Timothy W. Clark, MS

Title: Director of Bioinformatics, MassGeneral Institute for Neurodegenerative Disease & Co-Director, Data Management and Statistics Core, Massachusetts Alzheimer's Disease Research Center & Assistant Professor of Neurology, Harvard Medical School
Telephone: (617) 724-3685
Biography:

Tim trained as a computer scientist at Johns Hopkins, and began his work in life science informatics as one of the initial developers of the National Center for Biotechnology Information (NCBI) Genbank and a collaborator on the initial NCBI prototype of PubMed. He subsequently served as Vice-President of Informatics at Millennium Pharmaceuticals, where his team built one of the first integrated bio- and chemi-informatics software platforms in the pharmaceutical industry.

 

Tim is a founding Editorial Board member of the journal Briefings in Bioinformatics, an Advisory Committee member of the World Wide Web Consortium (http://w3.org), and an Advisory Board member for the Neuroscience Information Framework (http://nif.nih.gov).

Interests:

Tim Clark's research program focuses on multi-modal semantic integration of biomedical web communities, scientific discourse and experimental results.  He is the Principal Investigator of the Semantic Web Applications in Neuromedicine (SWAN) (http://swan.mindinformatics.org) and Science Collaboration Framework (www.sciencecollaboration.org) projects.

 

Tim's informatics group built the reusable software platform for Stembook (www.stembook.org), an online review of stem cell biology published by the Harvard Stem Cell Institute, and created the Parkinson's Disease (PD) Online Research website (http://pdonlineresearch.org) in collaboration with the Michael J. Fox Foundation for Parkinson's Research.

Publications:

Clark T, Martin S, Liefeld T. Globally Distributed Object Identification for Biological Knowledge Bases. Briefings in Bioinformatics. 2004; 5:  59-70. [PMC Journal - In Process].

 

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. J Web Semantics. 2006; 4:  222-228.

 

Clark T, Kinoshita J. Alzforum and SWAN:  The Present and Future of Scientific Web Communities.  Briefings in Bioinformatics. 2007; 8:  163-171. [PMC Journal - In Process].

 

Kinoshita J, Clark T. Alzforum. Methods Mol Biol 2007; 401:  365-381.

 

Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Fosberg 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. [PMCID:  1892099].

 

Ciccarese P, Wu E, Kinoshita J, Wong G, Ocana M, Ruttenberg A, Clark T. The SWAN Biomedical Discourse Ontology. J Biomed Informatics 2008; 41:  739-751.

 

Das S, Girard L, Green T, Weitzmann L, Lewis-Bowen A, Clark T. Building Biomedical Web Communities Using A Semantically-Aware Content Management System. Briefings in Bioinformatics 2009; 10:  129-138. [PMCID Journal - In Process].

 

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.

 

Ciccarese P, Ocana M, Castro LJG, Das S ,Clark T. An Open Annotation Ontology for Science on Web 3.0. J Biomed Semantics; 2 Suppl 2: S4. [PMCID:  3102893].

 

Sinha A, Merrill ME, Armstrong S, Clark T, Das S. eXframe:  Reusable Framework for Storage, Analysis and Visualization of Genomics Experiments. BMC Bioinformatics; 12:  452. [PMCID:  3235155].

 

Ciccarese P, Ocana M, Clark T (Accepted for Publication).  Open Semantic Annotation of Scientific Publications Using DOMEO.  J Biomedical Informatics.

 

More publications may be accessed at www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed