Alexander A. Morgan, PhD
Training
Stanford University
MD (in progress)
Stanford University
Postdoctoral Fellow in Biochemistry & Genetics
Postdoctoral Advisor: Ronald W. Davis
Stanford University
PhD in Biomedical Informatics
Research Advisor: Atul J. Butte
Thesis Title: Methods of Research Synthesis in Molecular Medicine
Stanford University
MS in Biomedical Informatics
Tufts University
MS in Biology
Brandeis University
BA in Physics
Business and Consulting
8/14-Present
7/12-9/13
4/09-4/11
5/98-9/98
Research Experience
10/11-9/12
9/10-9/11
9/06-9/10
5/00-9/06
5/99-9/99
5/97-9/97
5/96-8/96
5/95-9/95
DigiSight, Portola Valley, CA
Advisory board member & consultant on product development
Personalis, Menlo Park, CA
Consultant on bioinformatics and genomic medicine
Stimulomics, Portola Valley, CA
Co-Founder & Chief Scientist
Opal Financial Group, New York, NY
Vice President & Chief Financial Officer
Stanford Genome Technology Center, Palo Alto, CA
Dean's Postdoctoral Fellow, School of Medicine
Systems Medicine & Pediatrics, Stanford University, Stanford, CA
Research Assistant
Stanford University School of Medicine, Stanford, CA
National Library of Medicine Trainee Fellow
MITRE Corporation, San Diego, CA & Bedford, MA
Senior Artificial Intelligence Engineer
UNH Experimental Space Plasma Group, Durham, NH
Research Assistant
Brandeis Complex Fluids Group, Waltham, MA
Research Technician
Stanford Linear Accelerator Center, Stanford, CA
Lab Research Assistant
Harvard-Smithsonian Astrophysics Center, Cambridge, MA
Physical Science Aide
Clinical Experience
5/07-8/09
Teaching Experience
8/12-10/12
9/08-6/09
4/08-6/08
1/98-12/01
1/99-12/01
9/95-12/97
Arbor Free Clinic, Menlo Park, CA
Clinic Manager; IT & Specialty Clinics Coordinator
Department of Pathology, Stanford University, Stanford, CA
Teaching Assistant for Cells to Tissues, an introductory course in
histology, microscopy and cellular physiology
Stanford Biomedical Informatics, Stanford, CA
Teaching Assistant for Biomedical Informatics for Medicine
Stanford Biomedical Informatics, Stanford, CA
Teaching Assistant for Representations and Algorithms for Computational
Molecular Biology
Brandeis University Physics Department, Waltham, MA
Lab Instructor for Introductory Physics and Consultant on Curriculum
UNH Physics Department, Durham, NH
Lab Instructor for Introductory Physics and Introductory Electronics
Brandeis University Physics Department, Waltham, MA
Undergraduate Teaching Assistant for Introductory Physics
Invited Talks
2nd Annual 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"
Refereed Research Publications
1. MD Li, TC Burns, AA Morgan, PJ Khatri, "Integrated Multi-Cohort Transcriptional Meta-Analysis of
Neurodegenerative Diseases" Acta Neuropathologica Communications, Sept 2014.
2. AA Morgan, AS Achrol, MD Li, PJ Khatri, SH Cheshier, “Multiplex meta-analysis of medulloblastoma
expression studies with external controls” Proceedings of the Pacific Symposium for Biocomputing, Jan 2014.
PubMedID: 24297537.
3. A Patwardhan, M Clark, A Morgan, S Chervitz, M Pratt, G Bartha, G Chandratillake, S Garcia, N Leng,
R Chen, “Variant priorization and analysis incorporating problematic regions of the genome” Proceedings
of the Pacific Symposium for Biocomputing, Jan 2014. PubMedID: 24297554.
4. S Yan, A Tsurumi, YA Que, CM Ryan, A Banyopadhaya, AA Morgan, PJ Flaherty, RG Tompkins, LG
Rahme, “Prediction of multiple infections after severe burn trauma” Annals of Surgery, 2014.
PubMedID: 24950278.
5. LY Liu, T Yang, J Ji, Q Wen, AA Morgan, B Jin, G Chen, DJ Lyel, D Stevenson, XB Ling, AJ Butte,
“Integrating multiple ‘omics' analyses identifies serological protein biomarkers for preeclampsia” BMC
Medicine, Nov 6, 2013. PubMedID: 24195779.
6. CJ Patel, A Sivada, R Tabassum, T Preeprem, J Zhao, D Arafat, R Chen, AA Morgan, GS Martin, KL
Brigham, AJ Butte, G Gibson, "Whole genome sequencing in support of wellness and health
maintenance" Genome Medicine, 2013. PubMedID: 23806097.
7. P Khatri, S Roedder, N Kimura, K De Vusser, AA Morgan, Y Gong, M Fischbein, R Robbins, M
Naesens, A Butte, M Sarwal, "A common rejection module (CRM) across multiple transplant organs
identifies therapeutics for treatment of acute rejection in solid organ transplantation" Journal of
Experimental Medicine, 2013. PubMedID: 24127489.
8. JA Jenks, S Seki, T Kanai, J Huang, AA Morgan, RC Scalco, R Nath, R Bucayu, JM Wit, W Al-Herz, D
Ramadan, AA Jorge, R Bacchetta, V Hwa, R Rosenfeld, KC Nadeau, "Differentiating the roles of
STAT5B and STAT5A in human CD4(+) T cells" Clinical Immunology, 2013. PubMedID: 23773921.
9. E Corona, R Chen, M Sikora, AA Morgan, CJ Patel, A Ramesh, CD Bustamante, AJ Butte, “Analysis of
the genetic basis of disease in the context of worldwide human relationships and migration” PLoS
Genetics, 2013. PubMedID 23717210.
10. AA Morgan, E Rubenstein, “Proline: The distribution, frequency, positioning, and common functional
roles of proline and polyproline sequences in the human genome” PLoS One, Jan 1, 2013. PubMedID:
23372670
11. DAM Salih, AJ Rashid, D Colas, L Torre-Ubieta, RP Zhu, AA Morgan, EE Santo, D Ucar, K
Devarajan, CJ Cole, DV Madison, M Shamloo, AJ Butte, A Bonni , SA Josselyn, A Brunet. “FoxO6
regulates memory consolidation and synaptic function” Genes & Development, 2012. PubMedID:
23222102.
12. K Kodama, M Horikoshi, K Toda, S Yamadae, K Hara, J Iriee, Marina Sirota, AA Morgan, R Chen, H
Ohtsu, S Maeda, T Kadowaki, AJ Butte, "Expression-based genome-wide association study links the
receptor CD44 in adipose tissue with type 2 diabetes" PNAS, 2012. PubMedID: 22499789.
13. HP Kang, AA Morgan, R Chen, EE Schadt, AJ Butte. “Coanalysis of GWAS with eQTLs reveals
disease-tissue associations”, Proceedings of the AMIA Summit on Translational Science, 2012. PubMedID:
22779046.
14. R Chen, E Corona, M Sikora, JT Dudley, AA Morgan, A Moreno-Estrada, GB Nilsen, D Ruau, SE
Lincoln, CD Bustamante, AJ Butte, "Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional
Differentiation among Human Populations, Compared to Other Diseases" PLoS Genetics, 2012.
PubMedID: 22511877.
15. AA Morgan, R Chen, AJ Butte, "Clinical utility of sequence-based genotype compared with that
derivable from genotyping arrays",The Journal of the American Medical Informatics Association, 2012. Also
presented at the American Medical Informatics Association’s 2012 Summit on Translational Bioinformatics,
March 2012: San Francisco, CA; won Marco Ramoni Memorial Best Paper Award. PubMedID:
22718036.
16. 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" The Journal of the
American Medical Informatics Association, 2011; also presented at the Translational Bioinformatics Conference,
November 2011: Seoul, South Korea, won Best Paper Award.
17. JM Engreitz, R Chen R, AA Morgan, JT Dudley, R Mallelwar, AJ Butte. “ProfileChaser: searching
microarray repositories based on genome-wide patterns of differential expression” Bioinformatics, 2011.
PubMedID: 21967760.
18. 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, 2011. PubMedID: 21849665.
19. 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, 2011. PubMedID: 21849664.
20. 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, 2011.
PubMedID: 21737883.
21. JM Engreitz, AA Morgan, JT Dudley, R Chen, R Thathoo, RB Altman, AJ Butte. "Content-based
microarray search using differential expression profiles” BMC Bioinformatics, 2010. PubMedID:21172034.
22. AA Morgan, P Khatri, RH Jones, MM Sarwal, AJ Butte, "Comparison of Multiplex Meta-analysis
Techniques for Understanding the Acute Rejection of Solid Organ Transplants" BMC Bioinformatics,
2010; also presented at the AMIA Summit on Translational Bioinformatics, March 2010: San Francisco,
California; selected as a top presentation at the conference. PubMedID: 21044364.
23. J Dudley, Y Pouliot, R Chen, AA Morgan, A Butte "Translational bioinformatics in the cloud: an
affordable alternative" Genome Medicine, 2010. PubMedID: 20691073.
24. R Chen, TK Sigdel, L Li, N Kambham, JT Dudley, SC Hsieh, RB Klassen, A Chen, T Caohuu, AA
Morgan, HA Valantine, KK Khush, M Sarwal, AJ Butte. "Differentially Expressed RNA from Public
Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other
Conditions" PLoS Computational Biology, 2010. PubMedID: 20885780.
25. EA Ashley, AJ Butte, MT Wheeler, R Chen, TE Klein, FE Dewey, JT Dudley, KE Ormond, A
Pavlovic, L Hudgins, L Gong, LM Hodges, DS Berlin, CF Thorn, K Sangkuhl, JM Hebert, M Woon, H
Sagreiya, R Whaley, AA Morgan, D Pushkarev, NF Neff, JW Knowles, M Chou, J Thakuria, A
Rosenbaum, AW Zaranek, G Church, HT Greely, SR Quake, RB Altman, "Clinical evaluation
incorporating a personal genome" The Lancet, 2010. PubMedID: 20435227.
26. AA Morgan, R Chen, AJ Butte, "Likelihood Ratios for Genome Medicine" Genome Medicine, 2010.
PubMedID: 20497613.
27. DP Chen, AA Morgan, AJ Butte, "Validating pathophysiological models of aging using clinical
electronic medical records" Journal of Biomedical Informatics, 2009. PubMedID: 19958842.
28. AA Morgan, J Dudley, T Deshpande, AJ Butte, "Dynamism in Gene Expression Across Multiple
Studies" Physiological Genomics, 2009. PubMedID: 19920211.
29. VM Renault, VA Rafalski, AA Morgan, DAM Salih, JO Brett, AE Webb, SA Villeda, PU Thekkat, C
Guillerey, NC Denko, TD Palmer, AJ Butte, A Brunet. "FoxO3 regulates neural stem cell homeostasis"
Cell Stem Cell, November 6 2009. PubMedID: 19896443.
30. R Xu, AA 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.
31. R Chen, AA Morgan, J Dudley, AM Deshpande, L Li, K Kodama, AP Chiang, AJ Butte. "FitSNPs:
highly differentially expressed genes are more likely to have variants associated with disease" Genome
Biology, 2008. PubMedID: 19061490.
32. AA Morgan, et al. "Overview of BioCreative II Gene Normalization" Genome Biology, September 2008.
PubMedID: 18834494.
33. R Xu, K Supekar, AA Morgan, A Das, A Garber. "Unsupervised Method for Automatic Construction
of a Disease Dictionary from a Large Free Text Collection", Proceedings of the American Medical Informatics
Annual Symposium. Nov, 2008. PubMedID: 18999169.
34. M Krallinger, AA Morgan, L Smith, F Leitner, L Tanabe, J Wilbur, L Hirschman, A Valencia,
"Evaluation of text-mining systems for biology: overview of the Second BioCreative community
challenge" Genome Biology, 2008. PubMedID: 18834487.
35. P Wang, AA Morgan, A Sette, B Peters, "Automating Document Classification for the Immune
Epitope Database" BMC Bioinformatics, 2007. PubMedID: 17655769.
36. AA Morgan, B Wellner, JB Colombe, R Arens, ME Colosimo, L Hirschman; "Evaluating the
Automatic Mapping of Human Gene and Protein Mentions to Unique Identifiers" Proceedings of the Pacific
Symposium on Biocomputing, January 2007. PubMedID: 17990499.
37. B Wellner, M Huyck, S Mardis, J Aberdeen, AA Morgan, L Peshkin, A Yeh, J Hitzeman, L Hirschman,
"Rapidly Retargetable Approaches to De-identification" Journal of the American Medical Informatics
Association, 2007; also, presented at the NLP Challenge Workshop of the American Medical Informatics
Association Annual Symposium 2006: Washington, DC. PubMedID: 17600096.
38. M Colosimo, L Hirschman, AA Morgan, Alexander S. Yeh. "Data Preparation and Interannotator
Agreement BioCreAtivE Task 1B" BMC Bioinformatics, 2005. PubMedID: 15960824.
39. AS Yeh, L Hirschman, AA Morgan, M Colosimo. "BioCreAtIve Task 1A: Gene Mention Finding
Evaluation" BMC Bioinformatics, 2005. PubMedID: 15960832.
40. L Hirschman, M Colosimo, AA Morgan, AS Yeh. "Overview of BioCreAtIvE task 1B: Normalized
Gene Lists" BMC Bioinformatics, 2005. PubMedID: 15960823.
41. AA Morgan, L Hirschman, M Colosimo, AS Yeh, J Colombe. "Gene Name Identification and
Normalization Using a Model Organism Database" The Journal of Biomedical Informatics, 2004. PubMedID:
15542014
42. AS Yeh, L Hirschman, AA Morgan. "Evaluation of Text Data Mining for Database Curation: Lessons
Learned from the KDD Challenge Cup" Bioinformatics, 2003. PubMedID: 12855478.
43. AA Morgan, L Hirschman, AS Yeh, ME Colosimo. "Gene Name Extraction Using FlyBase Resources"
Proceedings of ACL 2003 Workshop on Natural Language Processing in Biomedicine, July 2003.
44. L Hirschman, AA Morgan, A Yeh. "Rutabaga By Any Other Name: Extracting Biological Names" The
Journal of Biomedical Informatics, 2002; won the MITRE Corporation Best Paper award for 2002..
PubMedID: 12755519.
45. W Greiff, AA Morgan, R Fish, M Richards, A Kundu. "Fine Grained Hidden Markov Modeling For
Broadcast-News Story Segmentation" Proceedings of Human Language Technology, January 2001.
Other Publications
1. AA Morgan, "The Wonder of the Human Hand", Journal of Hand Surgery, forthcoming in 2014.
2. AA Morgan, L Miller, "Chapter 3: Probability and Statistics", S Aerni (ed), M Sirota (ed), A
Bioinformatics Guide for Molecular Biologists, Cold Spring Harbor Laboratory Press, 2014. ISBN: 9781936113224.
3. AA Morgan, R Chen, AJ Butte, EA Ashley. "The personal genome—the future of personalised
medicine? Authors' reply" The Lancet. 11 September 2010.
4. AA Morgan, Lynette Hirschman, "Overview of BioCreative II Gene Normalization" Proceedings of the
Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 23-25, 2007.
5. AS Yeh, L Hirschman, AA Morgan. "Background and Overview for KDD Cup 2002 Task 1:
Information Extraction from Biomedical Articles" SIGKDD Explorations, 2003.
6. JD Burger, L Ferro, W Greiff, J Henderson, S Mardis, AA Morgan. "MITRE's Quanda at TREC-11"
Proceedings of the Eleventh Text Retrieval Conference, 2002: Gaithersburg, Maryland.
7. P Anand, D Anderson, J Burger, J Griffith, M Light, S Mardis, AA Morgan. "Qanda and the Catalyst
Architecture" Proceedings of the Tenth Text Retrieval Conference, 2001: Gaithersburg, Maryland.
8. W Greiff, AA Morgan, R Fish, M Richards, A Kundu. "MITRE TDT-2000 Segmentation System"
Proceedings of the Topic Detection and Tracking Workshop, 2000: Philadelphia, Pennsylvania.
Patents
1. JT Dudley, AJ Butte, AA Morgan. "United States Patent US8700337 B2 Method and system for
computing and integrating genetic and environmental health risks for a personal genome", The Board
Of Trustees Of The Leland Stanford Junior University; Apr 15, 2014
Awards & Fellowships
Travel Award
International Society for Computational Biology, Pacific Symposium
on Biocomputing, January 2014: The Big Island, Hawaii
Young Investigator Award
Sage Bionetworks Commons Congress, 2013
Marco Ramoni Memorial Best Paper
Award
AMIA Summit on Translational Bioinformatics, 19-21 March 2012:
San Francisco, CA
Dean’s Postdoctoral Fellowship
Stanford University School of Medicine, 2012
Best Paper Award
Translational Bioinformatics Conference, November 2011: Seoul,
South Korea
Outstanding Paper Award
AMIA Summit on Translational Bioinformatics, March 2010: San
Francisco, CA
Student Travel Award
International Society for Computational Biology, Pacific Symposium
on Biocomputing, January 2007: The Big Island, Hawaii
Best Paper of the Year Award
MITRE Corporation, 2002
National Merit Scholarship
National Merit Scholarship Corporation & Brandeis University, 1993
Research Community Involvement
Refereeing of Conference Submissions
SIGIR, ACL, PSB, AMIA Annual Symposium, ISMB, HLT/NAACL,
ICMLA
Refereeing of Journal Submissions
Bioinformatics, BMC Bioinformatics, Journal of Biomedical Informatics, Genome
Biology, Nucleic Acids Research, ACM TOS, Information Retrieval, Journal of
Investigative Medicine, Journal of the American Medical Informatics Association,
PLoS One, Journal of the American College of Cardiology
Society Memberships
(Past and Present)
American Geophysical Union, International Society for Computational
Biology, Association for Computational Linguistics, American Medical
Informatics Association, American Association of Neurological
Surgeons (student member)