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Clark Lab

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.

 

Tim Clark's research program focuses on multi-modal semantic integration of biomedical web communities, scientific discourse and experimental results.  He is the Director or the Center for Interdisciplinary Informatics, and 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.

researcher

Principal Investigator

Timothy W. Clark, MSc

  • Instructor in Neurology,
    Harvard Medical School
  • Director, Center for Interdisciplinary Informatics,
    MassGeneral Institute for Neurodegenerative Disease

 

 

 

Research Scientists

  • Sudeshna Das,
    Senior Program Manager  
  • Paolo Ciccarese,
    Biomedical Informatics Research & Development  
  • Marco Ocana,
    Software Developer  
  • Stephane Corlosquet,
    Bioinformatics Engineername - Post Doc Fellow

 

 

  1. Clark T, Ciccarese P, Goble C. Micropublications: A Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications. Journal of Biomedical Semantics
  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. PMID: 25062675 PubMed
  3. Ciccarese P, Soiland-Reyes S, Clark T. Web Annotation as a First-Class Object. IEEE Internet Computing, Nov/Dec 2013. 
  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 PubMed
  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) PubMed
  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 PubMed
  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 PubMed
  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 PubMed
  10. 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 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 PubMed

 


NCBI PubMed Publications