Timothy W. Clark, PhD

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 Clark, Ph.D., is a researcher in biomedical informatics with over 24 years of experience in the field. He is Director of Informatics at the MassGeneral Institute for Neurodegenerative Disease; Assistant Professor of Neurology at Harvard Medical School; directs the MGH Biomedical Informatics Core; and co-directs the Data and Statistics Core at the Massachusetts Alzheimer Disease Research Center.

 

Dr. Clark is also a Founding Editorial Board member of the journal Briefings in Bioinformatics, and an Advisory Board member for F1000 Research.

 

Before coming to Harvard, Tim was 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. He began his career in life science informatics at the NCBI/NIH, where he led the database development team for NCBI GenBank.

 

Tim's core research group is based in the Neurology Research Department of the Massachusetts General Hospital (MGH), where it works in the areas of neuroinformatics, semantic web, and social computing.

 

Dr. Clark’s academic training is in Computer Science.  He earned his M.S. at Johns Hopkins University; and his Ph.D. at the University of Manchester (UK) under Professor Carole Goble, with a dissertation on the sociotechnical architecture and computational semantics of biomedical communications.

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. Brief Bioinform. 2004; 5:  59-70.

 

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.  Brief Bioinform. 2007; 8:  163-171.

 

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. Brief Bioinform 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.  Open Semantic Annotation of Scientific Publications Using DOMEO.  J Biomed Semantics 2012; 3: S1. [PMCID:  3337259].

 

More publications may be found at www.ncbi.nlm.nih.gov/