Category: Uncategorized

  • Timothy Lo

    Timothy Lo
    Graduate student

    Lab: ESC 3068
    Email: timothy.lo@utoronto.ca






    Publications:

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  • Shalabh Thakur

    Shalabh Thakur
    Graduate student







    Publications:

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  • Amy Zhang

    Amy Zhang
    Graduate student

    B.Sc. University of British Columbia

    Lab: ESC 4039
    Email: amyxw.zhang@mail.utoronto.ca

  • Sylva Donaldson

    Sylva Donaldson, PhD.
    Project Manager

    B.Sc.Hon Queen’s University, Molecular Biology
    M.Sc. University of New Brunswick, Marine Biology
    Ph.D. University of Toronto, Botany

    Email: sylva.donaldson@utoronto.ca



    Publications:

    Detection of Covid-19 Outbreaks Using Built Environment Testing for SARS-CoV-2.
    Fralick, M, Nott, C, Moggridge, J, Castellani, L, Raudanskis, A, Guttman, DS, Hinz, A, Thampi, N, Wong, A, Manuel, D, McGeer, A, Doukhanine, E, Mejbel, H, Zanichelli, V, Burella, M, Donaldson, SL, Wang, PW, Kassen, R, MacFadden, DR.
    NEJM Evid.2,2023. PubMed PMID:38320044

    Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations.
    Layeghifard, M, Li, H, Wang, PW, Donaldson, SL, Coburn, B, Clark, ST, Caballero, JD, Zhang, Y, Tullis, DE, Yau, YCW, Waters, V, Hwang, DM, Guttman, DS.
    NPJ Biofilms Microbiomes.5,2019. PubMed PMID:30675371

    Penicillin-binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with β-lactams.
    Clark, ST, Sinha, U, Zhang, Y, Wang, PW, Donaldson, SL, Coburn, B, Waters, VJ, Yau, YCW, Tullis, DE, Guttman, DS, Hwang, DM.
    Int J Antimicrob Agents.53,2019. PubMed PMID:30664925

    A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans.
    Diaz Caballero, J, Clark, ST, Wang, PW, Donaldson, SL, Coburn, B, Tullis, DE, Yau, YCW, Waters, VJ, Hwang, DM, Guttman, DS.
    PLoS Pathog.14,2018. PubMed PMID:30532201

    Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung.
    Diaz Caballero, J, Clark, ST, Coburn, B, Zhang, Y, Wang, PW, Donaldson, SL, Tullis, DE, Yau, YC, Waters, VJ, Hwang, DM, Guttman, DS.
    mBio.6,2015. PubMed PMID:26330513

    Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis.
    Clark, ST, Diaz Caballero, J, Cheang, M, Coburn, B, Wang, PW, Donaldson, SL, Zhang, Y, Liu, M, Keshavjee, S, Yau, YC, Waters, VJ, Elizabeth Tullis, D, Guttman, DS, Hwang, DM.
    Sci Rep.5,2015. PubMed PMID:26047320

    Lung microbiota across age and disease stage in cystic fibrosis.
    Coburn, B, Wang, PW, Diaz Caballero, J, Clark, ST, Brahma, V, Donaldson, S, Zhang, Y, Surendra, A, Gong, Y, Elizabeth Tullis, D, Yau, YC, Waters, VJ, Hwang, DM, Guttman, DS.
    Sci Rep.5,2015. PubMed PMID:25974282

    Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.
    Maughan, H, Wang, PW, Diaz Caballero, J, Fung, P, Gong, Y, Donaldson, SL, Yuan, L, Keshavjee, S, Zhang, Y, Yau, YC, Waters, VJ, Tullis, DE, Hwang, DM, Guttman, DS.
    PLoS One.7,2012. PubMed PMID:23056217

    The BioPAX community standard for pathway data sharing.
    Demir, E, Cary, MP, Paley, S, Fukuda, K, Lemer, C, Vastrik, I, Wu, G, D’Eustachio, P, Schaefer, C, Luciano, J, Schacherer, F, Martinez-Flores, I, Hu, Z, Jimenez-Jacinto, V, Joshi-Tope, G, Kandasamy, K, Lopez-Fuentes, AC, Mi, H, Pichler, E, Rodchenkov, I, Splendiani, A, Tkachev, S, Zucker, J, Gopinath, G, Rajasimha, H, Ramakrishnan, R, Shah, I, Syed, M, Anwar, N, Babur, O, Blinov, M, Brauner, E, Corwin, D, Donaldson, S, Gibbons, F, Goldberg, R, Hornbeck, P, Luna, A, Murray-Rust, P, Neumann, E, Ruebenacker, O, Samwald, M, van Iersel, M, Wimalaratne, S, Allen, K, Braun, B, Whirl-Carrillo, M, Cheung, KH, Dahlquist, K, Finney, A, Gillespie, M, Glass, E, Gong, L, Haw, R, Honig, M, Hubaut, O, Kane, D, Krupa, S, Kutmon, M, Leonard, J, Marks, D, Merberg, D, Petri, V, Pico, A, Ravenscroft, D, Ren, L, Shah, N, Sunshine, M, Tang, R, Whaley, R, Letovksy, S, Buetow, KH, Rzhetsky, A, Schachter, V, Sobral, BS, Dogrusoz, U, McWeeney, S, Aladjem, M, Birney, E, Collado-Vides, J, Goto, S, Hucka, M, Le Novère, N, Maltsev, N, Pandey, A, Thomas, P, Wingender, E, Karp, PD, Sander, C, Bader, GD.
    Nat Biotechnol.28,2010. PubMed PMID:20829833

    Cytoscape Web: an interactive web-based network browser.
    Lopes, CT, Franz, M, Kazi, F, Donaldson, SL, Morris, Q, Bader, GD.
    Bioinformatics.26,2010. PubMed PMID:20656902

    The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
    Warde-Farley, D, Donaldson, SL, Comes, O, Zuberi, K, Badrawi, R, Chao, P, Franz, M, Grouios, C, Kazi, F, Lopes, CT, Maitland, A, Mostafavi, S, Montojo, J, Shao, Q, Wright, G, Bader, GD, Morris, Q.
    Nucleic Acids Res.38,2010. PubMed PMID:20576703

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  • Maggie Wolven (Middleton)

    Maggie Wolven (Middleton)
    Lab technician

    B.Sc.Hon. University of Toronto, Biology

    Office: 4037
    Lab: ESC 4039
    Email: maggie.middleton@utoronto.ca







    Publications:

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  • Anu Surendra

    Anuradha Surendra
    Bioinformatician
















    Publications:
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  • André Severino

    André Santos Severino
    Lab technician

    Office: 4037
    Lab: ESC 4039
    Email: andre.santos.severino@utoronto.ca






    Publications:

    Incipient stem cell niche conversion in tissue culture: using a systems approach to probe early events in WUSCHEL-dependent conversion of lateral root primordia into shoot meristems.
    Chatfield, SP, Capron, R, Severino, A, Penttila, PA, Alfred, S, Nahal, H, Provart, NJ.
    Plant J.73,2013. PubMed PMID:23181633

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  • David Guttman

    David S. Guttman, PhD.

    Canada Research Chair in Comparative Genomics
    Associate Chair for Research
    Director, Centre for the Analysis of Genome Evolution & Function

    Education:
    Ph.D. Stony Brook University 1994
    B.Sc. Washington University in St. Louis 1987

    Research Areas

    Bioinformatics & Computational Biology
    Comparative Genomics
    Evolutionary Biology
    Functional Genomics
    Genetics
    Microbiology
    Pathology
    Plant Biology

    Research
    The Guttman lab has two major foci. First, we are studying the evolution of host specificity and virulence in pathogenic bacteria. We are specifically interested in identifying the genetic determinants of host specificity, and determining what factors determine if a particular bacterial-host interaction is benign or results in disease. Our work will lead to a better understanding of where the genetic potential for virulence originates and how is it maintained in bacterial populations. Most of this work is done with the agriculturally important plant pathogen Pseudomonas syringae and the model plant Arabidopsis thaliana. Our second focus is on the structure, dynamics, and function of bacterial communities (microbiomes) associated with both humans and plants. We are specifically interested in understanding how polymicrobial communities influence the expression and course of disease. Microbiomes have been shown to dramatically influence immune development and disease resistance and progression. Most of this work is focused on cystic fibrosis, and plant resistance, although we also study a number of other human pathologies such as inflammatory bowel disease. We use a wide range of comparative, evolutionary and functional genomic approaches in the group. We have a particularly strong emphasis on using evolutionary and bioinformatic approaches to generate hypotheses that can then be functionally validated through traditional molecular and biochemical assays.