Alexander A. Morgan

Stanford Genome Technology Center
855 South California Avenue
Palo Alto, CA 94304

Education

Stanford UniversityPhD in Biomedical Informatics
Research Advisor: Atul Butte
Thesis Title: Method of Study Integration in Multiplex Molecular Medicine
Stanford UniversityMS in Biomedical Informatics
Tufts UniversityMS in Biology
Brandeis UniversityBA in Physics (National Merit Scholar)

Research Experience

10/11-PresentDept of Biochemistry, Genome Technology Center, Stanford University
Dean's Postdoctoral Fellowship
10/06-09/11Biomedical Informatics, Systems Medicine and Pediatrics, Stanford University
National Library of Medicine's Biomedical Informatics Training Grant (T15 LM007033)
5/00-10/06 MITRE Corporation, San Diego, CA & Bedford, MA
Senior Artificial Intelligence Engineer

Clinical Experience

5/07-8/09 Arbor Free Clinic, Menlo Park, CA
Clinic Co-Manager

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

  1. AA Morgan, VJ Pyrgos, KC Nadeau, PR Williamson and AJ Butte. "Multiplex Meta-Analysis of RNA Expression to Identify Genes With Variants Associated with Immune Dysfunction", accepted to The Journal of the American Medical Informatics Association; also presented at the Translational Bioinformatics Conference, November 2011: Seoul, South Korea, where it won the Best Paper Award.
  2. AA Morgan, R Chen, AJ Butte. "Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays", accepted to The Journal of the American Medical Informatics Association; will be presented at the Summit on Translational Bioinformatics, March 2012: San Francisco, CA.
  3. M Sirota, JT Dudley, J Kim, AP Chiang, AA Morgan, A Sweet-Cordero, J Sage, AJ Butte. "Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data", Science Translational Medicine, 17 Aug 2011.
  4. JT Dudley, M Sirota, M Shenoy, RK Pai, S Roedder, AP Chiang, AA Morgan, MM Sarwal, PJ Pasricha, AJ Butte. "Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease", Science Translational Medicine, 17 Aug 2011.
  5. M Yu , MR Eckart MR, AA Morgan, K Mukai, AJ Butte, M Tsai, SJ Galli, "Identification of Interferon-gamma mast cell axis in mouse of chronic asthma" Journal of Clinical Investigation, July 2011.
  6. Jesse M Engreitz, Alexander A Morgan, Joel T Dudley, Rong Chen, Rahul Thathoo, Russ B Altman, Atul J Butte. "Content-based microarray search using differential expression profiles", BMC Bioinformatics, 2010, 11:603.
  7. Alexander A. Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M. Sarwal, Atul J. Butte, "Comparison of Multiplex Meta-analysis Techniques for Understanding the Acute Rejection of Solid Organ Transplants," presented at the AMIA Summit on Translational Bioinformatics, San Francisco: March 2010 (selected as a top presentation at the conference), BMC Bioinformatics, 2010, 11(Suppl 9):S6.
  8. Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal M, Butte AJ. "Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions" PLoS Comput Biol 6(9), 2010.
  9. Dudley, J., Pouliot, Y., Chen, R., Morgan, A., & Butte, A. (2010). Translational bioinformatics in the cloud: an affordable alternative Genome Medicine, 2 (8)
  10. E. A. Ashley, A.J. Butte, M.T. Wheeler, R. Chen, T.E. Klein, F.E. Dewey, J.T. Dudley, K.E. Ormond, A. Pavlovic, L. Hudgins, L. Gong, L.M. Hodges, D.S. Berlin, C.F. Thorn, K. Sangkuhl, J.M. Hebert, M. Woon, H. Sagreiya, R. Whaley, A.A. Morgan, D. Pushkarev, N.F. Neff, J.W. Knowles, M. Chou, J. Thakuria, A. Rosenbaum, A. W. Zaranek, G. Church, H.T. Greely, S.R. Quake, R.B. Altman, "Clinical evaluation incorporating a personal genome" The Lancet, Vol. 375, Issue 9725: 1525-1535 (1 May 2010). PDF
  11. Alexander A. Morgan, Rong Chen, Atul J. Butte, "Likelihood Ratios in Genomic Medicine", Genome Medicine, 2010, 2:30 (17 May 2010) PDF
  12. David P. Chen, Alexander A. Morgan, Atul J. Butte, "Validating pathophysiological models of aging using clinical electronic medical records," Journal of Biomedical Informatics, Volume 43, Issue 3, June 2010:358-64.
  13. Alexander A. Morgan, Joel Dudley, Taragini Deshpande, Atul J. Butte, "Dynamism in Gene Expression Across Multiple Studies," Physiological Genomics, 2009.
  14. 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.
  15. 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).
  16. Alexander A. Morgan, et al. "Overview of BioCreative II Gene Normalization," Genome Biology (1 September 2008).
  17. 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 (1 September 2008).
  18. Peng Wang, Alexander A. Morgan, Alessandro Sette, Bjoern Peters, "Automating Document Classification for the Immune Epitope Database," BMC Bioinformatics, 2007, 8:269.
  19. 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.
  20. Marc Colosimo, Lynette Hirschman, Alex Morgan, Alexander S. Yeh. "Data Preparation and Interannotator Agreement BioCreAtivE Task 1B," BMC Bioinformatics (24 May 2005).
  21. Alexander S. Yeh, Lynette Hirschman, Alexander A. Morgan, Marc Colosimo. "BioCreAtIve Task 1A: Gene Mention Finding Evaluation," BMC Bioinformatics (24 May 2005).
  22. Lynette Hirschman, Marc Colosimo, Alexander A. Morgan, Alexander S. Yeh. "Overview of BioCreAtIvE task 1B: Normalized Gene Lists," BMC Bioinformatics (24 May 2005).
  23. 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.
  24. 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.
  25. 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.

Refereed Conference Publications

  1. 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.
  2. 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.
  3. 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 (ISCB Student Travel Award)
  4. 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.
  5. 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.

Other Publications, Presentations, ETC.

  1. Alexander A Morgan,Rong Chen,Atul J Butte,Euan A Ashley The Lancet - 11 September 2010 (Vol. 376, Issue 9744, Pages 869 - 870) DOI: 10.1016/S0140-6736(10)61405-5.
  2. AA Morgan, R Chen, AJ Butte, "Likelihood Ratios in Genomic Medicine", 13th International MGED Meeting, Boston, MA: July 14, 2010.
  3. Alexander A. Morgan, Lynette Hirschman, "Overview of BioCreative II Gene Normalization," Proceedings of the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 23-25, 2007.
  4. 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
  5. 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.
  6. 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.
  7. 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.
  8. Warren Greiff, Alex Morgan, Randall Fish, Marc Richards, Amlan Kundu. "MITRE TDT-2000 Segmentation System", Proceedings of the Topic Detection and Tracking Workshop 2000.

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, AMIA Translational Informatics
Refereeing of Journal Submissions Bioinformatics, BMC Bioinformatics, Journal of Biomedical Informatics, Genome Biology, Nucleic Acids Research, ACM TOS, Information Retrieval, Journal of the American Medical Informatics Association
Society Memberships
(Past and Present) 		American Geophysical Union, International Society for Computational Biology, Association for Computational Linguistics, American Medical Informatics Association