T.,
Kulkarni K.. 2021.
Investigating the gut microbial
community and genes in children with differing levels of
change in serum asparaginase activity during pegaspargase
treatment for acute lymphoblastic leukemia. Leuk
Lymphoma. 62(4):927-936. doi: 10.1080/10428194.2020.1850718.
Youssef N, Susko E, Bielawski JP. 2020.
Consequences of
stability-induced epistasis for substitution rates. Mol
Biol Evol. 37(11):3131-3148. doi: 10.1093/molbev/msaa151.
Douglas, G.M., Bielawski, J.P., Langille, M.G.I., 2020.
Re-evaluating
the Relationship Between “Missing Heritability” and the
Microbiome. Micorbiome Jun 8;8(1):87. doi:
10.1186/s40168-020-00839-4.
Cui, T.T., Dawson, T.J., McLatchie, S., Dunn, K.A., Bielawski,
J.P., Walsh, DA. 2020.
Modelling free-living
and particle-associated bacterial assemblages across the
deep and hypoxic Lower St. Lawrence Estuary. MSphere.
May 20;5(3):e00364-20. doi: 10.1128/mSphere.00364-20.
Jones CMA, Connors J, Dunn KA, Bielawski JP, Comeau AM,
Langille MGI, Van Limbergen J. 2020.
Bacterial Taxa and
Functions Are Predictive of Sustained Remission Following
Exclusive Enteral Nutrition in Pediatric Crohn's Disease.
Inflamm Bowel Dis. Jun 18;26(7):1026-1037. doi:
10.1093/ibd/izaa001.
Connors J, Dunn KA, Allott J, Bandsma R, Rashid M, Otley AR,
Bielawski JP, Van Limbergen J. 2020.
The relationship
between fecal bile acids and microbiome community structure
in pediatric Crohn's disease. ISME J. 2020
Mar;14(3):702-713.
Jones CT, Youssef N, Susko E, Bielawski JP. 2020.
A
phenotype-genotype codon model for detecting adaptive
evolution. Systematic Biology 69(4):722-738. doi:
10.1093/sysbio/syz075.
Levine A, Wine E, Assa A, Boneh RS, 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, Van Limbergen
J., 2019.
Crohn's Disease Exclusion Diet Plus
Partial Enteral Nutrition Induces Sustained Remission in a
Randomized Controlled Trial. Gastroenterology 2019. doi:
10.1053/j.gastro.2019.04.021.
Chen, W., Kenney T., Bielawski J.P., Gu H.
2019.
Testing adequacy for DNA substitution models.
BMC Bioinformatics 2019 20:349.
doi.org/10.1186/s12859-019-2905-3.
Mingrone, J., Susko E., Bielawski J.P., 2019.
ModL:
exploring and restoring regularity when testing for positive
selection. Bioinformatics, bty1019,
doi.org/10.1093/bioinformatics/bty1019.
Dunn KA, Kenney T, Gu H, Bielawski JP. 2019.
Improved
inference of site-specific positive selection under a
generalized parametric codon model when there are
multinucleotide mutations and multiple nonsynonymous rates.
BMC Evol Biol. 19(1):22. doi: 10.1186/s12862-018-1326-7.
Jones C.T., Susko E., Bielawski J.P., 2019.
Looking
for Darwin in genomic sequences: validity and success
depends on the relationship between model and data. In
Evolutionary Genomics: Statistical and Computational Methods.
Maria Anisimova (ed.) 2nd edition, pages: 339-426. Human
press.
Youssef, N., Budd, A., and Bielawski, J.P.,
2019.
Introduction to Genome Biology and Diversity.
In Evolutionary Genomics: Statistical and Computational
Methods. Maria Anisimova (ed.) 2nd edition, pages: 3-32, Human
press.
Dunn, K.A., Andrews, K., Bashwih, R.O. and Bielawski, J.P.,
2018.
Bayesian Inference of Microbial Community Structure
from Metagenomic data using BioMiCo. In Mircrobiome
Analysis: Methods and Protocols, Beiko, R., Hsiao, Willina,
& Parkinson, J. (eds), pages: 267-290, Humana Press,
Totowa, NJ.
Jones C.T., Youssef N., Susko E., Bielawski J.P., 2018.
Phenomenological Load on Model Parameters Can Lead to False
Biological Conclusions. Mol Biol Evol. 35(6):1473-1488.
Douglas, G.M., Hansen, R., Jones, C.M.A., Dunn, K.A., Comeau,
A.M., Bielawski, J.P., Tayler, R., El-Omar, E.M., Russell,
R.K., Hold, G.L., Langille, M.G.I., Van Limbergen, J., 2018.
Multi-omics
differentially classify disease state and treatment outcome
in pediatric Crohn's disease. Microbiome. 2018, 6(1):13.
Jones, C., Youssef, N., Susko, E. and Bielawski, J.,
2017.
Shifting balance on a static
mutation-selection landscape: a novel scenario of positive
selection. Molecular Biology and Evolution,
34(2):391-407.
Dunn, K.A., Moore-Connors, J., MacIntyre, B., Stadnyk, A.,
Thomas, N.A., Noble, A., Mahdi, G., Rashid, M. Otley, A.R.,
Bielawski, J.P. and Van Limbergen, J., 2017. T
he gut
microbiome of pediatric Crohn’s disease patients differs
from healthy controls in genes that can influence the
balance between a healthy and dysregulated immune response.
Inflammatory Bowel Diseases, 2(11):2607-2618.
Mingrone, J., Susko, E. and Bielawski, J., 2016.
Smoothed
bootstrap aggregation for assessing selection pressure at
amino acid sites. Molecular Biology and Evolution,
33(11):2976-2989.
Dunn, K.A., Moore-Connors, J., MacIntyre, B., Stadnyk, A.,
Thomas, N.A., Noble, A., Mahdi, G., Rashid, M. Otley, A.R.,
Bielawski, J.P. and Van Limbergen, J., 2016.
Early changes
in microbial community structure are associated with
sustained remission following nutritional treatment of
Pediatric Crohn’s Disease. Inflammatory Bowel Diseases,
22(12):2853-2862.
Bielawski, J.P., Baker, J.L. and Mingrone, J., 2016.
Inference
of episodic changes in natural selection acting on protein
coding sequences via CODEML. Current Protocols in
Bioinformatics, pp.6-15.
Moore-Connors, J., Dunn, K.A., Bielawski, J.P. and Van
Limbergen, J., 2016.
Novel strategies for applied
metagenomics. Inflammatory bowel diseases, 22(3),
pp.709-718.
Baker, J.L., Dunn, K.A., Mingrone, J., Wood, B.A., Karpinski,
B.A., Sherwood, C.C., Wildman, D.E., Maynard, T.M. and
Bielawski, J.P., 2016.
Functional divergence of the
nuclear receptor NR2C1 as a modulator of pluripotentiality
during Hominid evolution. Genetics, 203(2), pp.905-922.
Bielawski, J.P., 2016.
Evolutionary models. In: R.
Kliman, ed. Encyclopedia of Evolutionary Biology. Elsevier.
Volume 1, pp. 61-70.
Bielawski, J.P. and Jones., C.F., 2016.
Adaptive
evolution: detection methods. In: R. Kliman, ed.
Encyclopedia of Evolutionary Biology. Elsevier. Volume 1, pp.
16-25.
Shafiei, M., Dunn, K.A., Boon, E., MacDonald, S.M., Walsh,
D.A., Gu, H. and Bielawski, J.P., 2015.
BioMiCo: a
supervised Bayesian model for inference of microbial
community structure. Microbiome, 3(1), p.1.
El‐Swais, H., Dunn, K.A., Bielawski, J.P., Li, W.K. and Walsh,
D.A., 2015.
Seasonal assemblages and short‐lived blooms in
coastal north‐west Atlantic Ocean bacterioplankton.
Environmental Microbiology, 17(10), pp.3642-3661.
Garvin, M.R., Bielawski, J.P., Sazanov, L.A. and Gharrett,
A.J., 2015.
Review and meta‐analysis of natural selection
in mitochondrial complex I in metazoans. Journal of
Zoological Systematics and Evolutionary Research, 53(1),
pp.1-17.
Shafiei, M., Dunn, K.A., Chipman, H., Gu, H. and Bielawski,
J.P., 2014.
BiomeNet: A Bayesian model for inference of
metabolic divergence among microbial communities. PLoS
Computational Biology, 10(11), p.e1003918.
Yoder, A.D., Chan, L.M., dos Reis, M., Larsen, P.A., Campbell,
C.R., Rasoloarison, R., Barrett, M., Roos, C., Kappeler, P.,
Bielawski, J. and Yang, Z., 2014.
Molecular evolutionary
characterization of a V1R subfamily unique to strepsirrhine
primates. Genome Biology and Evolution, 6(1),
pp.213-227.
Garvin, M.R., Bielawski, J.P., Sazanov, L.A. and A.J.
Gharrett, 2014.
Positive Selection and Its Functional
Implications in Metazoan Mitochondrial Genomes. Journal
of Zoological Systematics and Evolutionary Research 52(3).
doi: 10.1111/jzs.12079
Bay R.A. and Bielawski J.P., 2013.
Inference of
functional divergence among proteins when the evolutionary
process is non-stationary. Journal of Molecular
Evolution 76(4):205-215.
Dunn K.A., Jiang W., Field C. and Bielawski J.P., 2013.
Improving
evolutionary models for mitochondrial protein data with
site-class specific amino acid exchangeability matrices.
PLoS One. 2013;8(1):e55816.
Bielawski J.P., 2013.
Detecting the signatures of adaptive
evolution in protein-coding genes. In: Current Protocols
in Bioinformatics, John Wiley & Sons, Chapter 19:Unit
19.1.
Bay, R.A. and J.P. Bielawski, 2012.
Recombination
Detection Under Evolutionary Scenarios Relevant to
Functional Divergence. Journal of Molecular Evolution.
73(5-6):273-286.
Garvin, M.R., J.P. Bielawski and A.J. Gharrett, 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.
Bielawski, J.P., H. Gu, and K. A. Dunn. 2011.
Likelihood
Based Clustering (LiBaC) for Codon Models. In: Codon
Evolution: Mechanisms and Models, Oxford University Press.
Dunn, K.A., J.P. Bielawski, T.J. Ward, C. Urquhart and
H. Gu. 2009.
Reconciling ecological and
genomic divergence among lineages of Listeria: the extended
mosaic genome concept. Molecular Biology and Evolution
68(5): 506-515.
Morine, M., H. Gu, R. Meyers, and J.P. Bielawski.
2009.
Niche breadth influences the functional
cartography of metabolic networks. Journal of Molecular
Evolution. 68:506-515.
Ward, T.J., T.F. Ducey, T. Usgaard, K.A. Dunn, and J.P.
Bielawski. 2008.
Multilocus genotyping assays
for SNP-based subtyping of Listeria monocytogenes.
Applied Environmental Microbiology, 74: 7629-7642.
Bao, L., H. Gu, K.A. Dunn, and J.P. Bielawski. 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.
Sullivan, M.B. , M.C. Coleman, V. Quinlivan, J.E. Rosenkrantz,
A.S. DeFrancesco, G. Tan, R. Fu, J.A. Lee, J.B. Waterbury,
J.P. Bielawski, S.W. Chisholm. 2008.
Portal protein
diversity and phage ecology. Applied Environmental
Microbiology: 10:2810-2823.
Anisimova, M., J.P. Bielawski, K.A. Dunn, and Z. Yang. 2007.
Phylogenomic
analysis of natural selection pressure in Streptococcus.
BMC Evolutionary Biology, 7:e154.
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 Suppl 1:S5.
Aguileta, G., J.P. Bielawski, and Z. Yang. 2006a.
Rate
variation and divergence dates among vertebrate β-globin
genes. Gene, 380:21-29.
Aguileta, G., J.P. Bielawski, and Z. Yang. 2006b.
Proposed
standard nomenclature for the β–globin gene family.
Genes and Genetic Systems, 81:367-371.
Aris-Brosou, S. and J.P. Bielawski. 2006.
Large-scale
analysis of synonymous substitution rates can be sensitive
to assumptions about the process of mutation. Gene,
378:58-64.
Field, S.F., M.Y. Bulina, I.V. Kelmanson, J.P. Bielawski, and
M.V. Matz. 2006.
Adaptive evolution of color diversity and
a putative binding site in fluorescent proteins from
reef-building corals. Journal of Molecular Evolution,
63:332-339.
Popescu, C.E., T. Borza, J.P. Bielawski, and R.W. Lee. 2006.
Synonymous
and nonsynonymous substitution rate variation among nuclear
genes in green algae: Chlamydomonas reinhardtii and C.
incerta. Genetics, 172:1567-1576.
Sullivan, M.B, D. Lindell, J.A. Lee, L.R. Thompson, J.P.
Bielawski, and S.W. Chisholm. 2006.
Prevalence
and evolution of core photosystem II genes in marine
cyanobacterial viruses and their hosts. PLoS Biology,
4:e234.
Bielawski, J.P. and Z. Yang. 2005.
Likelihood methods for
detecting adaptive evolution. In: Statistical methods in
Molecular Evolution, Springer Verlag Series in Statistics in
Health and Medicine. New York, New York.
Shi P., J.P. Bielawski, H. Yang, and Zhang Y.P. 2005.
Adaptive
diversification of vomeronasal receptor 1 genes in rodents.
Journal of Molecular Evolution, 60:566-576.
Zeidner G., J.P. Bielawski., M. Shmoish, D.J. Scanlan, G.
Sabehi, and O. Béjà. 2005.
Potential photosynthesis gene
recombination between Prochlorococcus and Synechococcus via
viral intermediates. Environmental Microbiology,
10:1505-1513.
Aguileta G., J.P. Bielawski, and Z. Yang. 2004.
Gene
conversion and functional divergence in the Beta-globin gene
family. Journal of Molecular Evolution, 59:177-189.
Bielawski J.P. and Z. Yang. 2004.
A maximum likelihood
method for detecting functional divergence at individual
codon sites, with application to gene family evolution.
Journal of Molecular Evolution, 59:121-132.
Bielawski J.P., K.A. Dunn, G. Sabehi, and O. Béjà. 2004.
Darwinian
adaptation of proteorhodopsin to different light intensities
in the marine environment. Proceedings of the National
Academy of Sciences, USA, 101:14824-14829.
Munad, L., J.P. Bielawski, R. Matyasek, A. Kovarík, R.A.
Nichols, A.R. Leitch, and C.P. Lichtenstein. 2004.
The
origin and evolution of geminivirus-related DNA sequences in
Nicotiana. Heredity, 92:352-358.
Bielawski, J.P. and Z. Yang. 2003a.
Maximum likelihood
methods for detecting adaptive evolution in gene
families. In: Gene and Genome Duplications and the
Evolution of Novel Gene Functions. A. Meyer and Y. Van De Peer
(eds). Pp. 201-212.
Bielawski, J.P. and Z. Yang. 2003b.
Maximum likelihood
methods for detecting adaptive evolution after gene
duplication. Journal of Structural and Functional
Genomics, 3:201-212.
Sabehi, G., M. Ramon, J.P. Bielawski, M. Rosenber, E. F.
Delong, and O. Béjà. 2003.
Novel proteorhodopsin variants
from the Mediterranean and Red Seas. Environmental
Microbiology, 5:842-849.
Yang, W., J.P. Bielawski, and Z. Yang. 2003.
Widespread
adaptive evolution in the human immunodeficiency virus
type-1 genome. Journal of Molecular Evolution,
57:212-221.
Anisimova, M., J.P. Bielawski, and Z. Yang. 2002.
Evaluation
of the Bayesian approach to detecting codon sites under
positive Darwinian selection. Molecular Biology and
Evolution, 19:950-958.
Bielawski, J.P. 2002.
Phylogenetic inference:
an overview. In: Oxford Encyclopaedia of
Evolution. M. Pagel (eds) Oxford University Press, Oxford. Pp.
891-895.
Bielawski, J.P. and J.R Gold. 2002.
Mutation patterns of
mitochondrial H- and L-strand DNA in closely related
cyprinid fishes. Genetics, 161:1589-1597.
Bielawski, J.P., A.C. Brault, and J.R Gold. 2002.
Phylogenetic
relationships within genus Pimephales (Cyprinidae:
Teleostei). Journal of Fish Biology, 61: 293-297.
Ward, T.J., J.P. Bielawski, H.C. Corby-Kistler, E. Sullivan,
and K. O’Donnell. 2002.
Ancient polymorphism and adaptive
evolution in the trichothecene gene cluster of
phytopathogenic Fusarium. Proceedings of the National
Academy of Sciences, USA, 99:9278-9283.
Anisimova, M., J.P. Bielawski, and Z. Yang. 2001.
The
accuracy and power of the likelihood ratio test to detect
adaptive molecular evolution. Molecular Biology and
Evolution, 18:1585-1592.
Bielawski, J.P. and J.R. Gold. 2001.
Phylogenetic
relationships of cyprinid fishes in subgenus Notropis as
inferred from nucleotide sequences of the mitochondrially
encoded cytochome b gene. Copeia, 2001(3): 656-667.
Bielawski, J.P. and Z. Yang. 2001.
The role of selection
in the evolution of the DAZ gene family. Molecular
Biology and Evolution, 18: 523-529.
Dunn, K.A., J.P. Bielawski, and Z. Yang. 2001.
Rates and
patterns of synonymous substitutions in Drosophila:
implications for translational selection. Genetics,
157:295-305.
Bielawski, J.P., K.A. Dunn, and Z. Yang. 2000.
Rates of
nucleotide substitution and mammalian nuclear gene
evolution: approximate and maximum-likelihood methods lead
to different conclusions. Genetics, 156:1299-1308.
Yang, Z. and J.P. Bielawski. 2000.
Statistical tests of
adaptive molecular evolution. Trends in Ecology and
Evolution, 15:496-502.
Ward, T.J., J.P. Bielawski, S.K. Davis, J. Templeton, and J.N.
Derr. 1999.
Identification of domestic cattle hybrids in
wild cattle and bison species: a general approach using
mtDNA and the parametric bootstrap. Animal Conservation,
2:51-57.
Schmidt, T.R., J.P. Bielawski, and J.R. Gold. 1998.
Molecular
phylogenetics and evolution of the cytochrome b gene in the
cyprinid genus Lythrurus (Actinoptergii: Cypriniformes).
Copeia, 1998(1): 14-22.
Bielawski, J.P. and J.R. Gold. 1996.
Unequal synonymous
substitution rates within and between two protein-coding
mitochondrial genes. Molecular Biology and Evolution,
13:889-892.
Bielawski, J.P. and D.E. Pumo. 1996.
Randomly Amplified
Polymorphic DNA (RAPD) analysis of Atlantic Coast striped
bass populations. Heredity, 78:32-40.
Bielawski, J.P., K. Noack, and D.E. Pumo. 1995.
Improving
amplification of Randomly Amplified Polymorphic DNA Markers
(RAPD) from vertebrate DNA. Biotechniques, 18:856-859.
Dunn K, Bielawski J, Bjorndahl P, 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 (SCFA) pathways during nutritional therapy in
paediatric Crohn´s disease patients. (Oral presentation)
UEG Week, Barcelona, Spain; (Poster of Distinction) 5th
International Symposium on Paediatric Inflammatory Bowel
Disease.
Levine A, Dunn K, Gerasimidis K, Bjorndahl P, Svolos V,
Bielawski J, Sigall Boneh R, Wine E, Van Limbergen J.
2019.
Fecal Short Chain Fatty Acids (SCFA)
measurement and microbiome metabotype shifts in nutritional
therapy of paediatric Crohn´s disease.
(Oral
Presentation) 5th International Symposium on Paediatric
Inflammatory Bowel Disease; (poster) UEG Week, Barcelona,
Spain.
Dunn KA, Bielawski JP, Boneh RS, Shamir R, Wine E, van
Limbergen JE, Levine A. 2019.
Exclusive
enteral nutrition (EEN) and Crohn´s disease exclusion diet
(CDED) produce broadly similar taxonomic and functional
changes during the induction of remission, with EEN showing
a pattern of rebound after return to free diet + partial
enteral nutrition (PEN). (ePoster) 52nd ESPGHAN
Annual Meeting; (Oral presentation) Digestive Disease Week,
San Diego, CA.
Dunn KA, Bielawski JP, Boneh RS, Shamir R, Wine E, van
Limbergen JE, 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. (Poster) 14th
Congress of ECCO Inflammatory Bowel Diseases, Copenhagen,
Denmark
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. (Oral presentation)
UEG, Vienna, Austria
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. (Oral presentation) Digestive Disease Week,
Chicago.
Dunn KA, Sigall-Boneh R, Bielawski JP, Turner D, Van Limbergen
J, Levine A. 2017
Microbiome community structure and
prediction of response to nutritional therapy in Pediatric
Crohn’s disease. (Oral presentation) Microbiome Human
Nutrition. Boston MA
MacLellan A, Connors J, MacIntyre B, Douglas G, Dunn KA,
Bielawski JP, Noble A, Mahdi G, Rashid M, Otley A, Cahill L,
Langille M, Van Limbergen J. 2017.
Fibre
intake is associated with microbiome changes in pediatric
Crohn’s disease patients following induction of remission
induction with exclusive enteral nutrition (EEN).
(Poster) Digestive Disease Week Chicago
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. (talk)
Journal of Crohn’s and Colitis 11(suppl_1):S29-S29. (digital
oral presentation)
MacLellan A, Connors J, MacIntyre B, Douglas G, Dunn KA,
Bielawski JP, Noble A, Mahdi G, Rashid M, Otley AR, Cahill L,
Langille MG, Van Limbergen, J. 2017.
Fibre Intake is
Associated with Microbiome Changes in Pediatric Crohn’s
Disease Patients Following Remission Induction with
Exclusive Enteral Nutrition (EEN). (Oral presentation)
J. European Crohn’s and Colitis Organization, Inflammatory
Bowel Disease, February 15-18 2017 Barcelona Spain
Dunn KA, Sigall Boneh R, Bielawski JP, Turner D, Van Limbergen
J, Levine A. 2017.
Enteral nutrition induces changes in
the functional repertoire of the human gut microbiome. (poster)
International Symposium on Pediatric Inflammatory Bowel
Disease (PIBD 2017) September 13-16 2017 Barcelona
Spain *awarded a PIBD Best Communication.
Hansen R, Douglas GM, Jones C, Dunn KA, Comeau AM, Bielawski
JP, Tayler R, El-Omar EM, Russell RK, Hold GL, Langille MGI,
Van Limbergen J. 2017. Shotgun Metagenomics,
16S
rRNA Gene Sequencing, and Human Genetics Differentially
Classify Pediatric Crohn’s Disease State and Treatment
Outcome. (poster) International Symposium on Pediatric
Inflammatory Bowel Disease (PIBD 2017) September 13-16 2017
Barcelona Spain.
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 are associated with sustained remission following
nutritional treatment of Pediatric Crohn’s Disease. (Oral
presentation) 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. (poster)
World Congress of Pediatric
Gastroenterology, Hepatology and Nutrition .
Dunn, K.A., J. Connors, B. MacIntyre, A. Stadnyk, J. P.
Bielawski, N. Thomas, A. R. Otley, J. Van Limbergen, 2015.
The
dysbiosis index does not distinguish children with Crohn’s
disease from healthy siblings. (Oral presentation)
United European Gastroenterology Journal 2015;3(5S):A133
(OP412).
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, K.A., J. Connors, B. MacIntyre, A. Stadnyk, J. P.
Bielawski, N. Thomas, A. R. Otley, J. Van Limbergen,
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.
(poster) United European Gastroenterology Journal
2015;3(5S):A441 (P1005) [This poster was featured as
'poster in the spolight', and won best e-poster in the session
on 'New insights into the management of paediatric and
adolescent IBD.]
Connors, J., K.A. Dunn, J.P. Bielawski, A. Stadnyk, N. Thomas,
A.R. Otley, J. Van Limbergen, 2015.
Clinical remission
induced by exclusive enteral nutrition (EEN) in pediatric
Crohn's disease is associated with microbiome metabolic
changes toward altered xenobiotic biodegradation and
metabolism. (poster) Digestive Disease Week,
Washington DC May 2015
Connors, J., R. Hansen, K.A. Dunn, M.G. Langille, R.K.
Russell, A.R. Otley, B. MacIntyre, E. El-Omar, J.P. Bielawski,
G.L. Hold, J. Van Limbergen, 2015. (poster)
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. (poster) 10th
Congress of European Crohn’s and Colitis Organization,
Barcelona, Spain.
Connors, J., K.A. Dunn, J.P. Bielawski, A. Stadnyk, N. Thomas,
A.R. Otley, J. Van Limbergen, 2015. (poster)
Clinical
remission induced by exclusive enteral nutrition (EEN) in
pediatric Crohn's disease is associated with microbiome
metabolic changes toward altered xenobiotic biodegradation
and metabolism. 10th Congress of European Crohn’s and
Colitis Organization, Barcelona, Spain.