Shoshana Wodak

Summary

Affiliation: The Hospital for Sick Children
Country: Canada

Publications

  1. ncbi request reprint Integrative bioinformatics: making sense of the networks
    Shoshana J Wodak
    Biochemistry Department, University of Toronto, Medical Sciences Building, 1 King s College Circle, Toronto, Ont, Canada M5S 1A8 Electronic
    Drug Discov Today Technol 1:179-87. 2004
  2. pmc Literature curation of protein interactions: measuring agreement across major public databases
    Andrei L Turinsky
    Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
    Database (Oxford) 2010:baq026. 2010
  3. 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
  4. pmc iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
    Brian Turner
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Database (Oxford) 2010:baq023. 2010
  5. 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
  6. pmc Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences
    Miguel A Santos
    Molecular Structure and Function Program, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
    Nucleic Acids Res 38:7927-42. 2010
  7. ncbi request reprint Protein-protein interaction networks: the puzzling riches
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5K 1X8, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada Electronic address
    Curr Opin Struct Biol 23:941-53. 2013
  8. doi request reprint Challenges and rewards of interaction proteomics
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Mol Cell Proteomics 8:3-18. 2009
  9. doi request reprint High-throughput analyses and curation of protein interactions in yeast
    Shoshana J Wodak
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Methods Mol Biol 759:381-406. 2011
  10. pmc Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    James Vlasblom
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
    BMC Bioinformatics 10:99. 2009

Collaborators

  • Shuye Pu
  • James Vlasblom
  • John Parkinson
  • Zhaolei Zhang
  • Yi an Chen
  • Stephen W Scherer
  • Dong Dong
  • Martha L Bulyk
  • Joel Janin
  • Sabry Razick
  • Yunchen Gong
  • Rosanna Weksberg
  • Carolyn A Bondy
  • Andrei L Turinsky
  • Brian Turner
  • Lila Aiyar
  • Jia Xin Jiang
  • Daria Grafodatskaya
  • Ian M Donaldson
  • Miguel A Santos
  • Benoit H Dessailly
  • Guillaume Launay
  • Lea Velsher
  • Annie Dupuis
  • Robin Hayeems
  • David Chitayat
  • Cheryl Shuman
  • Jill Davies
  • Cindy Skinner
  • Jill Hamilton
  • Charles E Schwartz
  • Chris Sotiropolous
  • Sarah J Goodman
  • Rageen Rajendram
  • Fatima E Abidi
  • Barian H Y Chung
  • James Stavropoulos
  • Darius J Bagli
  • Tyler Kirwan
  • Darci T Butcher
  • Trupti Panchal
  • Cornelia Tolg
  • Chunhua Zhao
  • Youliang Lou
  • Karen J Aitken
  • Nicole Zhang
  • Sana Choufani
  • Michael Heath
  • Xuejian Xiong
  • Jack Greenblatt
  • Tuan On
  • James A Gleeson
  • Rosanne C Borja
  • Andrew Emili
  • Thomas Switzer
  • Serene Ong
  • Andrew R Gehrke
  • Michael F Berger
  • Edgard K Crowdy
  • Gwenael Badis
  • Emerson Cho
  • Shaheynoor Talukder
  • Timothy R Hughes
  • Kyle Morrison
  • Jennifer Tsai
  • Thomas Simonson
  • Raul Mendez
  • Marc F Lensink

Detail Information

Publications16

  1. ncbi request reprint Integrative bioinformatics: making sense of the networks
    Shoshana J Wodak
    Biochemistry Department, University of Toronto, Medical Sciences Building, 1 King s College Circle, Toronto, Ont, Canada M5S 1A8 Electronic
    Drug Discov Today Technol 1:179-87. 2004
    ..The new exciting developments in bioinformatics show great promise in meeting the challenge of extracting biological insight from these data.: ..
  2. pmc Literature curation of protein interactions: measuring agreement across major public databases
    Andrei L Turinsky
    Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
    Database (Oxford) 2010:baq026. 2010
    ..Database URL: http://wodaklab.org/iRefWeb...
  3. 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...
  4. pmc iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
    Brian Turner
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Database (Oxford) 2010:baq023. 2010
    ..iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/..
  5. 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/...
  6. pmc Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences
    Miguel A Santos
    Molecular Structure and Function Program, Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
    Nucleic Acids Res 38:7927-42. 2010
    ..The availability of quantitative descriptions of molecular function, such as DNA-binding data, will be a key factor in exploiting this potential in the future...
  7. ncbi request reprint Protein-protein interaction networks: the puzzling riches
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5K 1X8, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada Electronic address
    Curr Opin Struct Biol 23:941-53. 2013
    ..Lastly, we present a brief overview of the literature-curated protein interaction data stored in public databases, which are often relied upon for independent validation of newly derived interaction networks. ..
  8. doi request reprint Challenges and rewards of interaction proteomics
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Mol Cell Proteomics 8:3-18. 2009
    ..The challenges and rewards of interaction proteomics are reviewed here using as an example the latest comprehensive high throughput analyses of protein interactions in yeast...
  9. doi request reprint High-throughput analyses and curation of protein interactions in yeast
    Shoshana J Wodak
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Methods Mol Biol 759:381-406. 2011
    ....
  10. pmc Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    James Vlasblom
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
    BMC Bioinformatics 10:99. 2009
    ....
  11. pmc Relating destabilizing regions to known functional sites in proteins
    Benoit H Dessailly
    Service de Conformation des Macromolécules Biologiques, Centre de Biologie Structurale et Bioinformatique, CP 263, Universite Libre de Bruxelles, Bruxelles, Belgium
    BMC Bioinformatics 8:141. 2007
    ..In addition, to relate destabilizing regions to known functional sites, a novel benchmark consisting of a diverse set of hand-curated protein functional sites is derived...
  12. pmc Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets
    Guillaume Launay
    Laboratoire de Biochimie UMR CNRS 7654, Department of Biology, Ecole Polytechnique, 91128, Palaiseau, France
    BMC Bioinformatics 8:270. 2007
    ....
  13. ncbi request reprint The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007
    Joel Janin
    Yeast Structural Genomics, IBBMC, CNRS UMR 8619, Bat 430, Universite Paris Sud, 91405 Orsay, France, and Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
    Structure 15:755-9. 2007
    ....
  14. pmc Phenotypic switching induced by damaged matrix is associated with DNA methyltransferase 3A (DNMT3A) activity and nuclear localization in smooth muscle cells (SMC)
    Jia Xin Jiang
    Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada Department of Physiology, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 8:e69089. 2013
    ..Matrix has a profound effect on the regulation of SMC phenotype, which is associated with altered expression, localization of DNMTs and discrete changes DNA methylation. ..
  15. pmc Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C
    Daria Grafodatskaya
    Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
    BMC Med Genomics 6:1. 2013
    ..Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment...
  16. doi request reprint Risk estimates for complex disorders: comparing personal genome testing and family history
    Lila Aiyar
    1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada 2 Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada 3 Fetal Diagnostic Center, Kapiolani Medical Center for Women and Children, Honolulu, Hawaii, USA
    Genet Med 16:231-7. 2014
    ..g., family history analysis). We sought to analyze the concordance of risk estimates generated by family history analysis and by personal genome testing...