Brett Trost

Brett Trost

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Brett Trost

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Glutaminase Deficiency Caused by Short Tandem Repeat Expansion in .

N Engl J Med 2019 04;380(15):1433-1441

From Amsterdam University Medical Centers, University of Amsterdam, Departments of Clinical Chemistry, Pediatrics, and Clinical Genetics, Emma Children's Hospital, Amsterdam Gastroenterology and Metabolism (A.B.P.K., R.L., J.K., J. Meijer, L.A.T., M.T., M.W., R.J.A.W., H.R.W., C.D.M.K.), and United for Metabolic Diseases (A.B.P.K., R.J.A.W., H.R.W., C.D.M.K.), Amsterdam, and the Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht (J.J.F.A.V., J.H.V.), and the Project MinE ALS Sequencing Consortium (J.J.F.A.V., J.H.V.), Utrecht - all in the Netherlands; the Departments of Biochemistry and Molecular Biology and Medical Genetics, Cumming School of Medicine, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary (M.T.-G.), Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute (P.A.R., M.J.J., M.S.K., J. MacIsaac, W.W.W., C.D.M.K.), the Faculty of Pharmaceutical Sciences (B.I.D., G.E.B.W., C.J.R.), and the Departments of Medical Genetics (C.M., I.-S.R.-B., W.W.W.) and Pediatrics (C.D.M.K.), University of British Columbia, Vancouver, the Zebrafish Centre for Advanced Drug Discovery, St. Michael's Hospital and University of Toronto (K.B.-A., F.K., M.L., Y.W., X.-Y.W.), the Centre for Applied Genomics, Genetics and Genome Biology, the Hospital for Sick Children (C.N., S.W.S., B.T., R.K.C.Y.), and the Department of Molecular Genetics (C.N., S.W.S., R.K.C.Y.), the McLaughlin Centre (S.W.S.), and the Departments of Medicine, Physiology, and Laboratory Medicine and Pathobiology, Institute of Medical Science (X.-Y.W.), University of Toronto, Toronto, and the Division of Medical Genetics, Department of Pediatrics, Children's Hospital Eastern Ontario, University of Ottawa, Ottawa (J.S.W., M.T.G.) - all in Canada; the Departments of Medicine and Physiology, National University of Singapore (M.A.P.), and the Translational Laboratory in Genetic Medicine, Agency for Science, Technology, and Research (M.A.P., B.S., X.X., J.Z.) - both in Singapore; Uppsala University, Department of Chemistry-Biomedical Center, Uppsala, Sweden (D.D.); Illumina, San Diego, CA (E.D., M.A.E.); Gene Structure and Disease Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (B.H., D.K., K.U.); and the Department of Clinical Inherited Metabolic Disorders, Birmingham Children's Hospital, Birmingham, United Kingdom (S.S.).

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http://dx.doi.org/10.1056/NEJMoa1806627DOI Listing
April 2019

Conservation of kinase-phosphorylation site pairings: Evidence for an evolutionarily dynamic phosphoproteome.

PLoS One 2018 14;13(8):e0202036. Epub 2018 Aug 14.

Vaccine and Infectious Disease Organization-International Vaccine Research Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202036PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091962PMC
January 2019

The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.

CMAJ 2018 02;190(5):E126-E136

The Centre for Applied Genomics (Reuter, Walker, Thiruvahindrapuram, Whitney, Yuen, Trost, Paton, Pereira, Herbrick, Wintle, Merico, Howe, MacDonald, Lu, Nalpathamkalam, Sung, Wang, Patel, Pellecchia, J. Wei, Strug, Bell, Kellam, Mahtani, Hosseini, Fiume, Marshall, Buchanan, Scherer); Divisions of Clinical Pharmacology and Toxicology (I. Cohn), or Clinical, and Metabolic Genetics (Sondheimer, Weksberg, Shuman, Bowdin, Meyn, Monfared), The Hospital for Sick Children; Departments of Paediatrics (Sondheimer, R. Cohn) and Molecular Genetics (Yuen, Weksberg, Shuman, R. Cohn, Ellis, Meyn), University of Toronto; Deep Genomics Inc. (Merico); Department of Psychiatry (Bassett), University Health Network and Centre for Addiction and Mental Health, University of Toronto; Li Ka Shing Knowledge Institute (Bombard), St. Michael's Hospital; Institute of Health Policy, Management and Evaluation (Bombard), University of Toronto; Centre for Genetic Medicine (Stavropoulos, Bowdin, Ray, Monfared); Molecular Genetics Laboratory (Stavropoulos, Ray, Marshall), Division of Genome Diagnostics, Paediatric Laboratory Medicine; Developmental and Stem Cell Biology (Hildebrandt, W. Wei, Romm, Pasceri, Ellis); Ted Rogers Cardiac Genome Clinic (Hosseini); Cytogenetics Laboratory (Joseph-George), Division of Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children; Departments of Biochemistry and Laboratory Medicine, and Pathobiology (Keeley), University of Toronto; DNAstack (Cook, Fiume); McLaughlin Centre (Lee, Scherer), University of Toronto; Medcan Health Management Inc. (Davies, Hazell); Dalla Lana School of Public Health (Szego), Department of Family and Community Medicine, and The Joint Centre for Bioethics, University of Toronto; Centre for Clinical Ethics (Szego), St. Joseph's Health Centre, Toronto, Ont.

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http://dx.doi.org/10.1503/cmaj.171151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798982PMC
February 2018

A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data.

Am J Hum Genet 2018 01;102(1):142-155

The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5G 0A4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777982PMC
January 2018

Technological advances for interrogating the human kinome.

Biochem Soc Trans 2017 02;45(1):65-77

Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada

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http://dx.doi.org/10.1042/BST20160163DOI Listing
February 2017

Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites.

PLoS One 2016 5;11(4):e0152809. Epub 2016 Apr 5.

Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152809PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821552PMC
August 2016

DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites.

J Proteome Res 2016 08 13;15(8):2760-7. Epub 2016 Jul 13.

Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada.

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http://dx.doi.org/10.1021/acs.jproteome.6b00304DOI Listing
August 2016

Peptide Arrays for Kinome Analysis of Livestock Species.

Front Vet Sci 2014 14;1. Epub 2014 Oct 14.

VIDO-InterVac, University of Saskatchewan , Saskatoon, SK , Canada ; Department of Biochemistry, University of Saskatchewan , Saskatoon, SK , Canada.

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http://dx.doi.org/10.3389/fvets.2014.00004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668848PMC
December 2015

A Comparison of the Chicken and Turkey Proteomes and Phosphoproteomes in the Development of Poultry-Specific Immuno-Metabolism Kinome Peptide Arrays.

Front Vet Sci 2014 13;1:22. Epub 2014 Nov 13.

United States Department of Agriculture, Southern Plains Agricultural Research Center (SPARC), Agricultural Research Service , College Station, TX , USA.

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http://dx.doi.org/10.3389/fvets.2014.00022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668846PMC
December 2015

Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.

R Soc Open Sci 2015 Sep 30;2(9):150402. Epub 2015 Sep 30.

Department of Life Sciences , Brunel University , Uxbridge UB8 3PH, UK ; Department of Food and Bioproduct Sciences , University of Saskatchewan , Saskatoon Canada S7N 5A8.

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http://dx.doi.org/10.1098/rsos.150402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593695PMC
September 2015

EpIC: a rational pipeline for epitope immunogenicity characterization.

Bioinformatics 2015 Jul 6;31(14):2388-90. Epub 2015 Mar 6.

Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, S7N 5E5 Canada, Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, S7N 5E3 Canada and.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495294PMC
July 2015

Induction of tissue- and stressor-specific kinomic responses in chickens exposed to hot and cold stresses.

Poult Sci 2015 Jun 1;94(6):1333-45. Epub 2015 Apr 1.

Department of Food and Bioproduct Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada.

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http://dx.doi.org/10.3382/ps/pev046DOI Listing
June 2015

Characterization of the host response to pichinde virus infection in the Syrian golden hamster by species-specific kinome analysis.

Mol Cell Proteomics 2015 Mar 8;14(3):646-57. Epub 2015 Jan 8.

§§Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA;

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http://dx.doi.org/10.1074/mcp.M114.045443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349984PMC
March 2015

PIIKA 2: an expanded, web-based platform for analysis of kinome microarray data.

PLoS One 2013 29;8(11):e80837. Epub 2013 Nov 29.

Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada ; Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080837PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843739PMC
September 2014

Ebola virus modulates transforming growth factor β signaling and cellular markers of mesenchyme-like transition in hepatocytes.

J Virol 2014 Sep 18;88(17):9877-92. Epub 2014 Jun 18.

Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA.

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http://dx.doi.org/10.1128/JVI.01410-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136307PMC
September 2014

Equivalent input produces different output in the UniFrac significance test.

BMC Bioinformatics 2014 Aug 13;15:278. Epub 2014 Aug 13.

Department of Computer Science, University of Saskatchewan, 176 Thorvaldson Bldg, 110 Science Place, Saskatoon, Canada.

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http://dx.doi.org/10.1186/1471-2105-15-278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141948PMC
August 2014

Identification of developmentally-specific kinotypes and mechanisms of Varroa mite resistance through whole-organism, kinome analysis of honeybee.

Front Genet 2014 21;5:139. Epub 2014 May 21.

Vaccine and Infectious Disease Organization, University of Saskatchewan Saskatoon, SK, Canada ; Department of Biochemistry, University of Saskatchewan Saskatoon, SK, Canada.

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http://dx.doi.org/10.3389/fgene.2014.00139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033134PMC
June 2014

Kinotypes: stable species- and individual-specific profiles of cellular kinase activity.

BMC Genomics 2013 Dec 5;14:854. Epub 2013 Dec 5.

Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada.

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http://dx.doi.org/10.1186/1471-2164-14-854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924188PMC
December 2013

Divergent immune responses to Mycobacterium avium subsp. paratuberculosis infection correlate with kinome responses at the site of intestinal infection.

Infect Immun 2013 Aug 28;81(8):2861-72. Epub 2013 May 28.

Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

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http://dx.doi.org/10.1128/IAI.00339-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719570PMC
August 2013

DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.

Bioinformatics 2013 Jul 8;29(13):1693-5. Epub 2013 May 8.

Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt265DOI Listing
July 2013

Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights.

Bioinformatics 2013 Mar 22;29(6):686-94. Epub 2013 Jan 22.

Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt031DOI Listing
March 2013

Comparing the similarity of different groups of bacteria to the human proteome.

PLoS One 2012 25;7(4):e34007. Epub 2012 Apr 25.

Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034007PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338800PMC
September 2012

Systems kinomics demonstrates Congo Basin monkeypox virus infection selectively modulates host cell signaling responses as compared to West African monkeypox virus.

Mol Cell Proteomics 2012 Jun 28;11(6):M111.015701. Epub 2011 Dec 28.

Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1074/mcp.M111.015701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433897PMC
June 2012

A systematic approach for analysis of peptide array kinome data.

Sci Signal 2012 Apr 17;5(220):pl2. Epub 2012 Apr 17.

Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada.

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http://dx.doi.org/10.1126/scisignal.2002429DOI Listing
April 2012

Computational prediction of eukaryotic phosphorylation sites.

Bioinformatics 2011 Nov 16;27(21):2927-35. Epub 2011 Sep 16.

Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btr525DOI Listing
November 2011

Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera.

BMC Microbiol 2010 Oct 13;10:258. Epub 2010 Oct 13.

Department of Computer Science, University of Saskatchewan, 176 Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada.

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http://dx.doi.org/10.1186/1471-2180-10-258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020658PMC
October 2010

No human protein is exempt from bacterial motifs, not even one.

Self Nonself 2010 Oct;1(4):328-334

Department of Computer Science; University of Saskatchewan; Saskatoon, Canada.

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http://dx.doi.org/10.4161/self.1.4.13315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062388PMC
October 2010

The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand.

BMC Bioinformatics 2010 Jul 20;11:383. Epub 2010 Jul 20.

Department of Biochemistry and Molecular Biology Ernesto Quagliariello, University of Bari, Bari, Italy.

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http://dx.doi.org/10.1186/1471-2105-11-383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919516PMC
July 2010

Bacterial peptides are intensively present throughout the human proteome.

Self Nonself 2010 Jan;1(1):71-74

Department of Computer Science; University of Saskatchewan; Saskatoon, SK CA.

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http://dx.doi.org/10.4161/self.1.1.9588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091599PMC
January 2010

Codon number shapes peptide redundancy in the universal proteome composition.

Peptides 2009 Oct 8;30(10):1940-4. Epub 2009 Jul 8.

Department of Computer Science, University of Saskatchewan, Saskatoon, Canada.

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http://dx.doi.org/10.1016/j.peptides.2009.06.035DOI Listing
October 2009

Statistical characterization of the GxxxG glycine repeats in the flagellar biosynthesis protein FliH and its Type III secretion homologue YscL.

BMC Microbiol 2009 Apr 16;9:72. Epub 2009 Apr 16.

Department of Computer Science, University of Saskatchewan, 110 Science Place, Saskatoon, S7N 5C9, Canada.

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http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-
Publisher Site
http://dx.doi.org/10.1186/1471-2180-9-72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674601PMC
April 2009

Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools.

Immunome Res 2007 Mar 24;3. Epub 2007 Mar 24.

Department of Computer Science, University of Saskatchewan, Saskatchewan, Canada.

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http://dx.doi.org/10.1186/1745-7580-3-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847428PMC
March 2007