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.

Publications

Export 51 results:
Author Title [ Type(Desc)] Year
Journal Article
Das S, Girard L, Green T, Weitzman L, Lewis-Bowen A, Clark T. Building Biomedical Web Communities Using a Semantically Aware Content Management System. Brief Bioinform 2009;10(2):129-38.
Ciccarese P, Shotton D, Peroni S, Clark T. CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships. [Internet]. Semantic Web Journal 2012;Available from: http://www.semantic-web-journal.net/system/files/swj175_1.pdf
Ciccarese P, Peroni S. The Collections Ontology: creating and handling collections in OWL 2 DL frameworks [Internet]. Semantic Web Journal 2013;Available from: http://www.semantic-web-journal.net/system/files/swj506.pdf
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. Neurobiol Dis 2007;26(3):606-14.
Sinha AU, Merrill E, Armstrong SA, Clark T, Das S. eXframe: reusable framework for storage, analysis and visualization of genomics experiments. BMC Bioinformatics 2011;12:452.
Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E, Shotton D. The Future of Research Communication and e-Scholarship. Dagstuhl reports 2011;1(8)
McFarland KN, Das S, Sun TTing, Leyfer D, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha J-HJ. Genome-wide histone acetylation is altered in a transgenic mouse model of Huntington's disease. PLoS One 2012;7(7):e41423.
McFarland KN, Das S, Sun TTing, Leyfer D, Kim M-O, Xia E, Sangrey GR, Kuhn A, Luthi-Carter R, Clark T, Sadri-Vakili G, Cha J-HJ. 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.
Clark T, Martin S, Liefeld T. Globally Distributed Object Identification for Biological Knowledgebases. Brief Bioinform 2004;5(1):59-70.
Sadri-Vakili G, Bouzou B, Benn CL, Kim M-O, Chawla P, Overland RP, Glajch KE, Xia E, Qiu Z, Hersch SM, Clark T, Yohrling GJ, Cha J-HJ. Histones Associated with Downregulated Genes are Hypo-acetylated in Huntington's Disease Models. Hum Mol Genet 2007;16(11):1293-306.
Benn CL, Sun T, Sadri-Vakili G, McFarland KN, DiRocco DP, Yohrling GJ, Clark T, Bouzou B, Cha J-HJ. Huntingtin modulates transcription, occupies gene promoters in vivo, and binds directly to DNA in a polyglutamine-dependent manner. J Neurosci 2008;28(42):10720-33.
Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database (Oxford) 2012;2012:bas005.
Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark T, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, López-Bigas N, Maojo V, Mons B, Musen M, Oliveira JL, Rowe A, Ruch P, Shabo A, Shortliffe EH, Valencia A, van der Lei J, Mayer MA, Sanz F. Improving data and knowledge management to better integrate health care and research. J Intern Med 2013;274(4):321-8.
Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E, Shotton D. Improving Future Research Communication and e-Scholarship: A Summary of Findings. Informatik-Spektrum 2012;35(1):56-57.
Clark T. Knowledge Integration in Biomedicine: Technology and Community. Brief Bioinform 2007;
Clark T, Ciccarese P, Goble C. Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications [Internet]. Journal of Biomedical Semantics Submitted;Available from: http://arxiv.org/abs/1305.3506
Ciccarese P, Ocana M, Castro LJael Garci, Das S, Clark T. An Open Annotation Ontology for Science on Web 3.0. J Biomed Semantics 2011;2 Suppl 2:S4.
Ciccarese P, Ocana M, Clark T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics 2012;3 Suppl 1:S1.
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. Front Neuroinform 2014;8:21.
Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJG, Goble C, Clark T. PAV ontology: Provenance, Authoring and Versioning [Internet]. Journal of Biomedical Semantics 2013;4(37)Available from: http://www.jbiomedsem.com/content/4/1/37
Merrill E, Corlosquet S, Ciccarese P, Clark T, Das S. Semantic Web repositories for genomics data using the eXframe platform [Internet]. Journal of Biomedical Semantics 2014;5(Supplement 1)Available from: http://www.jbiomedsem.com/content/5/S1/S3
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.
Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, Clark T. The SWAN Biomedical Discourse Ontology. J Biomed Inform 2008;41(5):739-51.
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman L-A, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Sui SJHo, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Toward interoperable bioscience data. Nat Genet 2012;44(2):121-6.
Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics 2011;2 Suppl 2:S1.

Pages