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Joanne Luciano Publications

Joanne S. Luciano
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Emailjluciano@cs.rpi.edu
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Homepagehttp://tw.rpi.edu/web/person/JoanneLuciano
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Wang, P., Zheng, J., Fu, L., Patton, E.W., Lebo, T., Ding, L., Luciano, J.S., and McGuinness, D.L. 2011. Next Generation Environmental Informatics as exemplified by the Tetherless World Semantic Water Quality Portal. In .
Patton, E.W., Wang, P., Zheng, J., Fu, L., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. Assessing Health Effects of Water Pollution Using a Semantic Water Quality Portal. In Proceedings of 10th International Semantic Web Conference (October 23-27 2011, Bonn, Germany).
Wang, P., Zheng, J., Fu, L., Patton, E.W., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. A Semantic Portal for Next Generation Monitoring Systems. In Proceedings of 10th International Semantic Web Conference (October 23-27 2011, Bonn, Germany).
Zheng, J., Wang, P., Patton, E.W., Lebo, T., Luciano, J.S., and McGuinness, D.L. 2011. A Semantically-Enabled Provenance-Aware Water Quality Portal. In .
Wang, P., Zheng, J., Fu, L., Patton, E.W., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. TWC-SWQP: A Semantic Portal for Next Generation Environmental Monitoring (Technical Report).
McCusker, J., Luciano, J.S., and McGuinness, D.L. 2011. Towards an Ontology for Conceptual Modeling. In Proceedings of International Conference on Biomedical Ontology (July 26-30 2011, Buffalo, NY, USA).
Luciano, J.S. and Stevens, R. 2008. OWL - PAX of mind or the AX that caused the split?. In .

2012

Matthias Samwald Matthias Samwald, PhD, Adrien Coulet, PhD, Robert R. Freimuth, PhD, Iker Huerga, MSc, Joanne S. Luciano, PhD, Elgar Pichler, PhD, Robert L. Powers, PhD, Eric Prud’hommeaux, PhD, Frederick Whipple, PhD, M. Scott Marshall, PhD, Michel Dumontier, PhD. "An informatics infrastructure for translating pharmacogenomic knowledge into clinical practice" 2012 AMIA Summit on Translational Bioinformatics, 2012 Joint Summits on Translational Science, San Francisco California, Parc 55 Hotel San Francisco, March 19, 2012 - March 23, 2012 Manuscript ID AMIA-077-T2012

Matthias Samwald, Adrien Coulet, Iker Huerga, Robert L Powers, Joanne S Luciano, Robert R Freimuth, Frederick Whipple, Elgar Pichler, Eric Prud’hommeaux, Michel Dumontier, and M Scott Marshall, "Semantically enabling pharmacogenomic data for the realization of personalized medicine"
Pharmacogenomics, January 2012, Vol. 13, No. 2 , Pages 201-212 (doi: 10.2217/pgs.11.179)

2011

Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine 165 - 169 Matthias Samwald, Holger Stenzhorn, Michel Dumontier, M. Scott Marshall, Joanne Luciano, Klaus-Peter Adlassnig User Centred Networked Health Care - Proceedings of MIE 2011 DOI: 10.3233/978-1-60750-806-9-165 http://arxiv.org/abs/1109.6626v1

ABSTRACT
Genetic dispositions play a major role in individual disease risk and treatment response. Genomic medicine, in which medical decisions are refined by genetic information of particular patients, is becoming increasingly important. Here we describe our work and future visions around the creation of a distributed infrastructure for pharmacogenetic data and medical decision support, based on industry standards such as the Web Ontology Language (OWL) and the Arden Syntax.

2010

  • "The BioPAX community standard for pathway data sharing" Dr. Emek Demir, Mr. Michael Cary , Ms. Suzanne Paley , Dr. Ken Fukuda , Dr. Christian Lemer , Dr. Imre Vastrik , Dr. Guanming Wu , Dr. Peter D'Eustachio , Carl Schaefer , Dr. Joanne Luciano, Dr. Frank Schacherer , Dr. Irma Martinez-Flores , Dr. Zhenjun Hu , Dr. Veronica Jimenez-Jacinto , Dr. Geeta Joshi-Tope , Kumaran Kandasamy , Dr. Alejandra Lopez-Fuentes , Dr. Huaiyu Mi , Dr. Elgar Pichler , Dr. Igor Rodchenkov , Dr. Andrea Splendiani , Dr. Sasha Tkachev , Dr. Jeremy Zucker , Dr. Gopal Gopinath , Dr. Harsha Rajasimha , Ms. Ranjani Ramakrishnan , Dr. Imran Shah , Dr. Mustafa Syed , Dr. Nadia Anwar , Dr. Özgün Babur , Prof. Michael Blinov , Dr. Erik Brauner , Dr. Dan Corwin , Dr. Sylva Donaldson , Dr. Frank Gibbons , Dr. Robert Goldberg , Dr. Peter Hornbeck , Augustin Luna , Dr. Peter Murray-Rust , Dr. Eric Neumann , Mr. Oliver Ruebenacker , Dr. Matthias Samwald , Mr. Martijn van Iersel , Mrs. Sarala Wimalaratne , Dr. Keith Allen , Mr. Burk Braun , Dr. Michelle Whirl-Carrillo , Dr. Kam Dahlquist , Andrew Finney , Dr. Marc Gillespie , Dr. Elizabeth Glass , Dr. Li Gong , Dr. Robin Haw , Dr. Michael Honig , Mr. Olivier Hubaut , Mr. David Kane , Dr. Shiva Krupa , Miss Martina Kutmon , Miss Julie Leonard , Dr. Debora Marks , Mr. David Merberg , Dr. Victoria Petri , Dr. Alexander Pico , Mr. Dean Ravenscroft , Miss Liya Ren , Nigam Shah , Miss Margot Sunshine , Miss Rebecca Tang , Mr. Ryan Whaley , Dr. Stanley Letovsky , Dr. Kenneth Buetow , Dr. Andrey Rzhetsky , Dr. Vincent Schachter , Dr. Bruno Sobral , Dr. Ugur Dogrusoz , Dr. Mirit Aladjem , Dr. Shannon mcweeney , Dr. Ewan Birney , Dr. Julio Collado-Vides , Susumu Goto , Dr. Michael Hucka , Dr. Nicolas Le Novere , Dr. Natalia Maltsev , Dr. Akhilesh Pandey , Dr. Paul Thomas , Dr. Edgar Wingender , Dr. Peter Karp , Dr. Chris Sander , Dr. Gary Bader. Nature Biotechnology, Volume 28, Number 9, September 2010. http://www.nature.com/nbt/journal/v28/n9/pdf/nbt.1666.pdf
  • Dumontier M, Andersson B, Batchelor C, Domarew C, Jentzsch A, Luciano J, Pichler E, Prud'hommeaux E, Whetzel PL, Bodenreider O, Clark T, Harland L, Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L, Tonellato PJ, Zhao J, Stephens S. The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench. Proceedings of the 13th ISMB'2010 SIG meeting "Bio-ontologies" 2010:120-123. http://www.lhncbc.nlm.nih.gov/lhc/docs/published/2010/pub2010004.pdf
  • Matthias Samwald, Michel Dumontier, Jun Zhao, Joanne Luciano, M. Scott Marshall, Kei Cheung. "Integrating findings from traditional medicine into modern pharmaceutical research: the potential role of linked open data. Chinese Medicine 5:43 (2010). http://www.cmjournal.org/content/pdf/1749-8546-5-43.pdf http://www.cmjournal.org/content/5/1/43
  • Translational Medicine: Using Systems of Differential Equations to Identify Patterns in Symptom Remission in Response to Treatment and the Underlying Dynamics of their Interactions. Luciano, et. al. 2010 Proceedings of AMIA Summit on Translational Bioinformatics. (2010)

In preparation:

  • InfluenzO: An Influenza Metadata Ontology for Biomedical Research and Biosurveillance. Joanne Luciano1, Lynn Schriml, Meredith Keybl, Eric Bortz, Torsten Staab, David Spiro, Marc Colosimo, Lynette Hirschman, Richard H. Scheuermann, R. Burke Squires. Keywords: Biosecurity, Influenza, Flu, Ontology, Metadata, Biosurveillance, Bioforensics, Disease Monitoring.
  • Characterizing novel compounds with antidepressant action from traditional medicine using semantic technologies. Matthias Samwald, Jun Zhao, Michel Dumontier, Joanne Luciano, Kei Cheung
  • Predictive Medicine and Bioinformatics - Current Trends and Future Implications. Joanne Luciano PhD, Christopher A Domarew, MBChB PharmD RPh North Cheshire NHS Hospital Trust, Christopher Wood PhD , Yale University
  • Ontology Evaluation and Reuse: A Science and Engineering Approach. This is based on work I did at The MITRE Corporation. Slides on slideshare.net at: Luciano pr 08-849_ontology_evaluation_methods_metrics

2009

2008

  • 2008 Special Issue of the Journal of Biomedical Informatics: Semantic BioMed Mashup. Volume 41, Issue 5, October 2008. Special Issue Editors: Kei-Hoi Cheung, Huajun Chen, Yimin Wang, Susie Stephens, Joanne Luciano, Vipul Kashyap. Semantic mashup of biomedical data. Science Direct
  • 2008 Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata. Lynette Hirschman, Cheryl Clark, K. Bretonnel Cohen, Scott Mardis, Joanne Luciano, Renzo Kottmann, James Cole, Victor Markowitz, Nikos Kyrpides, Norman Morrison, Lynn M. Schriml, Dawn Field, and the Novo Project OMICS: A Journal of Integrative Biology. June 2008, 12(2): 129-136. http://www.liebertonline.com/doi/pdfplus/10.1089/omi.2008.0016
  • 2008 Issues in learning an ontology from text. Christopher Brewster, Simon Jupp, Joanne Luciano, David Shotton Robert Stevens, and Ziqi Zhang. Bio-Ontologies 2008: Knowledge ion Biology, ISMB 2008, Toronto, Canada. Phillip Lord, Nigam Shah, Susanna-Assunta Sansone, Matthew Cockerill, Editors. pages 9-12. http://www.bio-ontologies.org.uk/download/Bio-Ontologies2008.pdf
  • 2008 Luciano, Joanne S. and Stevens, Robert D. OWL: PAX of mind or the AX? Experiences of Using OWL in the Development of BioPAX For the workshop OWL: Experiences and Directions, Gaithersburg, MD, USA, April 1-2, 2008. http://www.webont.org/owled/2008dc/papers/owled2008dc_paper_7.pdf

2007

  • 2007 Luciano, Joanne S. and Stevens, Robert D. e-Science and biological pathway semantics. BMC Bioinformatics 2007, 8 (Suppl 3):S3 http://www.biomedcentral.com/1471-2105/8/S3/S3
  • 2007 Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T Wong, Elizabeth Wu, Davide Zaccagnini1, Tonya Hongsermeier, Eric Neumann, Ivan Herman and Kei-Hoi Cheung. Advancing translational research with the Semantic Web. BMC Bioinformatics 2007, 8(Suppl 3):S2 http://www.biomedcentral.com/1471-2105/8/S3/S2
  • 2007 Matthias Samwald, William Bug, Jonathan Rees, Chris Mungall, John Barkley, Ray Hookway, Huajun Chen, Susie Stephens, Olivier Bodenreider, Kei-Hoi Cheung, Paolo Ciccarese, Tim Clark, Donald W Doherty, Kerstin Forsberg, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Eric Neumann, Eric Prud'hommeaux, Daniel Rubin, Michael Travers, Gwen Wong, Elizabeth Wu, Alan Ruttenberg, The Semantic Web Health Care and Life Sciences Interest Group work in progress: A large scale, OBO inspired, repository of biological knowledge based on Semantic Web technologies. Bio-Ontologies SIG Workshop 2007 Poster Abstract: http://bio-ontologies.man.ac.uk/abstracts.php
  • 2007 Vipul Kashyap, Kei-Hoi Cheung, Don Doherty, Matthias Samwald, M. Scott Marshall, Joanne Luciano, Susie Stephens, Ivan Herman and Ray Hookway, An Ontology-based approach for Data Integration - An Application in Biomedical Research, Book Chapter in Cardoso, J., Hepp, M., Lytras, M. (Eds.) Real-world Applications of Semantic Web Technology and Ontologies, Springer 2007. Hardcover ISBN-10: 0-387-48530-9, ISBN-13: 978-0-387-48530-0 http://empwr.org/2007-Chapter5.pdf
  • 2007 Ram D. Sriram, Mark A. Musen, and Joanne S. Luciano, Conrad Bock, Fabian Neuhaus, Evan Wallace, Mary Brady, (editors). Meeting Report: “NIST Workshop on Ontology Evaluation” NIST Ontology Evaluation Workshop, October 25-26, 2007

2006

2005

1993-1998

  • 1998 Rubin, Mark A., Cohen, Michael A., Luciano, Joanne S., and Samson, Jacqueline A. "Can we predict the outcome of treatment for depression?" IEEE Control Systems Society Technical Committee on Intelligent Control Intelligent Control Newsletter 98-3 (March 27, 1998) http://pami.uwaterloo.ca/~karray/newsl5.html
  • 1997 Luciano, J., Cohen, M. Samson, J. "Predictive Medicine: Initial Symptoms May Determine Outcome in Clinically Treated Depressions," 1997 International Conference on Neural Networks (ICNN'97), IEEE, Piscataway, NJ, vol. I, pp71-80.
  • 1996 Luciano, J.S. Neural Network Modeling of Unipolar Depression: Patterns of Recovery and Prediction of Outcome, Ph.D. Thesis, Boston University. To order a copy http://tinyurl.com/cpxwk8.
  • 1996 Luciano, J., Cohen, M. Samson, J. ”Neural Network Modeling of Unipolar Depression,” Neural Modeling of Cognitive and Brain Disorders, World Scientific Publishing Company, eds. J. Reggia and E. Ruppin and R. Berndt. Book cover; chapter pp 469-483.
  • 1994 Luciano, J., Cohen, M., Samson, J. and Hagan, P., “A Prototype and Nonlinear Neural Network Approach to Subtyping Depressive Illness by Initial Input Data and Treatment Outcome,” Proceedings of the Irish Neural Network Conference 1994, Dublin, Ireland
  • 1994 Luciano, J., Cohen, M., Samson, J. “A Neural Network Model of Unipolar Depression,” Proceedings of the Irish Neural Network Conference 1994, Dublin, Ireland.
  • 1993 Schiller, Ilya, Luciano, Joanne S., Draper, James S. "Flock autonomy for unmanned vehicles." Proc. SPIE Vol. 1831, p. 45-51, Mobile Robots VII, William J. Wolfe, Wendell H. Chun, Eds. (SPIE Homepage) Abstract Copyright: (c) 1993 SPIE--The International Society for Optical Engineering. http://adsabs.harvard.edu/abs/1993SPIE.1831...45S

Selected Presentations and Posters

2012

    SeeSaw: Audience comments at-a-glance
    Vivien Marx, M.A. 2011
    Joanne Luciano, PhD. Rensselaer Polytechnic Institute

    When people post comments about stories they read, see, or hear, the lists can get unwieldy. SeeSaw weighs the comments’ content and tone and delivers icons to readers that reflect these thoughts and emotions. For example: Why do readers love the subject of the article, or what makes people angry after reading the piece?Columbia University - Innovation Showcase 2012 http://towcenter.org/innovation-showcase/
    SeeSaw prototype website http://tryseesaw.wordpress.com/

2011

  • 2011 American Medical Informatics Association, Summit on Translational Bioinformatics. The Translational Medicine Ontology and Knowledge Base: Using Semantic Web Technology in Personalized Medicine for Data Integration. Luciano, Joanne. March 8, 2011. http://www.slideshare.net/joanneluciano/the-translational-medicine
  • 2011 Timothy Lebo and Joanne Luciano. "Semantic Web Methodologies Provide Access to FLU Data Without Getting You Sick Of Searching". American Medical Informatics Association, Summit on Translational Bioinformatics, San Francisco, CA, Monday, March 7, 2011. http://tw.rpi.edu/wiki.tw/images/a/a2/AMIA-148-T2011-lebo-flu-ISO-A1.pdf
  • 2011 Matthias Samwald, Jun Zhao, Michel Dumontier, Michael Scott Marshall, Kei Cheung, Joanne Luciano. "Translating ethnopharmacological findings into novel drug leads: the potential roles of linked open data and ontologies". American Medical Informatics Association, Summit on Translational Bioinformatics, San Francisco, CA, Monday, March 7, 2011. #

2010

  • 2010 American Medical Informatics Association, Summit on Translational Bioinformatics. Translational Medicine: Using Systems of Differential Equations to Identify Patterns in Symptom Remission in Response to Treatment and the Underlying Dynamics of their Interactions. Luciano, Joanne Thursday March 11. 2010. http://summit2010.amia.org/files/symposium2008/S05_Luciano.pdf

2009

2008

  • 2008 Infectious Disease Ontology Workshop September 16-17, 2008, Buffalo, N.Y., USA. Influenza Ontology (presented by Burke Squires) and Ontology Evaluation (presented by Joanne Luciano). Presentations available on IDO webiste.
  • 2008 July Poster T13 Utilizing the Ontology of Biomedical Investigations (OBI) for Influenza Sequence and Surveillance Analysis. Richard Squires- UT Southwestern Medical Center at Dallas, Richard Scheuermann (UT Southwestern, Pathology); Lynn Schriml (University of Maryland School of Medicine, Institute for Genome Sciences); Eric Bortz (Mount Sinai School of Medicine, Microbiology); Torsten Staab (Los Alamos National Laboratory, Applied Engineering and Technology ); Marc Colosimo (Mitre Corporation, Information Technology); Joanne Luciano (The MITRE Corporation, Information Technology);
  • 2008 BioOntologies [Poster 3] Joanne Luciano, Lynn Schriml, Burke Squires and Richard Scheuermann, The Influenza Infectious Disease Ontology (I-IDO). (http://www.bio-ontologies.org.uk/download/Bio-Ontologies2008.pdf) The 11th Annual Bio-Ontologies Meeting Organized by: Phillip Lord, Newcastle University, Nigam Shah, Stanford University, Susanna-Assunta Sansone, EMBL-EBI and Matthew Cockerill, BioMed Central, July 20, 2008, Colocated with ISMB 2008, Toronto, Canada
  • 2008 EBI Industry Programme Disease Ontology Workshop. June 19-20, 2008. Presentation available from [jluciano at MITRE dot org] if not on EBI website.
  • 2008 Luciano, Joanne S. and Stevens, Robert D. OWL: PAX of mind or the AX? Experiences of Using OWL in the Development of BioPAX For the workshop OWL: Experiences and Directions, Gaithersburg, MD, USA, April 1-2, 2008. http://www.EMPWR.org/OWL-ED-2008-Luciano.pdf
  • 2008 Lessons Learnt in Ontology Construction, Hunter Lab, University of Colorado Health Sciences Center, January 14, 2008.

2006

  • W3C Semantic web health care and life science F2F, Boston, MA Jan 2006
  • Pacific Symposium on Biocomputing, Maui, Hawaii, Jan 2006

2005

  • Experience Using OWL DL for the Exchange of Biological Pathway Information For the workshop 2005 OWL: Experiences and Directions, Galway, Ireland Nov. 11-12 2005, Dublin, Ireland
  • BioPAX Technical Workshop, Tokyo Japan, November 17, 2005: Review of the BioPAX Ontology: http://tinyurl.com/go94r (presented by Matthew Horridge)
  • Drug Discovery Technology Technical Scientific Workshop Series. Workshop 10: Systems Biology: Can it Deliver the Magic Bullet? Boston, August 10, 2005
  • Pasteur Institute, Paris France, July 2005
  • Biopathways Semantic Aggregation, Integration and Inference, Tutorial, ISMB Detroit Michigan, June 2005
  • Oracle Life Science Users Group (BioIT), Boston, MA, May 2005 http://www.olsug.org/Presentations/May_2005/Workshops/RDF_Workshop05.pdf
  • W3C Life Science Meeting, BioIT, Boston, MA, May 2005
  • Molecular Medicine Tri Confrence (poster), San Francisco, CA April 2005
  • DARPA Workshop on Computable Semantics for Systems Biology (Invited Speaker), Arlington, VA, March 3-4, 2005

2004

Other

(selected list)

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