MIND Informatics develops and applies integrative computational methods in biomedical and brain research, working with leading clinicians and researchers to understand and cure neurological disorders.

Publications

Export 51 results:
Author Title Type [ Year(Desc)]
2011
Ciccarese P, Ocana M, Clark T. DOMEO: a web-based tool for semantic annotation of online documents. In: Bio-Ontologies 2011, July 15-16, Vienna Austria. 2011
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.
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)
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, Attwood T, de Waard A, Pettifer S. A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications. In: Beyond the PDF, San Diego, 19-21 Jan 2011. 2011
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.
Luciano JS, Andersson D, Batchelor C, Bodenreider O, Clark T, Denney C, Domarew C, Gambet T, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Marshall MS, McCusker JP, McGuinness DL, Lebo T, Ogbuji C, Pichler E, Powers RL, Prud’hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzelm PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: Using Semantic Web Technology in Personalized Medicine for Data Integration. In: AMIA Summit on Translational Bioinformatics, March 7-9, 2011, San Francisco CA, USA. 2011
2012
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
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.
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.
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.
Ciccarese P, Ocana M, Clark T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics 2012;3 Suppl 1: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.
2013
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 2013;
Clark T. Collaborative and distributed biomedical applications. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.), Encyclopedia of Systems Biology. Heidelberg, DE: Springer; 2013
Ciccarese P, Peroni S. The Collections Ontology: creating and handling collections in OWL 2 DL frameworks [Internet]. Semantic Web Journal 2013;Available from: http://www.semantic-web-journal.net/system/files/swj506.pdf
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.
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. J Intern Med 2013;274(4):321-8.
Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJG, Goble C, Clark T. PAV ontology: Provenance, Authoring and Versioning [Internet]. Journal of Biomedical Semantics 2013;4(37)Available from: http://www.jbiomedsem.com/content/4/1/37
Ciccarese P, Soiland-Reyes S, Clark T. Web Annotation as a First Class Object. Internet Computing, IEEE 2013;
Clark T, Goble C. The World-Wide Web. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.), Encyclopedia of Systems Biology. Heidelberg, DE: Springer; 2013

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