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Timothy William Clark, M.SC.

TitleAssistant Professor of Neurology
InstitutionMassachusetts General Hospital
DepartmentNeurology
AddressPartners Research Building
Room 219
65 Landsdowne St
Cambridge MA 02139
Phone617/947-7098

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Yan Y, Clark TW, Mondschein JI, Shlansky-Goldberg RD, Dagli MS, Soulen MC, Stavropoulos SW, Sudheendra D, Mantell MP, Cohen RD, Kobrin S, Chittams JL, Trerotola SO. Outcomes of percutaneous interventions in transposed hemodialysis fistulas compared with nontransposed fistulas and grafts. J Vasc Interv Radiol. 2013 Dec; 24(12):1765-72; quiz 1773.
    View in: PubMed
  2. Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJ, Goble C, Clark T. PAV ontology: provenance, authoring and versioning. J Biomed Semantics. 2013; 4(1):37.
    View in: PubMed
  3. Clark T and Goble C. Encyclopedia of Systems Biology, Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho & Hiroki Yokota eds. The World-Wide Web. 2013.
  4. Clark T. Encyclopedia of Systems Biology. Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho & Hiroki Yokota (eds.),. Collaborative and distributed biomedical application. 2013.
  5. Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark T, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, López-Bigas N, Maojo V, Mons B, Musen M, Oliveira JL, Rowe A, Ruch P, Shabo A, Shortliffe EH, Valencia A, van der Lei J, Mayer MA, Sanz F. Improving data and knowledge management to better integrate health care and research. Journal of Internal Medicine. 2013; 4(274):321-8.
  6. Ciccarese P, Soiland-Reyes S, Clark T . Web Annotation as a First-Class Object. IEEE Internet Computing. 2013; (Nov/Dec).
  7. McFarland KN, Das S, Sun TT, Leyfer D, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark TW, Sadri-Vakili G, Cha JH. Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease. PLoS One. 2012; 7(7):e41423.
    View in: PubMed
  8. Ciccarese P, Ocana M, Clark T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics. 2012; 3 Suppl 1:S1.
    View in: PubMed
  9. Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database (Oxford). 2012; 2012:bas005.
    View in: PubMed
  10. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Toward interoperable bioscience data. Nat Genet. 2012 Feb; 44(2):121-6.
    View in: PubMed
  11. Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E, Shotton D. Improving Future Research Communication and e-Scholarship: A Summary of Findings. Informatik Spectrum. 2012; 1(35):56-57.
  12. Ciccarese P, Shotton S, Peroni S, Clark T . CITO+SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships. Semantic Web Journal. 2012.
  13. Sinha AU, Merrill E, Armstrong SA, Clark TW, Das S. eXframe: reusable framework for storage, analysis and visualization of genomics experiments. BMC Bioinformatics. 2011; 12:452.
    View in: PubMed
  14. Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T. An open annotation ontology for science on web 3.0. J Biomed Semantics. 2011; 2 Suppl 2:S4.
    View in: PubMed
  15. Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E, Shotton D. The Future of Research Communication and e-Scholarship. Dagstuhl Reports. 2011; 8(1).
  16. Das S, Girard L, Green T, Weitzman L, Lewis-Bowen A, Clark T. Building biomedical web communities using a semantically aware content management system. Brief Bioinform. 2009 Mar; 10(2):129-38.
    View in: PubMed
  17. Benn CL, Sun T, Sadri-Vakili G, McFarland KN, DiRocco DP, Yohrling GJ, Clark TW, Bouzou B, Cha JH. Huntingtin modulates transcription, occupies gene promoters in vivo, and binds directly to DNA in a polyglutamine-dependent manner. J Neurosci. 2008 Oct 15; 28(42):10720-33.
    View in: PubMed
  18. Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, Clark T. The SWAN biomedical discourse ontology. J Biomed Inform. 2008 Oct; 41(5):739-51.
    View in: PubMed
  19. Clark T. Knowledge Integration in Biomedicine: Technology and Community. Brief Bioinform. 2007 May 25.
    View in: PubMed
  20. Clark T, Kinoshita J. Alzforum and SWAN: the present and future of scientific web communities. Brief Bioinform. 2007 May; 8(3):163-71.
    View in: PubMed
  21. Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH. AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics. 2007; 8 Suppl 3:S4.
    View in: PubMed
  22. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing translational research with the Semantic Web. BMC Bioinformatics. 2007; 8 Suppl 3:S2.
    View in: PubMed
  23. Sadri-Vakili G, Bouzou B, Benn CL, Kim MO, Chawla P, Overland RP, Glajch KE, Xia E, Qiu Z, Hersch SM, Clark TW, Yohrling GJ, Cha JH. Histones associated with downregulated genes are hypo-acetylated in Huntington's disease models. Hum Mol Genet. 2007 Jun 1; 16(11):1293-306.
    View in: PubMed
  24. Cantuti-Castelvetri I, Keller-McGandy C, Bouzou B, Asteris G, Clark TW, Frosch MP, Standaert DG. Effects of gender on nigral gene expression and parkinson disease. Neurobiol Dis. 2007 Jun; 26(3):606-14.
    View in: PubMed
  25. Kinoshita J, Clark T. Alzforum. Methods Mol Biol. 2007; 401:365-81.
    View in: PubMed
  26. Gao Y, Kinoshita J, Wu E, Miller E, Lee R, Seaborne A, Cayzer S, Clark T. SWAN: A Distributed Knowledge Infrastructure for Alzheimer Disease Research. Journal of Web Semantics. 2006; 3(4):222-228.
  27. Clark T, Martin S, Liefeld T. Globally distributed object identification for biological knowledgebases. Brief Bioinform. 2004 Mar; 5(1):59-70.
    View in: PubMed
  28. Ficenec D, Osborne M, Pradines J, Richards D, Felciano R, Cho RJ, Chen RO, Liefeld T, Owen J, Ruttenberg A, Reich C, Horvath J, Clark T. Computational knowledge integration in biopharmaceutical research. Brief Bioinform. 2003 Sep; 4(3):260-78.
    View in: PubMed
  29. Clark T. Identity and interoperability in bioinformatics. Brief Bioinform. 2003 Mar; 4(1):4-6.
    View in: PubMed
  30. Das S, McCaffrey PG, Talkington MWT, Andrews NA, Corlosquet S, Ivinson AJ, Clark T. Pain Research Forum: Application of Scientific Social Media Frameworks in Neuroscience. Frontiers in Neuroinformatics.
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