Parkinson, John - University of Toronto - Department of Biochemistry

个人简介

Dr John Parkinson is a computational biologist whose research interests focus on the impact of microbiota on human health. After completing his PhD at the University of Manchester, studying molecular self-assembly, John spent a year at the University of Manitoba investigating diatom morphogenesis. In 1997, John moved to Edinburgh where he applied computer models to study the evolution of complement control proteins with Dr Paul Barlow. With the emergence of high throughput sequencing, John then led the bioinformatics efforts associated with the parasitic nematode expressed sequence tag project, responsible for the processing and curation of sequence data from 30 species of parasitic nematodes. John was recruited to the Hospital for Sick Children in 2003 and was promoted to Senior Scientist in 2009. He holds cross-appointments in both the departments of Biochemsitry and Molecular Genetics at the University of Toronto. Current lab interests center on the role of the microbiome in health and disease as well as the mechanisms that allow pathogens and parasites to survive and persist in their human hosts. Key to this research is the integration of computational systems biology analyses with comparative genomics to explore the evolution and operation of microbial pathways driving pathogenesis. Findings from our research programs are helping guide new strategies for therapeutic intervention.

研究领域

Research in the Parkinson lab is largely driven through the development and application of computational methods.We work with an extensive network of clinicians, parasitologists and immunologists to generate and analyse genomic, metagenomic, metatranscriptomic and metabolomic datasets from a variety of patient and environmental samples. Exploiting the University of Toronto’s high performance computing platform (SciNet), these datasets are integrated to develop new insights into the evolution of parasites, pathogens and microbiomes and how their interact with their host. Trainees in our lab typically possess expertise in programming (C++/Java/Perl / Python); cloud computing; relational database management; maths and statistics. Over the course of their studies, trainees typically acquire skills in machine learning algorithms; genome annotation; next generation sequencing; metagenomics; phylogenetics; sequence processing; network biology; metabolic reconstruction; and constraints based modelling. In addition to our dry lab activities, we also maintain a wet lab with tissue culture facilities for the culturing of Toxoplasma strains for biochemical and proteomic investigations. Below is an image of a GFP-tagged strain of parasites growing in HFF cells.

近期论文

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Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality Jiang Y, Xiong X, Danska J, Parkinson J. Microbiome 2016 4:2 Read The genome of Onchocerca volvulus, agent of river blindness. Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. Nature Microbiology 2016 2:16216. Read Hyperscape: visualization for complex biological networks Cromar GL, Zhao A, Yang A, Parkinson J. Bioinformatics 2015 31: 3390-3391 Read Panorama of ancient metazoan macromolecular complexes. Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Nature 2015 525:339-344. Read New tricks for ‘old’ domains: How novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM Cromar G, Wong KC, Loughran N, On T, Song H, Xiong X, Zhang Z, Parkinson J. Genome Biology and Evolution 2014 Oct 15. pii: evu228. Read Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii. Song C, Chiasson MA, Nursimulu N, Hung SS, Wasmuth J, Grigg ME, Parkinson J. Molecular Systems Biology 2013 9: 708. Read The genomes of four tapeworm species reveal adaptations to parasitism. Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai J, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernández C, Holland PW, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, Kiss F, Koziol U, Lambert O, Liu K, Luo X, Luo Y, Macchiaroli N, Nichol S, Paps J, Parkinson J, Pouchkina-Stantcheva N, Riddiford N, Rosenzvit M, Salinas G, Wasmuth JD, Zamanian M, Zheng Y; Taenia solium Genome Consortium., Cai X, Soberón X, Olson PD, Laclette JP, Brehm K, Berriman M. Nature 2013 496. 57-63. Read A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. Parkinson J, Wasmuth JD, Salinas G, Bizarro CV, Sanford C, Berriman M, Ferreira HB, Zaha A, Blaxter ML, Maizels RM, Fernández C. PLoS Neglected Tropical Diseases 2012 6(11): e1897. Read