PUBLICATIONS

2010

Das S, Rogan M, Kawadler H, Corlosquet S, Brin S and Clark T. PD Online: a case study in scientific collaboration on the Web. Workshop on the Future of the Web for Collaborative Science, 19th International World Wide Web Conference, Raleigh, North Carolina USA - April 26-30, 2010 (accepted)

Ciccarese P, Ocana M, Das S, Clark T. AO: An Open Annotation Ontology for Science on the Web. Paper at Bio-ontologies 2010 (accepted)

2009

Das S, Girard L, Green T, Weitzmann L, Lewis-Bowen A, and Clark T. Building Biomedical Web Communities Using a Semantically-Aware Content Management System. Briefings in Bioinformatics. 2009 Mar;10(2):129-38. Epub 2008 Dec 6. PMID: 19060302

Das S, Goetz M, Girard L, Clark T. Scientific Publications on Web 3.0. 13th International Conference on Electronic Publishing (ELPUB 2009), 10-12 June 2009, Milan, Italy.

Corlosquet S, Delbru R , Clark T, Polleres A, and Decker S. Produce and Consume Linked Data with Drupal. 8th International Semantic Web Conference (ISWC 2009); October 25-29, 2009, Washington DC.

Passant A, Ciccarese P, Breslin J, Clark T. SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics. Workshop on Semantic Web Applications in Scientific Discourse, 8th International Conference on Semantic Web (ISWC 2009), Oct 25-29 2009, Washington DC.

Groza T, Handschuh S, Clark T and Shum SB. A Short Survey of Scientific Discourse Representation Models. Workshop on Semantic Web Applications in Scientific Discourse, 8th International Conference on Semantic Web (ISWC 2009), Oct 25-29 2009, Washington DC.

2008

Ciccarese, P, Wu E, Kinoshita J, Wong G, Ocana M, Ruttenberg A and Clark T. (2008) The SWAN Biomedical Discourse Ontology. Journal of Biomedical Informatics 2008 Oct; 41(5):739-51. PMID: 18583197.

Das S, Green T, Lewis-Bowen A, Weitzman L and Clark T. Linked data in a scientific collaboration framework. Workshop on Health Care and Life Sciences Data Integration for the Semantic Web, WWW2008. 17th International World Wide Web Conference, 2008; April 21-25; Beijing, China.

2007

Benn CL, Sun T, Sadri-Vakili G, McFarland K, DiRocco DP, Yohrling G, Clark T, Bouzou B, and Cha JH (2008) Huntingtin modulates transcription, occupies gene promoters in vivo and binds directly to DNA in a polyglutamine-dependent manner. The Journal of Neuroscience. 2008 Oct 15;28(42):10720-33. PMID: 18923047

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. Neurobiology of Disease 2007 Jun; 26(3):606-14. PMID: 17412603

Ciccarese P, Wu E, Clark T. An Overview of the SWAN 1.0 Discourse Ontology. Workshop on Health Care and Life Sciences Data Integration for the Semantic Web, WWW2007. 16th International World Wide Web Conference, 2007; May 8-12; Banff, Canada. http://www2007.org/workshops/paper_145.pdf

Clark T. Knowledge Integration: Technology and Community. Briefings in Bioinformatics 2007; 8: E1-E3; doi:10.1093/bib/bbm019. PMID: 17526592

Clark T and Kinoshita J. Alzforum and SWAN: The Present and Future of Scientific Web Communities. Briefings in Bioinformatics 2007; 8:163-171 doi:10.1093/bib/bbm012. PMID: 17510163

Kinoshita J and Clark T. Alzforum. Methods Mol Biol. 2007;401:365-81. PMID: 18368375

Lam YK, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong G, Liu N, Crasto C, Morse T, Stephen S, Cheung KH (2006) AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 2007; 8(Suppl 3):S4 doi:10.1186/1471-2105-8-S3-S4. PMID: 17493287

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 doi:10.1186/1471-2105-8-S3-S2. PMID: 17493285
Sadri-Vakili G, Bouzou B, Benn CL, Cattaneo E, Kim MO, Chawla P, Overland RP, Glajch KE, Xia E, Qiu Z, Hersch SM, Clark TW, MacDonald ME, Yohrling GJ, Cha JH (2007) Histones Associated with Downregulated Genes are Hypo-acetylated in Huntington’s Disease Models. Human Molecular Genetics 2007 Jun 1;16(11):1293-306. PMID: 17409194

2006

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.

Lam YK, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong G, Liu N, Crasto C, Morse T, Stephens S, Cheung KH. Semantic Web Meets e-Neuroscience: An RDF Use Case. Semantic Web - ASWC 2006: First Asian Semantic Web Conference, Beijing, China, September 3-7, 2006 Proceedings. Mizoguchi R, Giunchiglia F, Shi Z (eds). Lecture Notes in Computer Science #4185. Springer-Verlag, New York. pp 158-170.

2004

Clark T, Martin S, Liefeld T. Globally Distributed Object Identification for Biological Knowledge Bases, Briefings in Bioinformatics 2004; 5(1):59-70. PMID: 15153306