MassGeneral Institute for Neurodegenerative Disease

Translating today's discoveries into tomorrow's cures

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Publications

Export 47 results:
Author Title [ Type(Asc)] Year
Journal Article
Ciccarese P, Soiland-Reyes S, Clark T. Web Annotation as a First Class Object. IEEE Internet Computing In Press;
Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics 2011;2 Suppl 2:S1.
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 L-A, 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, Sui SJHo, 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;44(2):121-6.
Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, Clark T. The SWAN Biomedical Discourse Ontology. J Biomed Inform 2008;41(5):739-51.
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;4(3):222-228.
Ciccarese P, Ocana M, Clark T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics 2012;3 Suppl 1:S1.
Ciccarese P, Ocana M, Castro LJael Garci, Das S, Clark T. An Open Annotation Ontology for Science on Web 3.0. J Biomed Semantics 2011;2 Suppl 2:S4.
Clark T, Ciccarese P, Goble C. Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications [Internet]. Journal of Biomedical Semantics Submitted;Available from: http://arxiv.org/abs/1305.3506
Clark T. Knowledge Integration in Biomedicine: Technology and Community. Brief Bioinform 2007;
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-Spektrum 2012;35(1):56-57.
Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, 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. J Intern Med 2013;274(4):321-8.
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.
Sadri-Vakili G, Bouzou B, Benn CL, Kim M-O, Chawla P, Overland RP, Glajch KE, Xia E, Qiu Z, Hersch SM, Clark T, Yohrling GJ, Cha J-HJ. Histones Associated with Downregulated Genes are Hypo-acetylated in Huntington's Disease Models. Hum Mol Genet 2007;16(11):1293-306.
Clark T, Martin S, Liefeld T. Globally Distributed Object Identification for Biological Knowledgebases. Brief Bioinform 2004;5(1):59-70.
McFarland KN, Das S, Sun TTing, Leyfer D, Kim M-O, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha J-HJ. Genome-Wide Increase in Histone H2A Ubiquitylation in a Mouse Model of Huntington's Disease. Journal of Huntington's Disease 2013;2(3):263-277.
McFarland KN, Das S, Sun TTing, Leyfer D, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha J-HJ. Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease. PLoS One 2012;7(7):e41423.
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;1(8)
Sinha AU, Merrill E, Armstrong SA, Clark T, Das S. eXframe: reusable framework for storage, analysis and visualization of genomics experiments. BMC Bioinformatics 2011;12:452.
Cantuti-Castelvetri I, Keller-McGandy C, Bouzou B, Asteris G, Clark T, Frosch MP, Standaert DG. Effects of Gender on Nigral Gene Expression and Parkinson Disease. Neurobiol Dis 2007;26(3):606-14.
Ciccarese P, Peroni S. The Collections Ontology: creating and handling collections in OWL 2 DL frameworks [Internet]. Semantic Web Journal In Press;Available from: http://www.semantic-web-journal.net/system/files/swj506.pdf
Ciccarese P, Shotton D, Peroni S, Clark T. CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships. [Internet]. Semantic Web Journal 2012;Available from: http://www.semantic-web-journal.net/system/files/swj175_1.pdf
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;10(2):129-38.
Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. Database In Press;
Lam HYK, 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 K-H. AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 2007;8 Suppl 3:S4.
Clark T, Kinoshita J. Alzforum and SWAN: The Present and Future of Scientific Web Communities. Brief Bioinform 2007;8(3):163-71.

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