| Education |
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| Stanford University | PhD program in Biomedical Informatics,
currently enrolled
Research Advisor: Atul Butte |
| Tufts University | MS in biology |
| Brandeis University | BA in physics |
| Research Experience |
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| 10/06-Present | Stanford Biomedical Informatics, Palo Alto, CA
National Library of Medicine Trainee Fellowship Researcher |
| 5/00-10/06 | MITRE Corporation, San Diego, CA & Bedford, MA
Senior Artificial Intelligence Engineer |
| 5/99-9/99 | UNH Experimental Space Plasma Group, Durham, NH
Research Assistant, Summer Intern |
| 5/97-9/97 | Brandeis Complex Fluids Group, Waltham, MA
Research Technician, Summer Intern |
| 5/96-8/96 | Stanford Linear Accelerator Center, Stanford, CA
Lab Research Assistant, Summer Intern |
| 5/95-9/95 | Harvard-Smithsonian Astophysics Center, Cambridge, MA
Physical Science Aide, Summer Intern |
| |
| Clinical Experience |
|---|
| 5/07-8/09 | Arbor
Free Clinic, Menlo Park, CA
Clinic Manager, IT and Specialty Clinics Coordinator |
| Teaching Experience |
|---|
| 9/08-6/09 | Stanford Biomedical Informatics, Stanford,
CA
Teaching Assistant for Biomedical Informatics for Medicine |
| 4/08-6/08 | Stanford Biomedical Informatics, Stanford, CA
Teaching
Assistant for Representations and Algorithms for Computational Molecular Biology |
| 1/98-12/01 | Brandeis University Physics Department, Waltham, MA
Consultant for Introductory Physics Lab & Teaching Assistant |
| 1/99-12/01 | UNH Physics Department, Durham, NH
Teaching Assistant, Lab Instructor for Introductory Physics and Introductory Electronics |
| 9/95-12/97 | Brandeis University Physics Department, Waltham, MA
Undergraduate Teaching Assistant |
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| Consulting |
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| 4/09-Present | Stimulomics Bioinformatics
Consulting, Portola Valley, CA |
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| Invited Talks |
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| 2nd Anuual
International Symposium on Semantic Mining in Biomedicine, Jena, Germany: 2006, Invited Tutorial on the Evaluation of
Text Mining Systems (with Martin Krallinger) |
| e-Biology Initiative: Towards New Frontiers
of Biology, Tokyo: March 11, 2005: "Linking Text Mentions to Biological Identifiers" |
| Ontario Centre for Genomic Computing's Text Mining Tools for Bioinformaticians and Biologists workshop,
Toronto: February 4, 2005: "Linking Text Mentions to Biological Identifiers" |
| Joint
Conference on Digital Libraries, TREC-Genomics
Pre-Track Workshop, 2002: "KDD Cup 2002: Lessons Learned" |
| Journal Publications |
|---|
| David P. Chen, Alexander A. Morgan, Atul J. Butte,
"Validating pathophysiological models of aging using clinical
electronic medical records," Journal of Biomedical Informatics, 2009. |
| Alexander A. Morgan, Joel Dudley, Taragini Deshpande, Atul J. Butte,
"Dynamism in Gene Expression Across Multiple Studies," Physiological Genomics, 2009. |
| V. M. Renault, V. A. Rafalski, A. A.
Morgan, D. A. M. Salih, J. O. Brett, A. E. Webb, S. A.
Villeda, P. U. Thekkat, C. Guillerey, N. C. Denko, T.D. Palmer, A. J. Butte, A. Brunet. "FoxO3 regulates neural stem cell
homeostasis", Cell Stem Cell, November 6 2009. |
| R. Chen, A. A. Morgan, J. Dudley, A. M. Deshpande,
L. Li, K. Kodama, A. P. Chiang, A. J. Butte. "FitSNPs: highly
differentially expressed genes are more likely to have variants associated
with disease", Genome Biology, Vol. 9, No. 12. (2008). |
| Alexander A. Morgan, et al. "Overview of BioCreative II
Gene Normalization," Genome Biology, 2008, 9 (Suppl 2):S3 (1
September 2008). |
| Peng Wang, Alexander A. Morgan, Alessandro Sette, Bjoern Peters, "Automating Document Classification for the Immune Epitope Database," BMC Bioinformatics, 2007, 8:269. |
| Ben Wellner, Matt Huyck, Scott Mardis, John Aberdeen,
Alex Morgan, Leon Peshkin, Alex Yeh, Janet Hitzeman, Lynette
Hirschman, "Rapidly Retargetable Approaches to
De-identification," Journal of the American Medical
Association, 2007:;14:564-573. |
| Marc Colosimo, Lynette Hirschman, Alex Morgan, Alexander S. Yeh. "Data Preparation and Interannotator Agreement BioCreAtivE Task 1B," BMC Bioinformatics 2005, 6(Suppl 1):S12 (24 May 2005). |
| S. Yeh, Lynette Hirschman, Alexander A. Morgan, Marc Colosimo. "BioCreAtIve Task 1A: Gene Mention Finding Evaluation," BMC Bioinformatics 2005, 6(Suppl 1):S2 (24 May 2005). |
| Lynette Hirschman, Marc Colosimo, Alexander A. Morgan, Alexander S. Yeh. "Overview of BioCreAtIvE task 1B: Normalized Gene Lists," BMC Bioinformatics 2005, 6(Suppl 1):S11 (24 May 2005). |
Journal of the American Medical Informatics Association, 2007;14:564-573. /td>
| Alexander A. Morgan, Lynette Hirschman, Marc Colosimo, Alexander Yeh, Jeff Colombe. "Gene Name Identification and Normalization Using a Model Organism Database," The Journal of Biomedical Informatics, 2004 Dec;37(6):396-410. |
| Alexander S. Yeh, Lynette Hirschman, Alexander A. Morgan. "Evaluation of Text Data Mining for Database Curation: Lessons Learned from the KDD Challenge Cup," Bioinformatics, 2003. |
| Lynette Hirschman, Alex Morgan, Alexander Yeh. "Rutabaga By Any Other Name: Extracting Biological Names," The Journal of Biomedical Informatics: 2002 Aug;35(4):247-59. |
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| Refereed Conference Publications
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| R. Xu, A. A. Morgan, A. Das, A. Garber, "Investigation of Unsupervised Pattern Learning Techniques
for Bootstrap Construction of a Medical Treatment Lexicon", Proceedings of the BioNLP 2009 Workshop, June
2009;
Boulder, Colorado: 63-70. |
|
Rong Xu, Kaustubh Supekar, Alex Morgan, Amar Das, Alan Garber.
"Unsupervised Method for Automatic Construction of a Disease Dictionary
from a Large Free Text Collection", American Medical Informatics Annual
Symposium. Nov 8-12, 2008: Washington, DC.
|
| Alexander A. Morgan, Benjamin Wellner, Jeffrey B. Colombe, Robert Arens, Marc E. Colosimo, Lynette Hirschman;"Evaluating the Automatic Mapping of Human Gene and Protein Mentions to Unique Identifiers," Proceedings of the Pacific Symposium on Biocomputing 2007 7 |
| Alex Morgan., Lynette Hirschman., Alexander Yeh., Marc Colosimo. "Gene Name Extraction Using FlyBase Resources", Proceedings of ACL 2003 Workshop on Natural Language Processing in Biomedicine, Sapporo, Japan: July 2003. |
| Warren Greiff, Alex Morgan, Randall Fish, Marc Richards, Amlan Kundu. "Fine Grained Hidden Markov Modeling For Broadcast-News Story Segmentation" Proceedings of Human Language Technology 2001. |
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| Other Publications, Presentations, et cetera |
|---|
| Martin Krallinger, Alexander Morgan, Larry Smith,
Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso
Valencia, "Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge", Genome Biology, 2008, 9 (Suppl 2):S1 (1 September 2008). |
| Alexander A. Morgan, Lynette Hirschman, "Overview of
BioCreative II Gene Normalization," Proceedings of the
SecondBioCreative Challenge Evaluation Workshop, Madrid, Spain,
April 23-25, 2007. |
| Ben Wellner, Matt Huyck, Scott Mardis, John Aberdeen, Alex Morgan, Leon Peshkin, Alex Yeh, Janet Hitzeman and Lynette Hirschman "Rapidly Retargetable Approaches to De-identification," NLP Challenge Workshop; American Medical Informatics Association Annual Symposium 2006. Washington DC, Nov 10-11 2006 |
| Alexander S. Yeh, Lynette Hirschman, Alex Morgan. "Background and Overview for KDD Cup 2002 Task 1: Information Extraction from Biomedical Articles," SIGKDD Explorations, Vol 4 Issue 2, 2003. |
| John D. Burger, Lisa Ferro, Warren Greiff, John Henderson, Scott Mardis, Alex Morgan. "MITRE's Quanda at TREC-11". Proceedings of the Eleventh Text Retrieval Conference, TREC 2002. |
| Pranav Anand, Doug Anderson, John Burger, John Griffith, Marc Light, Scott Mardis, Alex Morgan. "Qanda and the Catalyst Architecture". Proceedings of the Tenth Text Retrieval Conference, TREC 2001. |
| Warren Greiff, Alex Morgan, Randall Fish, Marc Richards, Amlan Kundu. "MITRE TDT-2000 Segmentation System" Proceedings of the Topic Detection and Tracking Workshop 2000, 2000. |
| Alex Morgan, Lynette Hirschman, Alexander Yeh. "Gene Name Finding Using FlyBase" Poster at The Pacific Symposium for Biocomputing, Kaua'i: 2003 |
| Alexander A. Morgan, Christian Blaschke, Jeff Colombe, Marc Colosimo, Lynette Hirschman, Alfonso Valencia, Alex Yeh. "The BioCreAtIve Evaluation" Poster at the Pacific Symposium for Biocomputing, Big Island of Hawai'i: 2004 |
| Research Community Involvement |
|---|
| Refereeing of Conference Submissions | Pacific Symposium on Biocomputing (Linking Biomedical Information Through Text Mining), AMIA Annual Symposium, SIGIR, ISMB BioLink, HLT/NAACL BioNLP, HLT/NAACL Biolink |
| Refereeing of Journal Submissions | Bioinformatics, BMC Bioinformatics, Journal of Biomedical Informatics, Genome Biology, Nucleic Acids Research, ACM TOS, Information Retrieval |
| Society Memberships(Past and Present) | American Geophysical Union, International Society for Computational Biology, Association for Computational Linguistics, American Medical Informatics Association |
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