CURRICULUM VITAE

OREGON HEALTH & SCIENCE UNIVERSITY

Undergraduate, Graduate and Postgraduate Education (Include Year, Degree, and Institution):

1. 1980-1983, Interdisciplinary Engineering, College of Engineering, University of Michigan, Ann Arbor, Michigan

2. 1983-1987, M.D., University of Michigan, School of Medicine

3. 1987-1988, Transition Year Resident, Internal Medicine Department, Carney Hospital, Boston, Massachusetts

4. 1989-1991, Computer Engineering, Department of Computer and Electrical Engineering, Northeastern University, Boston, Massachusetts

5. 2002-2005, National Library of Medicine Medical Informatics Fellow, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon

6. 2002-2005, M.S. Biomedical Informatics, Oregon Health & Science University, Portland, Oregon

Certification (Include Board, Number, Date, and Re-certification):

• National Boards, Part I/II/III (1985/87/88)

Licenses (Include State, Date, Status, Number, and Renewal Date):

• Medicine, Massachusetts, 1988, Inactive

III.  PROFESSIONAL EXPERIENCE

Academic (Include Year, Position, and Institution):

1. 2016-present, Professor, Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon

2. 2014-present, Research Member, Quantitative Oncology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon

3. 2012-present, Director of DMICE Informatics Discovery Lab (IDL), Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon

4. 2010-2016, Associate Professor, Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon

5. 2005-2010, Assistant Professor, Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon

6. 2002-2004, Teaching Assistant and Lecturer, Computer Science, Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon

Other (Include Year, Position, and Institution):

1. 1998-2002, Senior Staff Software Engineer, Intel Labs, Intel Corporation, Hillsboro, Oregon

2. 1995-1998, Staff Software Engineer, Business Video Conferencing Products, Intel Corporation, Hillsboro, Oregon

3. 1993-1995, Member of Technical Staff, Aware Corporation, Cambridge, Massachusetts

4. 1991-1993, Associate, Advanced Technology Group, Coopers and Lybrand, Boston, Massachusetts

5. 1990-1991, Senior Software Engineer, Advanced Video Products, Littleton, Massachusetts

6. 1988-1990, Chief Computer Engineer, Nuclear Medicine Department, Beth Israel Hospital, Brookline, Massachusetts

IV. SCHOLARSHIP

Area(s) of Research/Scholarly Interest:

Application of text mining, machine learning (ML), and natural language processing (NLP) techniques to the scientific literature, curated databases, clinical text and other biomedical data for aiding researchers in effectively using, exploring, and contributing to the ever-expanding biomedical knowledge base.

Funded Grants/Publications/Other Creative Work:

Applying Machine Learning to EHR Data for the identification of patients with previously undiagnosed AADC deficiency
PTC Therapeutics
Project Period: 11/1/2021 – 5/20/2023
Role: PI

Cardiac Arrhythmia Project - Project Irregular
GE Medical
Project Period: 07/01/2020 – 06/30/2021
Role: Lead Data Scientist

Text Mining Pipeline to Accelerate Systematic Reviews in Evidence-Based Medicine
National Library of Medicine (NLM) Grant Number R01LM010817
Project Period: 09/30/2010 – 06/30/2021
Principal Investigators: Aaron M. Cohen, MD, MS, Neil R. Smalheiser, MD, PhD
Final Year Total Project Funding: $599,995

Porphyria Recruitment Project
Alnylam Pharmaceuticals, Inc.
Research Collaboration
Project Period: 11/1/2018 - 12/31/2019
Principal Investigators: William R. Hersh, MD, Aaron M. Cohen, MD, MS

Cochrane Evidence Crowds & Machine Learning
Robert Wood Johnson Foundation
Project Period 1/15/2017 – 1/14/2018
Principal Investigators: Helfand, Elliott
Role: OHSU Machine Learning Lead Scientist
Total Funding: $400,000

Latent Dirichlet Allocation for Protein Inference in Quantitative Proteomics
National Cancer Institute (NCI) Grant Number R21 CA181382 01
Project Period: 01/01/2014 - 12/31/2016
Principal Investigator: Aaron M. Cohen, MD, MS
Final Year Total Funding: $167,475

Development of the CTSA Pharmaceutical Assets Portal
Pfizer, Inc.
Project Period: 11/1/2009 - 10/31/2010
Principal Investigator: Aaron M. Cohen, MD, MS
Final Year Total Project Funding: $135,000

Exploring Novel Drug Targets with Social Networking Analysis
Subcontract Sub0800138 with University of California
National Center for Research Resources (NCRR) Grant Number UL1-RR024146-03S3
Project Period: 09/15/2008 – 06/30/2009
Principal Investigator: Aaron M. Cohen, MD, MS
Final Year Total Subcontract Funding: $43,883

Identifying Candidate Researchers for Collaboration in Clinical and Translational Research
Oregon Clinical and Translational Research Institute (OCTRI) Pilot Grant
Project Period: 06/01/2008 – 05/31/2009
Principal Investigator: Aaron M. Cohen, MD, MS
Final Year Total Project Funding: $25,300

Assisting Systematic Review Preparation Using Automated Document Classification
National Library of Medicine (NLM) Grant Number 1R01LM009501
Project Period: 07/15/2007 - 07/14/2010
Principal Investigator: Aaron M. Cohen, MD, MS
Final Year Total Project Funding: $318,898

Peer-reviewed Publications

1. Cohen AM, Kaner J, Miller R, Kopesky JW, Hersh WR, Automatically Pre-Screening Patients for the Rare Disease Aromatic L-amino Acid Decarboxylase (AADC) Deficiency Using Knowledge Engineering, Natural Language Processing and Machine Learning on a Large EHR Population, J Am Med Inform Assoc. https://doi.org/10.1093/jamia/ocad244, (in press).

2. Bottomly D, Long N, Schultz A R, Kurtz S E, Tognon C E, Johnson K, Abel M, Agarwal A, Avaylon S, Benton E, Blucher A, Borate U, Braun T P, Brown J, Bryant J, Burke R, Carlos A, Chang B H, Cho H J, Christy S, Coblentz C, Cohen AM, d'Almeida A, Cook R, Danilov A, Dao K-H T, Degnin M, Dibb J, Eide C A, English I, Hagler S, Harrelson H, Henson R, Ho H, Joshi S K, Junio B, Kaempf A, Kosaka Y, Laderas T, Lawhead M, Lee H, Leonard J T, Lin C, Lind E F, Liu S Q, Lo P, Loriaux M M, Luty S, Maxson J E, Macey T, Martinez J, Minnier J, Monteblanco A, Mori M, Morrow Q, Nelson D, Ramsdill J, Rofelty A, Rogers A, Romine K A, Ryabinin P, Saultz J N, Sampson D A, Savage S L, Schuff R, Searles R, Smith R L, Spurgeon S E, Sweeney T, Swords, R T, Thapa A, Thiel-Klare K, Traer E, Wagner J, Wilmot B, Wolf J, Wu G, Yates A, Zhang H, Cogle C R, Collins R H, Deininger M W, Hourigan C S, Jordan C T, Lin T L, Martinez M E, Pallapati R R, Pollyea D A, Pomicter A D, Watts J M, Weir S J, Druker B J, McWeeney S K, Tyner J W. Integrative analysis of drug response and clinical outcome in acute myeloid leukemia. Cancer Cell. 2022 Jul 20;S1535-6108(22)00312-9.

3. Hersh WR, Cohen AM, Nguyen MM, Bensching KL, Deloughery TG. Clinical study applying machine learning to detect a rare disease: results and lessons learned. JAMIA Open. 2022 Jul 1;5(2):ooac053.

4. Proescholdt R, Hsiao TK, Schneider J, Cohen AM, McDonagh MS, Smalheiser NR. Testing a filtering strategy for systematic reviews: evaluating work savings and recall. AMIA Annu Symp Proc. 2022;2022:406-13.

5. Schneider J, Hoang Linh, Kansara Yogeshwar, Cohen AM, Smalheiser NR. Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews. JAMIA Open. 2022 Apr 1;5(1):ooac015.

6. Goueth RC, Cohen AM, Weiskopf NG. An Analysis of Two Sources of Cardiology Patient Data to Measure Medication Agreement. AMIA Annu Symp Proc. 2021;2021:267-75.

7. Luo M, Cohen AM, Addepalli S, Smalheiser NR. Identifying main finding sentences in clinical case reports. Database (Oxford). 2020 Jan 1;2020.

8. Chamberlin SR, Bedrick SD, Cohen AM, Wang Y, Wen A, Liu S, et al. Evaluation of patient-level retrieval from electronic health record data for a cohort discovery task. JAMIA Open. 2020 Oct;3(3):395-404.

9. Cohen AM, Chamberlin S, Deloughery T, Nguyen M, Bedrick S, Meninger S, et al. Detecting rare diseases in electronic health records using machine learning and knowledge engineering: Case study of acute hepatic porphyria. PLOS ONE. 2020 Jul 2;15(7):e0235574.

10. Chamberlin SR, Bedrick SD, Cohen AM, Wang Y, Wen A, Liu S, Liu H, Hersh WR, A query taxonomy describes performance of patient-level retrieval from electronic health record data, Health Search and Data Mining (HSDM) Workshop, Web Search and Data Mining (WSDM) Conference, medRxiv 19012294, 2020.

11. Leung ET, Raboin MJ, McKelvey J, Graham A, Lewis A, Prongay K, Cohen AM, Vinson A. Modelling disease risk for amyloid A (AA) amyloidosis in non-human primates using machine learning. Amyloid. 2019 Jun 18;0(0):1-9.

12. Weiskopf NG, Cohen AM, Hamman J, Jarmon T, Dorr D. Towards augmenting structured EHR data: a comparison of manual chart review and patient self-report. AMIA Annu Symp Proc; 2019.

13. Smalheiser NR, Cohen AM, Bonifield G. Unsupervised Low-Dimensional Vector Representations for Words, Phrases and Text that are Transparent, Scalable, and produce Similarity Metrics that are not Redundant with Neural Embeddings. J Biomed Inform. 2019 Jan 14;103096.

14. Cohen AM, Smalheiser NR. UIC/OHSU CLEF 2018 Task 2 Diagnostic Test Accuracy Ranking using Publication Type Cluster Similarity Measures. In: CLEF 2018 Working Notes: Working Notes of CLEF 2018 - Conference and Labs of the Evaluation Forum, Editors  Linda Cappellato, Nicola Ferro, Jian-Yun Nie, Laure Soulier. Avignon, FRANCE, 2018. Available at: http://ceur-ws.org/Vol-2125/paper_174.pdf

15. Cohen AM, Dunivin ZO, Smalheiser NR. A probabilistic automated tagger to identify human-related publications. Database (Oxford). 2018 01;2018:1-8.

16. Smalheiser NR, Cohen AM. Design of a generic, open platform for machine learning-assisted indexing and clustering of articles in PubMed, a biomedical bibliographic database. Data and Information Management. 2018;2(1):27-36.

17. Edinger T, Demner-Fushman D, Cohen AM, Bedrick S, Hersh W. Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval. AMIA Annu Symp Proc. 2017;2017:660-9.

18. Martin S, Wagner J, Lupulescu-Mann N, Ramsey K, Cohen A, Graven P, et al. Comparison of EHR-based diagnosis documentation locations to a gold standard for risk stratification in patients with multiple chronic conditions. Appl Clin Inform. 2017 Aug 2;8(3):794-809.

19. Wallace BC, Noel-Storr A, Marshall IJ, Cohen AM, Smalheiser NR, Thomas J. Identifying reports of randomized controlled trials (RCTs) via a hybrid machine learning and crowdsourcing approach. J Am Med Inform Assoc. 2017 May 25;

20. Weiskopf NG, Khan FJ, Woodcock D, Dorr DA, Cigarroa JE, Cohen AM. A Mixed Methods Task Analysis of the Implementation and Validation of EHR-Based Clinical Quality Measures. AMIA Annu Symp Proc. 2017 Feb 10;2016:1229-37.

21. Lugli G, Cohen AM, Bennett DA, Shah RC, Fields CJ, Hernandez AG, et al. Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: Altered Expression and Prospects for Biomarkers. PLoS ONE. 2015 Oct 1;10(10):e0139233.

22. Cohen AM, Smalheiser NR, McDonagh MS, Yu C, Adams CE, Davis JM, et al. Automated confidence ranked classification of randomized controlled trial articles: an aid to evidence-based medicine. J Am Med Inform Assoc. 2015 Feb 5.

23. Shao W, Adams CE, Cohen AM, Davis JM, McDonagh MS, Thakurta S, et al. Aggregator: a machine learning approach to identifying MEDLINE articles that derive from the same underlying clinical trial. Methods. 2015 Mar;74:65-70.

24. Gamble BT, Brush M, Cohen AM, Haendel M, et al. Post-Traumatic Stress Disorder (PTSD) Ontology to Support Automated Annotation and Data Categorization. Paper presented at: International Conference on Biomedical Ontology (ICBO), 2014; Houston, TX. 

25. Jiang Y, Lin C, Meng W, Yu C, Cohen AM, Smalheiser NR. Rule-based deduplication of article records from bibliographic databases. Database: the journal of biological databases and curation. 2014;2014.

26. Smalheiser NR, Lin C, Jia L, Jiang Y, Cohen AM, Yu C, et al. Design and implementation of metta, a metasearch engine for biomedical literature retrieval intended for systematic reviewers. Health Information Science and Systems. 2014;2(1):1.

27. Ambert KH, Cohen AM, Burns GA, Boudreau E, Sonmez K. Finna: A Paragraph Prioritization System for Biocuration in the Neurosciences. 2013 AAAI Fall Symposium Series. 2013.

28. Ambert KH, Cohen AM, Burns GA, Boudreau E, Sonmez K. Virk: An Active Learning-based System for Bootstrapping Knowledge Base Development in the Neurosciences. Front Neuroinform. 2013;7:38.

29. Edinger T, Cohen AM. A Large-Scale Analysis of the Reasons Given for Excluding Articles that are Retrieved by Literature Search During Systematic Review. AMIA Annu Symp Proc. 2013.

30. Cohen AM, Demner-Fushman D, Iorio A, Sim I, Smalheiser NR. Tools for Identifying Reliable Evidence and Implementing it in Everyday Clinical Care. AMIA Summits Transl Sci Proc. 2013;2013:42-4.

31. Ambert KH, Cohen AM. Text-mining and neuroscience. Int. Rev. Neurobiol. 2012;103:109-32.

32. Cohen AM, Demner-Fushman D, Iorio A, Sim I, Smalheiser NR. Tools for Identifying Reliable Evidence and Implementing it in Everyday Clinical Care. AMIA Summits Transl Sci Proc. 2013;2013:42-4.

33. Edinger T, Cohen AM, Bedrick S, Ambert K, Hersh W. Barriers to retrieving patient information from electronic health record data: failure analysis from the TREC Medical Records Track. AMIA Annu Symp Proc. 2012;2012:180-8.

34. Cohen AM, Ambert K, McDonagh M. Studying the potential impact of automated document classification on scheduling a systematic review update. BMC Medical Informatics and Decision Making. 2012 Apr 19;12(1):33.

35. Wright H, Cohen A, Sonmez K, Yochum G, McWeeney S. Occupancy Classification of Position Weight Matrix-Inferred Transcription Factor Binding Sites. PLoS ONE. 2011 Nov 4;6(11):e26160.

36. Dorr D, Cohen AM, Pierre-Jacques Williams M, Hurdle J. From simply inaccurate to complex and inaccurate: complexity in standards-based quality measures. AMIA Annu Symp Proc; 2011.

37. Ambert KH, Cohen AM. k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents. IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011.

38. Cohen AM, Adams CE, Davis JM, Yu C, Yu P, Meng W, et al. Evidence-Based Medicine,  the Essential Role of Systematic Reviews, and the Need for Automated Text Mining Tools.  In: IHI'10.  Arlington, Virginia, USA, 2010.

39. Campbell E, Sittig D, Chapman W, Hazlehurst B, Cohen AM. Understanding Inter-rater Disagreement: A Mixed Methods Approach. AMIA Annu Symp Proc; 2010. (Distinguished Paper Award Nominee)

40. Cohen AM, Ambert K, McDonagh M. A Prospective Evaluation of an Automated Classification System to Support Evidence-based Medicine and Systematic Review. AMIA Annu Symp Proc; 2010.

41. Cohen AM, Ambert K, McDonagh MS. Cross-topic Learning for Work Prioritization in Systematic Review Creation and Update. J Am Med Inform Assoc 2009.

42. Ambert KH, Cohen AM. A System for Classifying Disease Co-morbidity Status from Medical Discharge Summaries Using Automated Hotspot and Negated Concept Detection. J Am Med Inform Assoc 2009.

43. Yu H, Agrarwal S, Johnston M, Cohen A. Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension. Journal of Biomedical Discovery and Collaboration 2009;4(1).

44. Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, et al. Overview of BioCreative II gene normalization. Genome Biology 2008;9(Suppl 2):S3.

45. Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, et al. Text mining for biology - the way forward: opinions from leading scientists. Genome Biology 2008;9(Suppl 2):S9.

46. Yang J, Cohen A, Hersh W. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets. BMC Bioinformatics 2009;10 Suppl 2:S5.

47. Bahr, N, Cohen AM. Discovering synergistic qualities of published authors to enhance translational research. AMIA Annu Symp Proc 2008:31-5.

48. Yang J, Cohen A, McDonagh MS. SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification. AMIA Annu Symp Proc 2008:825-9.

49. Cohen AM. Optimizing feature representation for automated systematic review work prioritization. AMIA Annu Symp Proc 2008:121-5. (Distinguished Paper Awardee)

50. Roberts P, Cohen AM, Hersh WR. Tasks, Topics and Relevance Judging for the TREC Genomics Track: Five years of experience evaluating biomedical text information retrieval systems. Information Retrieval, OnlineFirst: DOI 10.1007/s10791-008-9072-x.

51. Cohen AM, McWeeney SK. RMEQ: A tool for computing equivalence groups in repeated measures studies. In: Linking Literature, Information and Knowledge for Biology: Proceedings of the BioLINK2008 Workshop; Toronto, ON; 2008.

52. Rekapalli H, Hersh W, Cohen A. A Comparative Analysis of Retrieval Features Used in the TREC 2006 Genomics Track Passage Retrieval Task. AMIA Annu Symp Proc 2007.

53. Yang J, Hersh W, Cohen A. Automatic Summarization of Mouse Gene Information by Clustering and Sentence Extraction from MEDLINE Abstracts. AMIA Annu Symp Proc 2007.

54. Cohen AM. Five-way Smoking Status Classification using Text Hot-spot Identification and Error-Correcting Output Codes. J Am Med Inform Assoc 2008;15(1):32-35.

55. Cohen AM. Automatically Expanded Dictionaries with Exclusion Rules and Support Vector Machine Text Classifiers: Approaches to the BioCreAtIve 2 GN and PPI-IAS Tasks. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop; Madrid, Spain: CNIO Centro Nacional de Investigaciones Oncologicas. p. 169-174, 2007.

56. Yang J, Cohen AM, Hersh WR. Functional Gene Group Summarization by Clustering MEDLINE Abstract Sentences. AMIA Annu Symp Proc 2006:1151.

57. Cohen AM. An effective general purpose approach for automated biomedical document classification. AMIA Annu Symp Proc 2006:161-5.

58. Hersh WR, Bhupatiraju RT, Ross L, Roberts P, Cohen AM, Kraemer DF. Enhancing Access to the Bibliome: The TREC 2004 Genomics Track. Journal of Biomedical Discovery and Collaboration 2006;1(3).

59. Cohen AM, Hersh W. The TREC 2004 Genomics Track Categorization Task: Classifying Full Text Biomedical Documents. Journal of Biomedical Discovery and Collaboration 2006;1(4).

60. Cohen AM, Hersh WR, Peterson K, Yen PY. Reducing Workload in Systematic Review Preparation Using Automated Citation Classification. JAMIA 2006;13(2):206-219.

61. Cohen AM. Unsupervised gene/protein entity normalization using automatically extracted dictionaries. In: Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, Proceedings of the BioLINK2005 Workshop; Detroit, MI: Association for Computational Linguistics; 2005. p. 17-24.

62. Cohen AM, Hersh WR, Dubay C, Spackman K. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts. BMC Bioinformatics 2005;6(103).

63. Cohen AM, Hersh W. A Survey of Current Work in Biomedical Text Mining. Briefings in Bioinformatics 2005;6(1):57-71.

64. Cohen AM, Stavri PZ, Hersh WR. A categorization and analysis of the criticisms of Evidence-Based Medicine. Int J Med Inf 2004;73(1):35-43.

65. Cohen AM, Parker JA, Donohoe K, Jansons D, Kolodny GM. Three years' experience with an all-digital nuclear medicine department. Semin Nucl Med 1990;20(3):225-33.

Non-peer-reviewed Publications

1. Cohen AM, Chamberlin S, Deloughery T, Nguyen M, Bedrick S, Meninger S, Ko JJ, Amin J, Wei AH, Hersh WR. Detecting Rare Diseases in Electronic Health Records Using Machine Learning and Knowledge Engineering: Case Study of Acute Hepatic Porphyria. MedRxiv, January 1, 2020, 2020.04.09.20052449. https://doi.org/10.1101/2020.04.09.20052449.

2. Bedrick S, Edinger T, Cohen A, Hersh W. Identifying Patients for Clinical Studies from Electronic Health Records: TREC 2012 Medical Records Track at OHSU. In: Proceedings of the Twenty-First Annual Text REtrieval Conference - TREC 2012;  Gaithersburg, MD; 2012. http://trec.nist.gov/pubs/trec21/papers/OHSU.medical.final.pdf.

3. Cohen AM. Classifying Sentences for Sentiment in Suicide Notes . In: i2b2 2011 NLP  Challenge Task; 2011; Washington, D.C.

4. Bedrick S, Ambert K, Cohen A, Hersh W. Identifying Patients for Clinical Studies from Electronic Health Records: TREC Medical Records Track at OHSU. In: Proceedings of the Twentieth Annual Text REtrieval Conference - TREC 2011;  Gaithersburg, MD; 2011. http://trec.nist.gov/pubs/trec20/t20.proceedings.html.

5. Cohen AM. Performance of support-vector-machine-based classification on 15 systematic review topics evaluated with the WSS@95 measure. J Am Med Inform Assoc. 2011 Jan 1;18(1):104; author reply 104-105. https://dx.doi.org/10.1136%2Fjamia.2010.008177

6. Aaron M. Cohen, Kyle Ambert, Jianji Yang, Robert Felder, Richard Sproat, Brian Roark,  Kristy Hollingshead, Kari Baker. OHSU/Portland VAMC Team  Participation in the 2010 i2b2/VA Challenge Tasks. In: i2b2 2010 NLP  Challenge Task; 2010; Washington, D.C.

7. Ambert K, Cohen AM. Error-Correcting Output Codes with Automatic Hot-Spot Filtering for Identifying Disease Comborbidity Status. In: i2b2 2008 NLP Obesity Challenge Task; 2008; Washington, D.C.

8. Hersh W, Cohen A, Roberts P. TREC 2007 Genomics Track Overview. In: Proceedings of the Sixteenth Annual Text Retrieval Conference (TREC) 2007, Gaithersburg, MD.

9. Cohen AM, Yang J, Fisher S, Roark B, Hersh WR. The OHSU Biomedical Question Answering System Framework. In: Proceedings of the Sixteenth Annual Text Retrieval Conference (TREC) 2007, Gaithersburg, MD.

10. Hersh W, Cohen A, Roberts P, Rekapalli H. TREC 2006 Genomics Track Overview. In: Proceedings of the Fifteenth Annual Text REtrieval Conference - TREC 2006; 2006; Gaithersburg, MD; 2006.

11. Cohen AM, Yang J, Fisher S, Roark B, Hersh WR. Combining Lexicon Expansion, Information Retrieval, and Cluster-based Ranking for Biomedical Question Answering. In: Proceedings of the Fifteenth Annual Text REtrieval Conference - TREC 2006; 2006; Gaithersburg, MD; 2006.

12. HershW, Cohen A, Yang J, Bhupatiraju RT,  Roberts P, Hearst M. TREC 2005 Genomics Track Overview. In: Proceedings of the Fourteenth Annual Text REtrieval Conference, TREC 2005, Gaithersburg, MD; http://trec.nist.gov/pubs/trec14/papers/GEO.OVERVIEW.pdf.

13. Cohen AM, Yang J, Hersh WR. A Comparison of Techniques for Classification and Ad Hoc Retrieval of Biomedical Documents. In: Proceedings of the Fourteenth Annual Text REtrieval Conference, TREC 2005, Gaithersburg, MD; http://trec.nist.gov/pubs/trec14/papers/ohsu-geo.pdf.

14. Cohen AM, Hersh WR, Bhupatiraju RT. Feature generation, feature selection, classifiers, and conceptual drift for biomedical document triage. In: Proceedings of the Thirteenth Annual Text REtrieval Conference, TREC 2004, Gaithersburg, MD, NIST SP 500-261, http://trec.nist.gov/pubs/trec13/papers/ohsu-hersh.geo.pdf.

15. Hersh WR, Bhupatiraju RT, Ross L, Cohen AM, Kraemer DF. TREC 2004 Genomics Track Overview. In: The Thirteenth Text Retrieval Conference - TREC 2004; Gaithersburg, MD; http://trec.nist.gov/pubs/trec13/papers/GEO.OVERVIEW.pdf.

16. Cohen AM, Hersh WR. Guest Editorial: Criticisms of Evidence-Based Medicine. Evidence-based Cardiovascular Medicine 2004;8(3):197-198.

17. Aaron Michael Cohen, How do I Process Images with Java?, Dr. Dobb's Journal, #287, July 1998: pp. 109-113.

18. Cohen AM, Resnikoff HL. Image Compression for Radiology and Telemedicine. SPIE Applications of Digital Image Processing XVII 1994;2298:304.

Books

1. Marusina K, Welsch DJ, Rose L, Brock D, Bahr N, Cohen AM, et al. Partnerships for Drug Repositioning: Lessones from the CTSA Pharmaceutical Assets Portal. In: Collaborative innovation in drug discovery: strategies for public and private partnerships. John Wiley & Sons; 2014. p. 115–33. 

2. Aaron Cohen and Mike Woodring, Win32 Multithreaded Programming, O'Reilly & Associates, Inc, Sebastopol, CA, 1998.

Electronic Publications

1. Patrick Schmitz, Aaron Cohen, SMIL Animation, World Wide Web Consortium (W3C) Recommendation, September 4, 2001. Available at: http://www.w3c.org/TR/smil-animation/

2. Jeff Ayars, Dick Bulterman, Aaron Cohen, et al., Synchronized Multimedia Integration Language (SMIL 2.0), World Wide Web Consortium (W3C) Recommendation, August 7, 2001. Available at: http://www.w3c.org/TR/smil20/

Invited Lectures, Conference Presentations or Professorships: 

International and National

1. Weiskopf NG, Cohen AM, Hamman J, Jarmon T, Dorr D. Towards augmenting structured EHR data: a comparison of manual chart review and patient self-report. Presented at: the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 18, 2019.

2. Smalheiser NS, Cohen AM, Schneider J.  Automated Probabilistic Tagging of Research Papers for Publication Type and Study Design. Presented at: The International Collaboration for the Automation of Systematic Reviews (5th ICASR) workshop, November 4, 2019, Bergen, Norway.

3. Cohen AM. NLP for the Institute: Developing and Deploying an NLP Capability to Accelerate Cancer Research. Invited plenary presentation. Presented at: ICBO-BioCreative 2016, August 1, 2016, Corvallis, Oregon.

4. Gamble BT, Brush M, Cohen AM, Haendel M, et al.  Post-Traumatic Stress Disorder (PTSD) Ontology and Use Case. Poster presented at: The Intelligent Systems for Molecular Biology (ISMB) conference Bio-Ontologies Special Interest Group (SIG). 2014; Boston, MA.

5. Cohen AM, Smalheiser NS, Informatics Approaches to Evidence-based Medicine, with Emphasis on Systematic Reviews, tutorial presented at the ACM BCB 2014: The 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, Newport Beach CA, September 20, 2014.

6. Edinger T, Cohen AM. A Large-Scale Analysis of the Reasons Given for Excluding Articles that are Retrieved by Literature Search During Systematic Review. Presented at: the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 16-20, 2013.

7. Cohen AM, Smalheiser NS, A Text Mining Pipeline to Support Evidence-based Medicine and Systematic Review. Part of the invited panel "Tools for Identifying Reliable Evidence and Implementing it in Everyday Clinical Care", presented at the American Medical Informatics Association (AMIA) Clinical Research Informatics (CRI) Summit, Parc 55 Hotel, San Francisco, CA, USA, March 21, 2013.

8. Cohen AM, Ambert K, McDonagh M. Studying the potential impact of automated document classification on scheduling a systematic review update (poster). Presented at OHSU Research Week, May 8, 2012, Portland, Oregon.

9. Dorr D, Cohen AM, Pierre-Jacques Williams M, Hurdle J. From simply inaccurate to complex and inaccurate: complexity in standards-based quality measures. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 22-26, 2011.

10. Cohen AM, Ambert K, McDonagh M. A Prospective Evaluation of an Automated Classification System to Support Evidence-based Medicine and Systematic Review. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 16, 2010.

11. Cohen AM, Adams CE, Davis JM, Yu C, Yu P, Meng W, et al. Evidence-Based Medicine, the Essential Role of Systematic Reviews, and the Need for Automated Text Mining Tools.  IHI'10 (poster).  Arlington, Virginia, USA, November 12, 2010.

12. Aaron M. Cohen, Kyle Ambert, Jianji Yang, Robert Felder, Richard Sproat, Brian Roark, Kristy Hollingshead, Kari Baker. OHSU/Portland VAMC Team  Participation in the 2010 i2b2/VA Challenge Tasks. i2b2 2010 Challenge Task Conference, Washington, D.C, November 12, 2010.

13. Wright H, Cohen A, Sonmez K, Yochum G, McWeeney S. Occupancy Classification of Position Weight Matrix-inferred Transcription Factor Binding Sites. Presented at ISMB 2010, the 18th Annual International Conference on Intelligent Systems for Molecular Biology, Boston MA, July 11-13, 2010.

14. Cohen AM, Ambert K, McDonagh MS. Cross-topic Learning for Work Prioritization in Systematic Review Creation and Update (poster). Presented at the National Library of Medicine Medical Informatics Fellow Annual Meeting, June 24, 2009, Portland, Oregon.

15. Cohen AM. Challenge Tasks for Biomedical Text Mining. Presented to the Veterans Administration Consortium for Health Informatics Research (CHIR), Work In Progress National Live Meeting, April 7, 2009.

16. Ambert K, Cohen AM. Error-Correcting Output Codes with Automatic Hot-Spot Filtering for Identifying Disease Comborbidity Status. Presented at the i2b2 2008 NLP Obesity Challenge Task, Washington, D.C., November 7, 2008.

17. Bahr N, Cohen AM. Discovering synergistic qualities of published authors to enhance translational research. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 12, 2008.

18. Yang J, Cohen AM, McDonagh M. SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 12, 2008.

19. Cohen AM. Optimizing Feature Representation for Automated Systematic Review Work Prioritization. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 12, 2008.

20. Cohen, AM. RMEQ: A tool for computing equivalence groups in repeated measures studies. BioLINK 2008 SIG Workshop, ISMB 2008, Toronto, ON, July 18, 2008.

21. Cohen, AM. The BioCreAtIve 2 GN and PPI-IAS Tasks: Approaches and Analysis (invited presentation). Presented at the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 23-25, 2007.

22. Cohen, AM. Enhancing access to the bibliome for genomics with evaluation tasks derived from user information needs: The TREC Genomics Track (invited presentation). Presented at the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 23-25, 2007.

23. Yang J, Cohen AM, Hersh WR. Functional Gene Group Summarization by Clustering Medline Abstract Sentences (poster). Presented at Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 14, 2006.

24. Craven CK, Smith CA, Cohen AM, Gorman J, Fiszman, M, Lehmann CU, Pevsner J. Careers in Medical Informatics (panel). Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 14, 2006.

25. Cohen AM. An Effective General Purpose Approach for Biomedical Document Classification. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 13, 2006.

26. Cohen AM, Yang J, Fisher S, Roark B, Hersh WR. Combining Lexicon Expansion, Information Retrieval, and Cluster-based Ranking for Biomedical Question Answering (poster). Presented at Text Retrieval Conference (TREC) 2006, November 15-17, 2006, Gaithersburg, Maryland.

27. Carson SM, Cohen AM, Hersh WR, Brown N, Helfand M. Systematic evaluation of web-based, publicly accessible clinical trial results databases (oral presentation). Presented at XIV Cochrane Colloquium, Dublin, Ireland, 2006.

28. Cohen AM, Carson SM, Hersh WR, Brown N, Peterson K, Helfand M. Elements and features of results databases recommended by experienced systematic reviewers (poster). Presented at XIV Cochrane Colloquium, Dublin, Ireland, 2006.

29. Cohen AM. Literature Based Discovery (invited presentation and panelist), American Medical Informatics Association Spring Congress, Phoenix, AZ, May 16-18, 2006.

30. Cohen AM, Hersh WR. Enhancing Access to the Genomics Literature: The TREC 2005 Genomics Track (poster). Presented at the American Medical Informatics Association (AMIA) Spring Congress, May 16-18, 2006, Phoenix, AZ.

31. Cohen AM, Yang J, Hersh WR. A Comparison of Techniques for Classification and Ad Hoc Retrieval of Biomedical Documents (poster). Presented at Text Retrieval Conference (TREC) 2005, November 15-16. 2005, Gaithersburg, Maryland.

32. Cohen, AM. Introduction to Biomedical Text Mining. Presented at the American Medical Informatics Association Annual Symposium, Washington D.C., October 26, 2005.

33. Cohen, AM. Unsupervised gene/protein entity normalization using automatically extracted dictionaries. Presented at BioLINK 2005 SIG ACL-05/ISMB-05, June 24, 2005, Detroit, Michigan.

34. Cohen, AM, Bhupatiraju RT, Hersh WR. Feature Generation, Feature Selection, Classifiers, and Conceptual Drift for Biomedical Document Triage (poster). Presented at the Text Retrieval Conference (TREC) 2004, November 17-19, 2004, Gaithersburg, Maryland.

35. Cohen, AM. Knowledge Extraction from MEDLINE with Symbolic Network Logical Analysis. Presented at the National Library of Medicine Medical Informatics Fellow Annual Meeting, June 9, 2004, Indianapolis, Indiana.

Regional and Local

1. Cohen AM, Kaner J, Miller R, Kopesky JW, Hersh WR. Using the EHR to Automatically Pre-Screen Patients for the Rare Disease Aromatic L-amino Acid Decarboxylase Deficiency (AADCd), Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, July 6 2023, Portland, Oregon.

2. Cohen AM, Practical Machine Learning Model Development and TEsting for Clinical Data Science, invited guest lecture HIP523, Oregon Health & Science University, October 26, 2022, Portland, Oregon.

3. Hersh WR, Chamberlin S, Cohen AM, Bedrick S. Re-Use of EHR Data for Cohort Discovery and Rare Disease Detection, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, November 7 2019, Portland, Oregon.

4. Cohen AM, Hagler S, McWeeney S. OCTRI NLP Evaluation: Results of the BeatAML Use Case, Druker Lab, Oregon Health & Science University, November 1 2019, Portland, Oregon.

5. Cohen AM. The State of the IDL 2016, DMICE Informatics Conference, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, January 14, 2016, Portland, Oregon.

6. Cohen AM. The State of the IDL: the OHSU Informatics Discovery Lab,
   DMICE Informatics Conference, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, February 26, 2015, Portland, Oregon.

7. Hersh WR, Cohen AM, Mohan V. Informatics at the Cutting Edge: Update from OHSU. HiMSS Northwest Annual Meeting, October 15, 2013, Portland, Oregon.

8. Edinger T, Cohen AM. Large-Scale Analysis of Reasons Given for Excluding Articles Retrieved by Literature Search During Systematic Review (poster). Presented at the OHSU Research Week, May 20-24, 2013, Portland, Oregon.

9. Edinger T, Cohen AM. Large-Scale Analysis of Reasons Given for Excluding Articles Retrieved by Literature Search During Systematic Review (poster). Presented at the OHSU School of Medicine 125th Anniversary Lecture Series: Accelerating personal health, An entrepreneurial patients's view of disruptive technologies and the promise of "OHSU Everywhere", April 1, 2013, Portland, Oregon.

10. Cohen AM. IDL: an Informatics Discovery Lab in the Department of Medical Informatics & Clinical Epidemiology (DMICE) at OHSU, part of the panel, A Decade of Excellence: The Department of Medical Informatics
    & Clinical Epidemiology, April 1, 2013, Portland, Oregon.

11. Cohen AM. An Informatics Innovation Lab in the Department of Medical Informatics & Clinical Epidemiology (DMICE) at OHSU.  Innotech Conference Oregon, May 3, 2012, Portland, Oregon.

12. Cohen AM, Ambert K, McDonagh M. A Prospective Evaluation of an Automated Classification System to Support Evidence-based Medicine and Systematic Review. DMICE Informatics Conference, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, November 4, 2010, Portland, Oregon.

13. Cohen AM. AMIA with Aaron: Highlights of the 2009 AMIA Symposium, DMICE Informatics Conference, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, November 19, 2009, Portland, Oregon.

14. Cohen AM. Introduction to biomedical text mining, Guest Lecture, CSE 554/654, Oregon Graduate Institute, May 5, 2008, Portland, Oregon.

15. Cohen AM. Why Python?, BioDev Research Group, Oregon Cancer Institute, Oregon Health & Science University, March 27, 2008, Portland, Oregon.

16. Cohen AM, Hersh WR, Research challenges and collaboration opportunities in information retrieval and text mining, Cancer Research Group, Oregon Cancer Institute, Oregon Health & Science University, December 12, 2007, Portland, Oregon.

17. Cohen AM. Reducing workload in systematic review preparation using automated citation classification, Systematic Reviews Discussion Group, Oregon Health & Science University, February 28, 2006, Portland, Oregon.

18. Cohen AM. Introduction to Biomedical Informatics, Oregon Biosciences Association Bioinformatics Special Interest Group, May 3, 2005, Portland, Oregon.

19. Cohen AM. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts, Oregon Health & Science University, Masters degree thesis defense, July 1, 2004, Portland, Oregon.

Patents

1. Cohen, Aaron M., Gorman, Christopher L., Hybrid procedural/pixel based textures, U.S. Patent Number 7,123,268, awarded October 17, 2006.

2. Cohen, Aaron M., Gupta, Ajay G., Video conferencing method and apparatus with improved initialization through command pruning, U.S. Patent Number 6,774,927, awarded August 10, 2004.

3. Cohen, Aaron M., Gorman, Christopher L., Hybrid procedural/pixel based textures, U.S. Patent Number 6,765,582, awarded July 20, 2004.

4. Woodring, Michael C., Cohen, Aaron M., Menon, Rama, Information streaming in a multi-process system using shared memory, U.S. Patent Number 6,519,686, awarded February 11, 2003.

5. Cohen, Aaron M., Gorman, Christopher L., Apparatus and method for progressively rendered procedural textures, U.S. Patent Number 6,459,434, awarded October 1, 2002.

6. Cohen, Aaron M., Method and Apparatus for Software Licensing Electronically Distributed Programs, U.S. Patent Number 6,233,567, awarded May 15, 2001.

Awards

1. November 2008, Distinguished Paper Award, Optimizing Feature Representation for Automated Systematic Review Work Prioritization. American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 12, 2008.

2. May 2005, Outstanding Masters Thesis Award, Using Symbolic Network Logical Analysis as a Knowledge Extraction Method on Medline Abstracts, Oregon Health & Science University, Portland, Oregon.

3. September 2001, Intel ASL Divisional Award, "In recognition of his outstanding accomplishment in leading the SMIL 2.0 spec to completion". Intel Corporation, Hillsboro, Oregon, September 27, 2001.

V. SERVICE

Membership in Professional Societies:

1. 2005-present, Full Member, American Medical Informatics Association

2. 2003-2005, Student Member, American Medical Informatics Association

Granting Agency Review Work:

1. December 2022, NIH Early Investigator Awards, Invited Reviewer.

2. May 2021- present, Shriners Children's Research Advisory Board.

3. May 23, 2019, NLM (National Library of Medicine), R01 PAR COMPUTATIONAL CURATION, ZLM1 YW-R(01).

4. October 30, 2018, NCI (National Cancer Institute), Special Emphasis Panel, ZDE1CF05.

5. February 23, 2017. National Institute of Health. Big Data to Knowledge (BD2K) Enhancing the Efficiency and Effectiveness of Digital Curation for Biomedical Big Data (U01), RFA-LM-17-001.

6. October 22, 2015, NIEHS (National Institute of Environmental Health Science), Ad hoc grant reviewer.

7. June 16 2015, NIEHS (National Institute of Environmental Health Science) Board of Science Review, Ad hoc reviewer.

8. April 2013, IWT (http://www.iwt.be) Invited Proposal Reviewer.

9. March 2012, Agency for Healthcare Research and Quality (AHRQ) Effective Health Care Invited Reviewer.

10. September 2008, External Peer Reviewer, National Institute of Standards and Technology (NIST).

Editorial and Ad Hoc Review Activities:

Journal article reviews: Over 50 manuscripts reviewed

Bioinformatics

BMC Bioinformatics

IEEE Computational Biology and Bioinformatics

International Journal of Medical Informatics

Information Processing and Management

Information Retrieval

Journal of the American Medical Informatics Association (JAMIA)

JAMIA Open

Journal of the American Society for Information Science and Technology (JASIST)

Journal of Biomedical Discovery and Collaboration

Medical Decision Making

PLOS One
Research Synthesis Methods

Toxicology

Conference program committees: Over 60 manuscripts reviewed

Association for the Advancement of Artificial Intelligence, Information Retrieval and Knowledge Discovery in Biomedical Text

American Medical Informatics Association Annual Symposium

Association for Computing Machinery (ACM) International Conference on Machine Learning and Applications (ICMLA)

Association for Computing Machinery (ACM) SIGIR

Association for Computing Machinery (ACM) SIGCHI

Association for Computing Machinery (ACM) SIGBIOMED

Association for Computational Linguistics (ACL)

BioCreative

BioLINK

BioNLP

BioTxtM

Brazilian Symposium on Bioinformatics

ISMB

Louhi Workshop on Text and Data Mining of Health Documents

Pacific Symposium on Biocomputing (PSB)

TMBio

Editorial Boards:

2005-present, Journal of Biomedical Discovery and Collaboration (JBDC)

2018-present, JAMIA Open

Award Reviews:

Houtchen Competition, University of Utah

Homer Warner Award, University of Utah

Committees:

International/National

1. July 2011-August 2012, SIGIR 2012 Sponsorships Chairman.

2. January 2011-present, Steering Commitee Memer, NIST Text REtrieval Conference (TREC) Medical Records Track.

3. January 2011-present, Program Committee Member, BioCreative IV.

4. November 2010 - November 2011, Scientific Program Commitee, American Medical Informatics Association (AMIA) Fall Symposium 2011, Washington, D.C.

5. 2002, Intel Lead Representative, Java Community Process (JCP)

6. 1999-2002, Chairman, World Wide Web Consortium (W3C), Synchronized Multimedia Working Group

Institutional

1. 2014-2017, OHSU Faculty Senate Executive Committee

2. 2013, OHSU Faculty Senate Awards Committee, School of Medicine Service Award Selection Committee

3. 2012, OHSU Faculty Senate Awards Committee, School of Medicine Service Award Selection Committee

4. 2011-2013, OHSU Biolibrary Development Committee (BDC), BDC Informatics Sub-Committee

5. 2011-2013, OHSU Faculty Senate Executive Committee

6. 2010-2017, OHSU Faculty Senate, School of Medicine Representative

7. 2006, OHSU Outstanding Masters Thesis Review Committee

8. 2006, Bioinformatics Subcommittee, OHSU Clinical and Translational Science Award Grant Proposal Committee

Departmental

1. 2023-present, Chairman, Promotion and Tenure Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

2. 2008-2023, Mentorship Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

3. 2007-2015, Internship Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

4. 2006-2023, Department Web Site Committee, Chairman, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

5. 2005-2023, NLM Fellowship Selection Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

6. 2005-2023, PhD Selection Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

7. 2005-present, Professional Conduct Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

8. 2005-2023, PhD Qualifying Exam Review Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Community Service:

1. Where the Jobs Are...Biosciences, Social Sciences, Mathematics, Panel discussion and Q & A, Reed College, February 13, 2007.

2. September 2005, Susan G. Komen, Race for the Cure, Portland, Oregon

VI. TEACHING (also see OHSU Educator's Portfolio):

Scholarship of Teaching:

Thesis and Exam Committees for Masters Students (Completed):
Michael Shapiro, MS, Department of Medical Informatics and Clinical Epidemiology, 2008. (thesis committee)
Nathan Bahr, MS, Department of Medical Informatics and Clinical Epidemiology, 2009. (thesis committee chair)
Daniel Bottomly, MS, Department of Medical Informatics and Clinical Epidemiology, 2009. (thesis committee)
John Koerner, MBI, Department of Medical Informatics and Clinical Epidemiology, 2009. (advisor)
Yongshun Chen, MS (Computer Science), Department of Biomedical Engineering, 2011. (thesis exam committee)
Tracy Edinger, MS, Department of Medical Informatics and Clinical Epidemiology, 2013-2014. (thesis committee, advisor)
Ravi Madhira, Department of Medical Informatics and Clinical Epidemiology. 2015-2016 (thesis advisor)

Dissertation and Exam Committees for PhD Students (Completed):
Jianji Yang, PhD, Department of Medical Informatics and Clinical Epidemiology, 2007. (dissertation committee)
Emily Campbell, PhD, Department of Medical Informatics and Clinical Epidemiology, 2009. (dissertation committee chair)
Hollis Wright, Department of Medical Informatics and Clinical Epidemiology, 2010. (dissertation committee)
Joshua Richardson, Department of Medical Informatics and Clinical Epidemiology, 2010. (dissertation committee)
Steven Bedrick, Department of Medical Informatics and Clinical Epidemiology, 2011. (dissertation exam committee)
Kyle Ambert, Department of Medical Informatics and Clinical Epidemiology. (dissertation committee chair)
James McKanna, Department of Medical Informatics and Clinical Epidemiology. (dissertation committee)
David Gibbs, Department of Medical Informatics and Clinical Epidemiology. (mentored project)
Travis Gamble, Department of Medical Informatics and Clinical Epidemiology. (primary mentor, dissertation committee)
Aurora Blucher, Department of Medical Informatics and Clinical Epidemiology. (dissertation committee, dissertation exam chair)

Summer Interns:
Ignatz Reicht, 2007
David Gibbs, 2008

Katie Shimaura, 2023

Masters Students:
Shahim Essaid, Department of Medical Informatics and Clinical Epidemiology. (thesis committee)
Andrew Lemieux, Department of Medical Informatics and Clinical Epidemiology. (thesis committee)
Katya Staroseltseva, Department of Medical Informatics and Clinical Epidemiology. (mentored project)
Jason Hwee, Department of Medical Informatics and Clinical Epidemiology. (mentored project)
Eric Leung, Department of Medical Informatics and Clinical Epidemiology. (mentored project)
Benjamin Cordier, Department of Medical Informatics and Clinical Epidemiology. (mentored project)

David Boston, Department of Medical Informatics and Clinical Epidemiology, 2019. (mentored capstone project)
Colman Hilton, Department of Medical Informatics and Clinical Epidemiology, 2019. (mentored capstone project)

Current PhD and Post-doctoral Students:
Nathan Bahr, Department of Medical Informatics and Clinical Epidemiology. (mentored project, mentored teaching, post-doc mentor)

Eric Leung, Department of Medical Informatics and Clinical Epidemiology. (mentored project)

Steven Chamberlin, Department of Medical Informatics and Clinical Epidemiology. (research and K99 mentor)
Benjamin Cordier, Department of Medical Informatics and Clinical Epidemiology. (dissertation committee chair)

Caroline King, Department of Biomedical Engineering. (mentored project)

Past Post-doctoral Advisees:
Armand Bankhead, Department of Medical Informatics and Clinical Epidemiology.

Curriculum Development

1. Software Engineering, BMI 546/646, 2007-present

2. Scripting for Scientists, BMI 507/607, Fall 2009 (Mentored teaching for students Kyle Ambert and Steven Bedrick) 

3. Advanced Topics: Biomedical Text Mining, BMI 607, Spring 2006 

4. Assisted in design of Bioinformatics Masters and PhD curriculum, 2005-present

Educational Activity:

1. Spring 2009 - present, BMI 505/605, Co-Course Director, Doctoral Fellows Meeting, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

2. Spring 2006 - present, BMI 546/646, Course Director and Instructor, Software Engineering, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

3. Fall 2002 - 2004, BMI 540, On-campus lecturer, Advanced Computer Programming, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Service and Membership on Educational Committees:

1. 2020-2023, OHSU School of Medicine Graduate Council, DMICE Representative

2. September 2014-2017, University Curriculum Committee, Faculty Senate Representative, Oregon Health & Science University

3. September 2012-2017, Educational Policy Committee Chairman, Faculty Senate, Oregon Health & Science University

4. October 2010-2012, Educational Policy Committee, Faculty Senate, Oregon Health & Science University

5. August 2005-present, Bioinformatics Curriculum Track Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

6. August 2005-present, Clinical Informatics Curriculum Track Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Honors and Awards for Education:

2011-2012 Teaching Excellence Award, OHSU School of Medicine, awarded October 2012.