John Parkinson

Summary

Affiliation: The Hospital for Sick Children
Country: Canada

Publications

  1. pmc NEMBASE: a resource for parasitic nematode ESTs
    John Parkinson
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King s Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK
    Nucleic Acids Res 32:D427-30. 2004
  2. ncbi request reprint A transcriptomic analysis of the phylum Nematoda
    John Parkinson
    Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
    Nat Genet 36:1259-67. 2004
  3. ncbi request reprint PartiGene--constructing partial genomes
    John Parkinson
    School of Biological Sciences, Ashworth Laboratories, King s Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
    Bioinformatics 20:1398-404. 2004
  4. pmc Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human
    Shuye Pu
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
    PLoS ONE 5:e14122. 2010
  5. ncbi request reprint Comparative genomics of elastin: Sequence analysis of a highly repetitive protein
    David He
    Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario Canada M5G 1X8
    Matrix Biol 26:524-40. 2007
  6. doi request reprint Phylogenomic analysis of EST datasets
    Jose M Peregrin-Alvarez
    Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Methods Mol Biol 533:257-76. 2009
  7. doi request reprint The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
    Tuan On
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Proteins 78:2075-89. 2010
  8. pmc Bacteriome.org--an integrated protein interaction database for E. coli
    Chong Su
    Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
    Nucleic Acids Res 36:D632-6. 2008
  9. pmc DAnCER: disease-annotated chromatin epigenetics resource
    Andrei L Turinsky
    Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Nucleic Acids Res 39:D889-94. 2011
  10. doi request reprint PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya
    Xuejian Xiong
    Program in Molecular Structure and Function, Hospital for Sick Children, Canada
    Bioinformatics 27:877-8. 2011

Detail Information

Publications47

  1. pmc NEMBASE: a resource for parasitic nematode ESTs
    John Parkinson
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King s Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK
    Nucleic Acids Res 32:D427-30. 2004
    ..Other developments include access to accurate peptide predictions, improved functional annotation and incorporation of automated processes allowing rapid analysis of nematode-specific gene families...
  2. ncbi request reprint A transcriptomic analysis of the phylum Nematoda
    John Parkinson
    Hospital for Sick Children, 555 University Avenue, Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada
    Nat Genet 36:1259-67. 2004
    ..Nematode-specific families are particularly interesting as drug and vaccine targets...
  3. ncbi request reprint PartiGene--constructing partial genomes
    John Parkinson
    School of Biological Sciences, Ashworth Laboratories, King s Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
    Bioinformatics 20:1398-404. 2004
    ..nematodes.org/PartiGene and also forms part of the EST analysis software, associated with the Natural Environmental Research Council (UK) Bio-Linux project (http://envgen.nox.ac.uk/biolinux.html)...
  4. pmc Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human
    Shuye Pu
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
    PLoS ONE 5:e14122. 2010
    ..Information on all the candidate CM domains and genes reported here is publicly available...
  5. ncbi request reprint Comparative genomics of elastin: Sequence analysis of a highly repetitive protein
    David He
    Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario Canada M5G 1X8
    Matrix Biol 26:524-40. 2007
    ..The success of this approach for elastin offers a promising route to the elucidation of sequence, structure, function and evolutionary relationships for many other proteins with sequences of low complexity...
  6. doi request reprint Phylogenomic analysis of EST datasets
    Jose M Peregrin-Alvarez
    Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Methods Mol Biol 533:257-76. 2009
    ..The second focuses on the use of phylogenetic profiles to identify groups of taxonomically related sequences...
  7. doi request reprint The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
    Tuan On
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Proteins 78:2075-89. 2010
    ..As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems...
  8. pmc Bacteriome.org--an integrated protein interaction database for E. coli
    Chong Su
    Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
    Nucleic Acids Res 36:D632-6. 2008
    ..Bacteriome.org is available online at http://www.bacteriome.org...
  9. pmc DAnCER: disease-annotated chromatin epigenetics resource
    Andrei L Turinsky
    Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Nucleic Acids Res 39:D889-94. 2011
    ..DAnCER is freely available at http://wodaklab.org/dancer/...
  10. doi request reprint PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya
    Xuejian Xiong
    Program in Molecular Structure and Function, Hospital for Sick Children, Canada
    Bioinformatics 27:877-8. 2011
    ..PhyloPro thus provides a valuable resource for the evolutionary and comparative studies of biological systems...
  11. ncbi request reprint SimiTri--visualizing similarity relationships for groups of sequences
    John Parkinson
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    Bioinformatics 19:390-5. 2003
    ..SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors...
  12. ncbi request reprint 400000 nematode ESTs on the Net
    John Parkinson
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King s Buildings, West Mains Rd, University of Edinburgh, EH9 3JT, Edinburgh, UK
    Trends Parasitol 19:283-6. 2003
    ..Over 400000 nematode ESTs are now available and at least another 130000 are planned. Here, an update is provided on the status of the project and describes the database tools being developed to disseminate these data...
  13. pmc Polymorphisms in the human tropoelastin gene modify in vitro self-assembly and mechanical properties of elastin-like polypeptides
    David He
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    PLoS ONE 7:e46130. 2012
    ....
  14. pmc The Modular Organization of Protein Interactions in Escherichia coli
    Jose M Peregrin-Alvarez
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    PLoS Comput Biol 5:e1000523. 2009
    ..Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks...
  15. doi request reprint DETECT--a density estimation tool for enzyme classification and its application to Plasmodium falciparum
    Stacy S Hung
    Program in Molecular Structure and Function, Hospital for Sick Children, 15 704 MaRS TMDT East, 101 College Street, Toronto, ON M5G 1L7, Canada
    Bioinformatics 26:1690-8. 2010
    ..As such, these methods are often error-prone and lack useful measures of reliability for the prediction...
  16. pmc Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing
    Xuejian Xiong
    Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Canada
    PLoS ONE 7:e36009. 2012
    ..These maps identified bacterial processes with components that were well-represented in the datasets. In summary this study highlights the potential of exploiting the economy of HTS platforms for metatranscriptomics...
  17. pmc The origins of apicomplexan sequence innovation
    James Wasmuth
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 2L3, Canada
    Genome Res 19:1202-13. 2009
    ..Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival...
  18. doi request reprint SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences
    David He
    Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
    Bioinformatics 24:1016-7. 2008
    ..Given their abundance, we suggest that SubSeqer represents a valuable resource for the study of typically neglected low-complexity sequences...
  19. pmc Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites
    Yvonne M Harcus
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
    Genome Biol 5:R39. 2004
    ..Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity...
  20. pmc Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays
    Avinash Persaud
    Programs in Cell Biology and Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
    Mol Syst Biol 5:333. 2009
    ..g. FGFR), suggesting Nedd4-1 suppresses their signalling. These results demonstrate the feasibility of identifying substrates and deciphering substrate specificity of mammalian E3 ligases...
  21. pmc Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures
    Hongyan Song
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    PLoS Comput Biol 8:e1002406. 2012
    ..In addition to providing insights into the evolution of elastomeric proteins, simulations such as those presented here may prove valuable for the tuneable design of new molecules that may be exploited as useful biomaterials...
  22. pmc The conservation and evolutionary modularity of metabolism
    Jose M Peregrin-Alvarez
    Program in Molecular Structure and Function, Hospital for Sick Children, College Street, Toronto, ON M5G1L7, Canada
    Genome Biol 10:R63. 2009
    ..Here we supplement existing genome and protein resources with partial genome datasets derived from 193 eukaryotes to present a comprehensive survey of the conservation of metabolism across 26 taxa representing the three domains of life...
  23. pmc Making sense of EST sequences by CLOBBing them
    John Parkinson
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Bioinformatics 3:31. 2002
    ..To increase the amount of information obtainable from ESTs and reduce sequencing errors, it is necessary to cluster ESTs into groups sharing significant sequence similarity...
  24. ncbi request reprint Expressed sequence tags: analysis and annotation
    John Parkinson
    Institute of Cell, Animal, and Population Biology, Ashworth Laboratories, University of Edinburgh, UK
    Methods Mol Biol 270:93-126. 2004
    ..The systems are written to use the public-domain LINUX environment and other openly available analytical tools...
  25. pmc IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype
    P ng Loke
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
    BMC Immunol 3:7. 2002
    ..Due in part to a lack of markers, these cells have not been well characterized in vivo and their function remains unknown...
  26. pmc A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation
    John Parkinson
    Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
    PLoS Negl Trop Dis 6:e1897. 2012
    ..granulosus larval stages. We report the salient features of this study with a focus on genes reflecting physiological adaptations of different parasite stages...
  27. doi request reprint Toward a systems level view of the ECM and related proteins: a framework for the systematic definition and analysis of biological systems
    Graham L Cromar
    Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Proteins 80:1522-44. 2012
    ..In addition to demonstrating an effective workflow for defining biological systems, this study crystallizes our current knowledge surrounding the organization of the ECM...
  28. pmc Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways
    Mohan Babu
    Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Canada
    PLoS Genet 7:e1002377. 2011
    ....
  29. pmc The global landscape of sequence diversity
    José Manuel Peregrín-Alvarez
    Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
    Genome Biol 8:R238. 2007
    ....
  30. pmc Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast
    Ronish Gupta
    Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
    Mol Syst Biol 3:116. 2007
    ..The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets...
  31. ncbi request reprint The Brugia malayi genome project: expressed sequence tags and gene discovery
    Mark Blaxter
    Institute of Cell, Animal and Population Biology, Ashworth Laboratories, Kings Buildings, University of Edinburgh, Edinburgh EH9 3JT, UK
    Trans R Soc Trop Med Hyg 96:7-17. 2002
    ..Building on the success of the B. malayi EST programme, significant EST datasets are being generated for a number of other major parasites of humans and domesticated animals, and model parasitic species...
  32. doi request reprint A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators
    Zhou Yu
    Department of Molecular Genetics, University of Toronto, 4285 Medical Sciences Building, 1 King s College Circle, Toronto, Ontario, Canada
    J Mol Biol 400:847-64. 2010
    ..Finally, our analysis of TFR structures highlights their flexibility and provides insight into a conserved allosteric mechanism for this family...
  33. pmc PartiGeneDB--collating partial genomes
    Jose M Peregrin-Alvarez
    Program in Genetics and Genomic Biology, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
    Nucleic Acids Res 33:D303-7. 2005
    ..PartiGeneDB currently contains the assembled partial genomes derived from 1.83 million sequences associated with 247 different eukaryotes...
  34. ncbi request reprint Cell++--simulating biochemical pathways
    Chris Sanford
    Hospital for Sick Children, 555 University Avenue Toronto, ON, M5G 1X8, Canada
    Bioinformatics 22:2918-25. 2006
    ..Here, we introduce Cell++, a novel stochastic simulation environment with the capacity to study a wide variety of biochemical processes within a spatial context...
  35. ncbi request reprint Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: Clues to the evolutionary history of elastins
    Martin I S Chung
    Cardiovascular Research Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada M5G1X8
    Matrix Biol 25:492-504. 2006
    ....
  36. ncbi request reprint Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    Nevan J Krogan
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada
    Nature 440:637-43. 2006
    ..The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology...
  37. doi request reprint Expressed sequence tags: an overview
    John Parkinson
    Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
    Methods Mol Biol 533:1-12. 2009
    ..Chapters are presented which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis of ESTs; and their application to phylogenetics and transcript profiling...
  38. ncbi request reprint Interaction network containing conserved and essential protein complexes in Escherichia coli
    Gareth Butland
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Nature 433:531-7. 2005
    ..This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota...
  39. doi request reprint Characterization of the Arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies
    Yolanda T Chong
    Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2
    New Phytol 185:401-19. 2010
    ..Overall subcellular localization patterns were observed that were also found in yeast and animal cells, and this, coupled with the evolutionary relationships, suggests that the exocyst may perform similar conserved functions in plants...
  40. doi request reprint Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome
    Walter H A Kahr
    Department of Paediatrics, University of Toronto, Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
    Nat Genet 43:738-40. 2011
    ..NBEAL2 encodes a protein containing a BEACH domain that is predicted to be involved in vesicular trafficking and may be critical for the development of platelet α-granules...
  41. pmc The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet α-granule biogenesis
    Denisa Urban
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
    Blood 120:5032-40. 2012
    ..We conclude that VPS16B, similar to its binding partner VPS33B, is essential for megakaryocyte and platelet α-granule biogenesis...
  42. doi request reprint Post-genomics resources and tools for studying apicomplexan metabolism
    Stacy S Hung
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Trends Parasitol 27:131-40. 2011
    ..Furthermore, how these datasets can be utilized to explore the metabolic capabilities of apicomplexans are discussed and targets for therapeutic intervention are prioritized...
  43. ncbi request reprint Large-scale modelling as a route to multiple surface comparisons of the CCP module family
    Dinesh C Soares
    Biocomputing Research Unit, Michael Swann Building, University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    Protein Eng Des Sel 18:379-88. 2005
    ..This observation might reflect adaptive evolution of surface-exposed residues involved in protein-protein interactions. This illustrative example of a multiple surface-comparison was indeed able to pinpoint functional sites in CR1...
  44. pmc A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
    Isabel Aznarez
    Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
    Genome Res 18:1247-58. 2008
    ..Based on our results, we estimate that approximately 15% of alternative cassette exons are regulated by TIA1/TIAL1 via U-rich intronic elements...
  45. pmc Sequencing and annotation of the Ophiostoma ulmi genome
    Shima Khoshraftar
    Department of Cell and Systems Biology University of Toronto, Toronto, Canada
    BMC Genomics 14:162. 2013
    ..O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics...
  46. pmc Identification of a functional connectome for long-term fear memory in mice
    Anne L Wheeler
    Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada
    PLoS Comput Biol 9:e1002853. 2013
    ..This network is concurrently integrated and segregated and therefore has small-world properties, and contains hub-like regions in the prefrontal cortex and thalamus that may play privileged roles in memory expression...
  47. ncbi request reprint A critical review of financial measures as reported in the Ontario hospital balanced scorecard
    John Parkinson
    School of Administrative Studies, York University, Toronto, Ontario, Canada
    J Health Care Finance 34:48-56. 2007
    ..We suggest changes that focus on key drivers of performance and reflect the operational realities of Ontario hospitals...