Timothy W. Clark, PhD

  • Lab Phone: 617-947-7098

Research Investigator Profile

Timothy W. Clark, MSc

Timothy W. Clark, PhD

  • Assistant Professor of Neurology,
    Harvard Medical School
  • Director,
    Biomedical Informatics Core, Massachusetts General Hospital

 

 

Research Description

Tim Clark 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 the journal F1000 Research. 

Before coming to Harvard, he 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. 

His 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.

Visit Tim Clark's MIND Informatics Lab for more information.

Research interests Software interoperability, neuroinformatics, and semantic models of theory and evidence in biomedical research, social computing
Research techniques Integrative computational methods in biomedical and brain research
Diseases studied Alzheimer's disease
Selected publications
  1. Clark T, Ciccarese P, Goble C. Micropublications: A Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications. Journal of Biomedical Semantics 5:28?[http://www.jbiomedsem.com/content/5/1/28].)
  2. McFarland KN, Das S, Sun TT, Leyfer D, Kim M-O, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha JH: 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.
  3. Ciccarese P, Soiland-Reyes S, Clark T. Web Annotation as a First-Class Object. IEEE Internet Computing, Nov/Dec 2013. PMID: 25062675
  4. Das S, McCaffrey PG, Talkington MWT, Andrews NA, Corlosquet S, Ivinson AJ, Clark T. Pain Research Forum: Application of Scientific Social Media Frameworks in Neuroscience. Frontiers in Neuroinformatics Mar 11;8:21. doi: 10.3389/fninf.2014.00021. eCollection 2014. PMID:24653693; PMCID: PMC3949323
  5. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hide W, Oliver Hofmann, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster M, Gaudet P, Gilbert J, Goble CA, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Sui SH, Laederach A, Liang S, Merrill EM, Roux M, Saito JT, Scheuerman RH, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I. Towards interoperable bioscience data. Nature Genetics 2012 44,:21–126. doi:10.1038/ng.1054. PMID: 22281772. (Also accepted for presentation, Highlights Track, Intelligent Systems in Molecular Biology 2012)
  6. McFarland KN, Das S, Sun TT, Leyfer D, Kim M-O, Xia E, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha JH: (2012) Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease. PLoS One 7(7):e41423 July 2012. PMID: 22848491; PMCID: PMC3407195
  7. Ciccarese P, Ocana M, Garcia-Castro LJ, Das S, Clark T. An Open Annotation Ontology for Science on Web 3.0. Journal of Biomedical Semantics 2011 2(Suppl2):S4. http://www.jbiomedsem.com/content/2/S2/S4. PMID: 17493287, PMCID: PMC3102893. (2nd most-accessed paper in this journal for the past year).
  8. Sinha A, Merrill ME, Armstrong S, Clark T and Das S. eXframe: Reusable Framework for Storage, Analysis and Visualization of Genomics Experiments. BMC Bioinformatics 2011 Nov 21;12(1):452 (a BMC “Highly Accessed Article”). PMID 22103807, PMCID: PMC3235155
  9. 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, PMCID: PMC2586288
  10. 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
NCBI PubMed link NCBI PubMed Publications
Collaborators
E-mail address twclark@partners.org
Lab mailing address

Partners Research Building
Room 219
65 Landsdowne St
Cambridge, MA 02139

or

MassGeneral Institute for Neurodegenerative Disease
CNY B114 2012
114 16th Street
Charlestown, MA 02129

 

Updated 10/1/2014