| Education |
|---|
| 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 |
|---|
| 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-Present | 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 |
| |
| Consulting |
|---|
| 4/09-Present | Stimulomics Bioinformatics
Consulting, Portola Valley, CA |
| |
| Invited Talks |
|---|
| 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 |
|---|
| Alexander A. Morgan, Joel Dudley,Atul J. Butte.
"Hypo- and Hyper-Dynamic Gene Expression" in review. |
| Valerie M. Renault, Victoria A. Rafalski, Alex A.
Morgan, Dervis A. M. Salih, Jamie O. Brett, Ashley E. Webb, Saul A.
Villeda, Pramod U. Thekkat, Camille Guillerey, Nicholas C. Denko, Theo
D. Palmer, Atul J. Butte, Anne 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). 26 Citations |
| Peng Wang, Alexander A. Morgan, Alessandro Sette, Bjoern Peters, "Automating Document Classification for the Immune Epitope Database," BMC Bioinformatics, 2007, 8:269. 6 Citations |
| 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 Informatics Association, 2007;14:564-573. 5 Citations |
| 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. 44 Citations |
| 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. 63 Citations |
| 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). 19 Citations |
| 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). 78 Citations |
| 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). 71 Citations |
| |
| Refereed Conference Publications
|
|---|
| 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 Citations |
| Alexander S. Yeh, Lynette Hirschman, Alexander A. Morgan. "Evaluation of Text Data Mining for Database Curation: Lessons Learned from the KDD Challenge Cup," Intelligent Systems for Molecular Biology 2003, Brisbane.; Also appeared in the journal Bioinformatics, 2003;19 Suppl 1:i331-9. 91 Citations |
| 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. 27 Citations |
| 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. 17 Citations |
| |
| 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 |
| |
| |