A division of the Department of Biomedical Informatics and Medical Education  |  UW Medicine
Biomedical and Health Informatics

Faculty Profiles - All Faculty


Barry Aaronson, MD, FACP, SFHM
Hospitalist & Associate Medical Director for Clinical Informatics
- Virginia Mason Medical Center, Seattle
Clinical Associate Professor Department of Medicine
Clinical Associate Professor Dept. of Biomedical Informatics & Medical Education
- University of Washington, Seattle

Background: Working 1/2 time as a Hospitalist at Virginia Mason Medical Center and 1/2 time as the Associate Medical Director for Clinical Informatics at Virginia Mason. Completed in 2009 National Library of Medicine Post-Doctoral Fellowship within BHI. During fellowship completed a clinical trial of an EHR based tool to assist the UWMC and HMC Rapid Response Teams proactively identify deteriorating patients outside the intensive care units in an effort to reduce mortality, unexpected cardiac arrest and unexpected transfers to the intensive care units.

Current Research:  Currently leading clinical trial of a tool we deployed within the EHR called the "Quality Safety Dashboard." This dashboard is a real-time feedback system for hospital core measure compliance that is displayed on large wall mounted monitors to aid in situational awareness by all members of the care team in an effort to achieve 100% compliance with core measures.

Representative Publications:

  • Solti I, Aaronson BA, Fletcher G, Solti M, Gennari J, Cooper M, Payne T, “Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development” AMIA Annu Symp Proc. 2008; 2008: 687
  • Hanson D, Aaronson B, Krevat S. An EHR Structured Discharge Documentation Tool to Mistake Proof CHF Bundle Compliance. (2010), Innovations Poster Abstract. Journal of Hospital Medicine, 5: 84–110. doi: 10.1002/jhm.708
  •  White A, Aaronson B, Fletcher G. et. al. Initial Pilot of an Electronic Health Record Dashboard to Improve Compliance with Inpatient Quality Measures. (2010), Innovations Poster Abstract. Journal of Hospital Medicine, 5: 84–110. doi: 10.1002/jhm.708
  • Aaronson BA, Westley M, Spohnholtz M, Tyler L, Dunning, E. Evaluation of an Electronic Early Warning System for the Detection of Critically Ill Hospital Patients. (2008), Innovations Abstracts. Journal of Hospital Medicine, 3: 49–74. doi: 10.1002/jhm.330
  •  Aaronson B, Stone D, Schaft M, et. al. An Electronic Health Record Based Tool to Aid in the Prevention of Avoidable Deaths in Hospital Patients. (2009), Innovations Poster Abstracts. Journal of Hospital Medicine, 4: 73–92. doi: 10.1002/jhm.546

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Neil Abernethy, PhD
Associate Professor, Biomedical Informatics and Medical Education
Assistant Professor, Health Services, School of Public Health

Background:   B.S. Biochemistry (NCSU); B.S. Applied Mathematics (NCSU); Ph.D. Biomedical Informatics (Stanford University). Dr. Abernethy’s training included molecular evolution, knowledge representation for bioinformatics, network analysis, epidemiology of infectious disease, and interactive data visualization.

Research:  Models of infectious disease (including TB, HIV, and influenza), molecular epidemiology, network analysis, disease surveillance, data information, systems biology, data standards and integration, with a focus on infectious diseases and global health.

Other interests:  High-throughput (“Omics”) biology, evolutionary processes, bibliometrics, user interfaces, and artificial intelligence.

Representative Publications:

  • N. F. Abernethy; Automating Social Network Models for Tuberculosis Contact Investigation.  Ph.D. Dissertation, Stanford University, September, 2005.
  • Jeffries D, Abernethy NF, De Jong BC. Supervised learning for the automated transcription of spacer classification from spoligotype films. Medical Research Council (UK), The Gambia. BMC Informatics 2009 August;10:248.
  • Guidry A, Walson J, Abernethy NF. Linking information systems for HIV care and research in Kenya. ACM International Health Informatics 2010.
  • B.  Walther, S. Hossin, J. Townend, N. F. Abernethy, D. Parker, D. Jeffries, Comparison of Electronic Data Capture (EDC) with the Standard Data Capture Method for Clinical Trial Data ; PLOS One, Sep 23, 2011.
  • Abernethy NF, Dereimer K, Small PM: A National Survey of Data Standards in Contact Investigation Forms for Tuberculosis. Proceedings of the American Medical Informatics Association (AMIA) 2011 (in press).
  • Deanna Petrochilos, N. F. Abernethy; Assessing Network Characteristics of Cancer-Associated Genes in Metabolic and Signaling Networks; Proceedings of the 2012  IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

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Tania P Bardyn, MLIS, AHIP
Associate Dean of University Libraries
Director, UW Health Sciences Library
Affiliate Assistant Professor, Department of Biomedical Informatics and Medical Education

Background: BA (Hons.) (Queen's University), and Master of Library and Information Sciences (University of Western Ontario).  Director of the University of Washington Health Sciences Library.  Sixteen years’ experience in medical librarianship at universities and teaching hospitals affiliated with UCLA, NYU Langone Medical Center and the University of Texas Health Center at San Antonio (UTHSCSA). 

Current Primary Interests:  Assessing information needs in medical education, GME and CME; systematic reviews as a library service; identifying essential information resources by discipline; needs assessment to improve information seeking behavior and biomedical literature searching skills; using games to improve evidence based information seeking behavior and incorporating it into clinical practice. Most recently, conducted research on the information and data curation needs and practices of translational researchers.

Current Research:

RELM.  In collaboration with the UW School of Medicine, we are developing an online game to teach WWAMI faculty how to practice evidence based medicine (EBM).

Representative Publications:

  • Tania P. Bardyn , Taryn Resnick & Susan K. Camina (2012): Translational Researchers’ Perceptions of Data Management Practices and Data Curation Needs: Findings from a Focus Group in an Academic Health Sciences Library, Journal of Web Librarianship, 6:4, 274-287   DOI: http://dx.doi.org/10.1080/19322909.2012.730375
  • Chatfield A, M. Ratajeski, J. Wang, T. Bardyn. Communicating with faculty, staff, and students using library blogs: results from a survey of academic health sciences libraries. Internet Reference Services Quarterly, Jul-Sep2010, Vol. 15 Issue 3, p149-168.
  • Bardyn, T. Library blogs: what's most important for success within the enterprise? Computers in Libraries; June 2009; 29 (6):12-16.
  • Bardyn, TP., Resnick, T, Mazo R, and KA Egol. Building orthopedic journal collections: analyzing use and bibliometrics in a teaching hospital library. Journal of Hospital Librarianship, April 2009; 9(2):123-138. DOI: 10.1080/15323260902805686.
  • Bardyn T. CME Learning Needs of Physicians: Implications for Librarians. Journal of Hospital Librarianship. June 2007 7(3):65-73. DOI: 10.1300/J186v07n03_09.
  • Bardyn T. Electronic Desktop Delivery of Journal Articles: One Medical Library’s Experience. Journal of Interlibrary Loan, Document Delivery & Information Supply. May 2003; 13(4):7-19 DOI: 10.1300/J110v13n04_03.
  • Quintana, Y. and T. Bardyn. Evaluating Health Libraries on the World Wide Web: Design Guidelines and Future Development.  Biblioteca Medica Canadiana; 1996;18(2):61-64.

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James Brinkley, MD, PhD
Professor, Biological Structure
Joint Professor, Biomedical Informatics and Medical Education
Adjunct Professor, Computer Science and Engineering
Fellow, American College of Medical Informatics
Director, UW Structural Informatics Group
Associate Director, Biomedical Informatics Core, Institute of Translational Health Science (ITHS)

Background: Informatics research on 2-D and 3-D imaging and modeling, ontologies, data management, data integration and visualization; established in 1991 the subfield of biomedical informatics known as "structural informatics," whose fundamental premise is that the structure of the body is the most rational means for organizing biomedical information.

Education: M.D., University of Washington; Ph.D., Stanford University, Medical Computer Engineering.

Current primary interests: structural informatics with emphasis on multimedia data management, ontologies, data integration, and visualization as applied to translational medicine; practical data management and integration as a service.

Current major project that could use student help:  the Foundational Model of Anatomy (FMA), a large ontology of anatomy; semantic web based approaches for creating views and web-service access to large ontologies like the FMA; image annotation using semantic-web methods; ontology-based data management and integration; ontology-based visualization of 3-D anatomical scenes in virtual worlds for education and as a substrate for visualization of biomedical information.  Application areas depend on funding; currently include craniofacial development and malformation, brain mapping, proteomics, distributed anatomy education in virtual worlds, low cost/open source management and integration of clinical/translational data and knowledge.

For more information see http://sig.biostr.washington.edu (this page is currently out of date, so please contact me through email for updates).

Currently possibly accepting new MS students (check with Dr. Brinkley).  Not currently accepting new PhD students.

Representative Publications: 

  • Brinkley, J.F. 1991  Structural informatics and its applications in medicine and biology. Academic Medicine 66(10):589-591.
  • Rosse, C., Shapiro, L.G. and Brinkley, J.F. 1998 The Digital Anatomist foundational model: principles for defining and structuring its concept domain. Journal of the American Medical Informatics Association, Symposium Supplement, pp 820-824.
  • Detwiler LT, Suciu D, Franklin JD, Moore EB, Poliakov AV, Lee ES, Corina D, Ojemann GA, Brinkley JF. Distributed XQuery-based integration and visualization of multimodality data: Application to brain mapping. Frontiers in Neuroinformatics (2009) 3:2. doi:10.3389/neuro.11.002.2009. http://sigpubs.biostr.washington.edu/archive/00000234/.
  • Shaw MS, Detwiler LT, Noy NF, Brinkley JF, Suciu D. vSPARQL: A view definition language for the semantic web. Journal of Biomedical Informatics. 44(1):102-117. 2010 

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Annie T. Chen, PhD

Research Interests: : Chronic illness information behaviors, health-related uses of social media, research methods, natural language processing, patient education, alternative medicine, digital humanities Current research: I am interested in patient experience — how patients encounter, seek out and interpret information to help manage their condition, and especially, how patients' understandings and cognitive representations of health and wellness change over time in the context of chronic illness. I am currently working on analysis of data from an interview study of patients’ illness journeys. This research investigates themes including: patient-provider interaction, learning to listen to the body (body awareness), and the role of emotions in chronic illness. I am also engaged in research involving text mining of health-related social media, including content from Reddit and other discussion forums. These include chronic conditions such as fibromyalgia and diabetes, and tobacco products (e.g. e-cigarettes and hookah).

Representative publications:

Chen, A. T. (2015). Information use and illness representations: Understanding their connection in illness coping. Journal of the Association for Information Science and Technology, 66(2), 340-353. DOI: 10.1002/asi.23173

Chen, A. T. (2014). What’s in a Virtual Hug? – A Transdisciplinary Review of Methods in Online Health Discussion Forum Research. Library and Information Science Research, 36(2), 120-130. DOI: 10.1016/j.lisr.2013.10.007

Chen, A.T. (2012). Information seeking over the course of illness: The experience of people with fibromyalgia. Musculoskeletal Care, 10(4): 212-20. DOI: 10.1002/msc.1022

Chen, A.T. (2012). Exploring online support spaces: Using cluster analysis to examine breast cancer, diabetes and fibromyalgia support groups. Patient Education and Counseling, 87(2), 250-257. DOI: 10.1016/j.pec.2011.08.017

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Daniel Capurro, MD, PhD
Assistant Professor Department of Internal Medicine, Pontificia Universidad Católica de Chile.
Affiliate Assistant Professor Department of Biomedical Informatics and Medical Education, University of Washington, Seattle

Background: LIcentiate (BS) in Medicine, MD and Internal Medicine residency from Pontificia Universidad Católica de Chile, PhD in Biomedical Informatics from the University of Washington. Significant experience in patient care ranging from outpatient ambulatory care to the intensive care unit, now working full time time in clinical informatics (implementing healthcare information systems) and clinical research informatics (developing methods to better phenotype patients using EMR databases.) 

Research: My current research is focused on developing methods to improve patient phenotyping using EMR databases, in particular the use of temporal abstractions and time intervals to define and identify patient cohorts. My second focus is on developing better ways to interact with patients and individuals in between medical visits or healthy individuals, for example developing systems to monitor patients in palliative home care and studying the use of social networking sites for publc health research and practice.

Representative Publications:

  • Capurro D, Ganzinger M, Perez-Lu J, Knaup P. Effectiveness of eHealth interventions and information needs in palliative care: a systematic literature review. Journal of Medical Internet Research 2014;16(3):e72.
  • Capurro D, Cole K, Echavarría M, Joe J, Neogi T, Turner AM. The use of social networking sites for public health practice and research: a systematic review. Journal of Medical Internet Research 2014;16(3):e79.
  • Devine EB, Capurro D, van Eaton, E, Alfonso-Cristancho R, Devlin A, Yanez, ND, Yetisgen-Yildiz M, Flum DR, Tarczy-Hornoch P and the CERTAIN Collaborative. Preparing electronic clinical data for quality improvement and comparative effectiveness research: The SCOAP CERTAIN Automation and Validation Project. eGEMs (Generating Evidence & Methods to improve patient outcomes) 2013; 1(1) Article 16.
  • Rada G, Perez D, Capurro D. Epistemonikos: a free, relational, collaborative, multilingual database of health evidence. Stud Health Technol Inform 2013; 192: 486-490. 
  • Kirchhoff K, Capurro D, Turner AM. A conjoint analysis framework for evaluating user preferences in machine translation. Machine Translation 2013; Online First DOI 10.1007/s10590-013-9140-x
  • Demiris G, Parker Oliver D, Capurro D, Wittenberg-Lyles E. Implementation science: implications for intervention research in hospice and palliative care. The Gerontologist 2013; Online First DOI: doi:10.1093/geront/gnt022
  • Turner AM, Kirchhoff K, Capurro D.  Using crowdsourcing technology for testing multilingual public health promotion materials. Journal of Medical Internet Research 2012; 14(3):e79
  • Capurro D, Soto M, Vivent M, Lopetegui M, Herskovic JR. Biomedical informatics.Rev Med Chile 2011; 139: 1611-1616

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Jan Carline, PhD
Professor, Biomedical Informatics and Medical Education

Background: 30 yrs experience in support of medical education and its evaluation.

Research: a) evaluation of curricular innovations, b) use of program evaluation to improve education

Representative Publications:

  • Carline JD, Curtis JR, Wenrich MD, Shannon SE, Ambrozy DM, Ramsey PG.  Physicians’ interactions with health care teams and systems in the care of dying patients: Perspectives of dying patients, family members, and health care professionals.  Journal of pain and symptom management, 25:19-28, 2003.
  • Carline JD, Patterson DG.  Assessing Health Profession Partnerships: Characteristics of professions schools, public school systems and community-based organizations in successful partnerships.  Academic Medicine, 78(5): 467-482, 2003.
  • Carline JD: Funding medical education research: Opportunities and issues. Academic Medicine 79(10): 918-924, 2004.
  • Carline JD, O’Sullivan PS, Gruppen LD, Richardson-Nassif K. Crafting successful relationships with the IRB. Academic Medicine 82:10: S57-60, 2007.
  • Shi-Hao Wen, Jing-Song Xu, Carline JD, Fei Zhong, Yi-Jun Zhong, Sheng-Juan Shen. Wei-Min Ren, Li Qu, Yue Wang, Guo-En Fang. Effects of teaching evaluation: a case study. International Journal of Medical Education http://www.ijme.net/archive/2/teaching-evaluation-effects/
  • Amies AM, Dobie S, Smith S, Tamura GS, Carline JD.  Where do medical students turn? The role of the assigned mentor in the fabric of support. Teaching and Learning in Medicine 23(3); 105-111, 2011.

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David Chou, MD
Professor, Laboratory Medicine
Adjunct Professor, Biomedical Informatics and Medical Education

Background: 30+ years computer science, laboratory medicine, informatics. Dr. Chou is also the director, Informatics and Phlebotomy, UW and Harborview Medical Centers and is the Chief Technical Officer for Information Technology Services, UW Medicine

Funded research: co-PI of informatics research grants on a) the application of emerging technologies to clinical decision support and clinical biorepositories, b) intersection of laboratory information systems, clinical information systems, clinical lab automation.

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Daniel Cook, MD, PhD
Research Professor, Physiology/Biophysics
Adjunct Research Professor, Biomedical Informatics and Medical Education

Background:  Dr. Cook has been developing tools for the representation and analysis of complex dynamic systems for 40 years. He earned a BSME in mechanical engineering from the University of Michigan and spent 4 years as a Boeing while earning his Masters degree in Mechanical Engineering from the UW. To follow-up his masters thesis project on the simulation of glucose-induced insulin secretion, he entered the UW's Medical Scientist Training Program to earn his MD and a PhD in Physiology & Biophysics. After making seminal discoveries in the electrophysiology of insulin secretion,

Dr. Cook returned to his interests in the computational representation and analysis of complex systems. He authored two graphics-based applications for diagramming and analyzing cell networks and based one program, Chalkboard, on a linguistic metaphor of entity interactions using noun/verb constructs. He then connected with Dr. Cornelius Rosse and the FMA project to learn state-of-the-art knowledge representation and query methods as part of the DARPA-sponsored Virtual Soldier Project.

In subsequent collaborations with Drs. John Gennari, James Brinkley, and others, he is developing informatics methods for the declarative representation of physics-based biosimulation models as needed by, for example, the European Virtual Physiological Human and IUPS Physiome projects. The major contributions to this effort are an ontology of classical physics, the Ontology of Physics for Biology (OPB), and light-weight OWL representations (SemSim models) that map the biological and mathematical content of individual simulation models to the FMA and OPB.

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David Crosslin, PhD

Dr. Crosslin's academic and professional research experience have been focused on statistical genetics and bioinformatics with applications to complex diseases.  His doctorate research in Computational Biology and Bioinformatics at Duke University focused on the central theme of modeling metabolic pathways through dimension reduction techniques of genomics data to understand the etiology of complex traits such as cardiovascular disease.  Dr. Crosslin's postdoctoral training at the University of Washington (UW) focused on the areas of clinical applications of genetics, statistical genetics, and sequencing technologies.  This led to an Acting Instructor faculty position in Genome Sciences at UW.  Along with the BIME faculty appointment, Dr. Crosslin has an affiliate faculty appointment at Group Health Research Institute, Seattle, WA, and an adjunct faculty appointment in Genome Sciences.  Dr. Crosslin's research program focuses on translational bioinformatics with a combination of bioinformatics, statistical association analyses, and computational tools development for applied research.  Specifically, his research focuses on integrating genetic data into the electronic health record (EHR) for clinical decision support (CDS).  All efforts will advance the national electronic health information infrastructure in support of personalized medicine.  Dr. Crosslin has been and will continue to be affiliated with one such NHGRI effort.  The Electronic Medical Records & Genomics (eMERGE) Network is on the forefront of precision medicine and discovery using mined phenotypes, and has transitioned from discovery, to interpretation and integration into the EHR for CDS.  When not spending time with his daughters, Dr. Crosslin enjoys training, camping, kayaking, and college football.

Representative Publications:

Crosslin D.R., Shah S.H., Nelson S.C., et al., 2009: “Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis,” Human Genetics, 125:217-229. (PMCID: PMC2759090.)

Crosslin D.R., McDavid A., Weston N., et al., 2012: “Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network,” Human Genetics, 131(4):639-652. (PMCID: PMC3640990.)

Crosslin D.R., Carrell D.S., Burt A., et al., 2014: “Genetic variation in the HLA region is associated with susceptibility to herpes zoster,” Genes & Immunity, 16(1):1-7. (PMCID: PMC4308645.)

Crosslin D.R., Tromp G., Burt A., et al., 2014: “Controlling for population structure and genotyping platform bias in the eMERGE multi-institutional biobank linked to Electronic Health Records” Frontiers in Genetics, 5:352, eCollection. (PMCID: PMC4220165.)

Crosslin D.R., Robertson P.D., Carrell D.S., et al., 2015: “Prospective participant selection and ranking to maximize actionable pharmacogenetic variants and discovery in the eMERGE Network,” Genome Medicine, 7(1):67, eCollection. (PMCID: PMC4517371.)

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Walter H. Curioso, MD, MPH, PhD
Research Professor, Universidad Peruana Cayetano Heredia, Peru.
Affiliate Associate Professor, Biomedical Informatics and Medical Education, University of Washington.

Education: MD (Universidad Peruana Cayetano Heredia); Master's in Public Health (University of Washington); Certificate in Biomedical and Health Informatics (University of Washington); Ph.D. in Biomedical and Health Informatics, University of Washington.

Current research:  His latest projects involve using mobiles devices to support adherence among HIV and diabetic patients, using cell phones to support prenatal care among pregnant women, and using cell phones and the Internet to develop a real-time surveillance system for adverse events. Other past research descriptions available at home page. International consultant on eHealth, mHealth, and telemedicine.
Editorial board: PLoS ONE, Revista Peruana de Medicina Experimental y Salud Pública

Representative Publications:

  • Curioso WH, Fuller S, Garcia PJ, Holmes KK, Kimball AM. Ten Years of International Collaboration in Biomedical Informatics and Beyond: The AMAUTA Program in Peru. J Am Med Inform Assoc 2010;17(4):477-480. (PubMed / MEDLINE). 
  • Curioso WH, Quistberg DA, Cabello R, Gozzer E, Garcia PJ, Holmes KK, Kurth AE. "It´s time for your life": How should we remind patients to take medicines using short text messages? AMIA Annu Symp Proc 2009;:129-133. (PubMed / MEDLINE).
  • Curioso WH, Peinado J, Rubio CF, Lazo-Escalante M, Castagnetto JM. Biomedical and Health Informatics in Peru: Significance for Public Health. Health Info Libr J. 2009;26(3): 246-251. (PubMed / MEDLINE).  
  • Curioso WH, Kurth AE. Access, use and perceptions regarding Internet, cell phones and PDAs as a means for health promotion for people living with HIV in Peru. BMC Medical Informatics and Decision Making 2007; 7:24. (PubMed / MEDLINE). 
  • Curioso WH, Karras BT, Campos PE, Buendia C, Holmes KK, Kimball AM. Design and Implementation of Cell PREVEN: A Real-Time Surveillance System for Adverse Events Using Cell Phones in Peru. AMIA Annu Symp Proc 2005; 176-180. (PubMed / MEDLINE).  

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Twitter: @waltercurioso

Valerie Daggett, PhD
Professor, Bioengineering
Adjunct Professor, Biochemistry
Adjunct Professor, Biomedical Informatics and Medical Education
B.A. Reed College, PhD UCSF, Postdoctoral Fellow, Stanford University

Background: 25 yrs molecular modeling proteins/peptides. Dr. Daggett is on the editorial boards: Biochemistry, Structure, and Biomedical Computation Review (BCR). Senior Editor: Protein Engineering, Design, and Selection. Founding member of the Biomolecular Structure and Design Program. Editor of a 2003 volume on Protein Simulations for Advances in Protein Chemistry. Member of NIH Macromolecular Structure and Function B Study Section, July 2005 - 2008. Biophysical Society Fellow, 2011. Funded Research: a) Molecular dynamics simulations of protein unfolding (NIH)| b)  Characterization of prion protein conformational changes (NIH)| c)  Design and characterization of alpha-sheet compounds (NSF, CART, NIH)| d) Data exploration and visualization (Microsoft)| and e) Molecular Dynameomics (DOE).  Member of the Board of Reviewing Editors of eLife.

Representative Publications:

  • Van der Kamp M.W., Schaeffer R.D., Jonsson A.L., Scouras A.D., Simms A.M., Toofanny R.D., Benson N.C., Anderson P.C., Merkley E.D., Rysavy S., Bromley D., Beck D.A.C., and Daggett V. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 18:423-435, 2010.[DOI]
  • Schaeffer R.D, Jonsson A.L., Simms A.M., and Daggett V. Generation of a Consensus Protein Domain Dictionary. Bioinformatics 27:46-54, 2011. [DOI]
  • Toofanny, R.D., Simms, A.M., Beck, D.A.C. and V. Daggett, Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics, 12:334, 2011. [DOI]
  • Benson, N.C. and V. Daggett, Wavelet Analysis of Protein Motion. Int. J. Wavelets, Multiresol. Info. Processing, 10:1250040, 2012. [DOI]
  • Simms, A.M. and V. Daggett, Protein simulation data in the relational model. J. of Supercomp. In press: 1-24, 2011. [DOI]
  • Benson N.C. and Daggett V.  A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations.  Journal of Physical Chemistry B, 116, 8722-8731, 2012. [DOI]
  • Benson N.C. and Daggett V.  A Chemical Group Graph Representation for Efficient High-Throughput Analysis of Atomistic Protein Simulations.  Journal of Bioinformatics and Computational Biology 10:1250008-1250024, 2012. [DOI]

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Mark Del Beccaro, MD, FAAP
Professor,  Department of Pediatrics
Adjunct Professor, Department of Biomedical Informatics and Medical Education
University of Washington School of Medicine
VP, Medical Affairs, Seattle Children's Hospital
Attending Physician, Emergency Department, Seattle Children’s Hospital

Background: Undergraduate education (BS in Biologic Sciences) at Stanford University, MD degree from the University of Washington (Seattle).   Completed both a Pediatric residency and was the Chief Resident in Pediatrics at the University of Washington and Seattle Children’s Hospital.  Was the CMIO at Seattle Children’s and has over 15 years experience in clinical systems selection, design, and implementation.   Involved in numerous national Health IT groups including HL-7, past co-chair of CCHIT Inpatient group.   Currently past Chair of the American Academy of Pediatrics Council on Clinical Information Technology (COCIT) Executive Committee and current Chair of the AAP Council Management Committee.

Research Interests:  Clinical decision support, using clinical databases to measure and improve health care outcomes and resource utilization, improve patient safety and decrease readmission.  Currently on the Exec Committee for a consortium of children’s hospitals piloting a federated database structure for outcomes research.  Currently involved in a large strategic effort to combine evidence based medicine with lean concepts and clinical informatics to improve care along all the IOM domains of health care quality.

Representative Publications:

  • Del Beccaro MA, Jeffries HE, Eisenberg MA, Harry ED.  Computerized provider order entry implementation (CPOE): No association with increased mortality rates in an intensive care unit (ICU). Pediatrics 2006;118:290-295. 
  • Migita D, Postetter L, Hagan P, Health S, Del Beccaro MA.  Governing peripherally inserted central venous catheters by combining continuous performance improvement and computerized physician order entry.  Pediatrics 2009;123(4):1155-1161.
  • Yamamoto L, Pyles L, Del Beccaro MA, et al.  Emergency information forms (EIFs) and emergency preparedness for children with special health care needs (CSHCN). Pediatrics Vol 125 No. 4 April 2010, pp 829-837.
  • Del Beccaro MA. Villanueva R, Knudson KM, Harvey EM, Langle JM, Paul W.  Decision support alerts for medication ordering in a computerized provider order entry (CPOE) system: A systematic approach to decrease alerts.  Appl Clin Inf 2010;1 3:346-362.
  • Macy M, Hall M, Shah S, et al.  Differences in designations of observation care in US freestanding children's hospitals: are they virtual or real? J Hosp Med 2011 (in press).
  • Bailey LC, MD, Milov DE, Kelleher K, Kahn M, Del Beccaro MA, Yu F, Richards T, Forrest CB. Multi-Institutional Sharing of Electronic Health Record Data To Assess Childhood Obesity.  PLOS ONE 8(6): e66192. doi:10.1371/journal.pone.0066192.

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George Demiris, PhD
Professor, Biobehavioral Nursing and Health Systems
Joint Professor, Biomedical Informatics and Medical Education
Alumni Endowed Professor in Nursing
Fellow, American College of Medical Informatics

Background: MSc in Medical Informatics ( University of Heidelberg); PhD in Health Informatics ( University of Minnesota).  Dr. Demiris is the Graduate Program Director of Biomedical and Health Informatics, and the Director of Clinical Informatics and Patient Centered Technologies (CIPCT).

Research: His research focuses on the use of information technology for older adults and patients with chronic conditions, the design and evaluation of "smart homes" and telehealth applications in home care and hospice. He is also examining health informatics graduate education challenges.

Other: At the University of Washington, he has a joint appointment with the School of Nursing (Biobehavioral Nursing and Health Systems). He is the Chair of the International Medical Informatics Education Working Group on Smart Homes and Ambient Assisted Living, and the Lead Convener of the Technology and Aging Group of the Gerontological Society of America. 

Currently accepting new MS students and new PhD students.

Representative Publications:

  • Demiris G, Thompson H, Reeder B, Wilamowska K, Zaslavsky O. Using informatics to Capture Older Adults' Wellness. International Journal of Medical Informatics (in press).
  • Demiris G, Parker Oliver D, Wittenberg-Lyles E, Washington K, Doorenbos A, Rue T, Berry D. A Noninferiority Trial of a Problem-Solving Intervention for Hospice Caregivers: In Person versus Videophone. Journal of Palliative Medicine 2012;15(6):653-60.
  • Thompson HJ, Demiris G, Rue T, Shatil E, Wilamowska K, Zaslavsky O, Reeder B. A Holistic approach to assess older adults' wellness using e-health technologies. Telemed J E Health. 2011;17(10):794-800.
  • Demiris G, Thompson H. Smart Homes and Ambient Assisted Living Applications: From Data to Knowledge-Empowering or Overwhelming Older Adults? Yearb Med Inform 2011;6(1):51-7.
  • Demiris G, Charness N, Krupinski E, Ben-Arieh D, Washington K, Wu, J, Farberow B. The role of human factors in telehealth. Telemedicine and e-health 2010; 16(4): 446-453.

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Beth Devine, PhD, PharmD, MBA
Associate Professor, Pharmaceutical Outcomes Research & Policy Program, School of Pharmacy
Adjunct Associate Professor
Department of Biomedical Informatics & Medical Education, School of Medicine
Department of Health Services, School of Public Health
Department of Surgery, Surgical Outcomes Research Center, School of Medicine  

Background: Dr. Devine received her PhD in Health Services Research from the UW Department of Health Services, her doctorate in Pharmacy (PharmD) from the University of the Pacific, and her MBA from the University of San Francisco. She completed a residency in clinical pharmacy practice at the VA Medical Center in Palo Alto, CA; and a post-doctoral fellowship in pharmacoeconomics and outcomes research at the UW Pharmaceutical Outcomes Program, spending one year with Roche Pharma Business, Health Economics and Strategic Pricing Group, in Palo Alto, CA. Prior to launching her research career, Dr. Devine practiced clinical pharmacy with advanced practice (prescribing) privileges, and served in administrative positions related to formulary management, medication safety and quality improvement, in both academic and community medical center settings. She is a past recipient of an AHRQ Mentored Clinical Scientist Training Award (K-08) and served as co-investigator and project lead on an AHRQ THQIT (Transforming Healthcare Quality through Technology) implementation grant where her team studied the impact of a computerized provider order entry system in the largest independent medical group in Washington State.

Current research: Dr. Devine’s research program is centered at the intersection of clinical research informatics, comparative effectiveness research, medication safety, and quality. She is the lead co-investigator for the Comparative Effectiveness Research Methods Core of the Surgical Care and Outcomes Assessment Program Comparative Effectiveness Research Network (SCOAP-CERTAIN; PI: Flum) – one of two AHRQ-funded grants in the Enhanced Registries for Quality Improvement and CER portfolio. On this same grant she serves on the Health Information Technology Core, where she leads the research study to validate the extraction of semi-automated data from disparate electronic health records across select hospitals in Washington State. On the Washington State Collaborative to prevent and respond to medical injuries (PI: Gallagher), she is evaluating the effect of communication training on serious clinical adverse events across eight medical centers. A second area of research interest is evidence synthesis, where she conducts meta-analyses and network meta-analyses within the Bayesian framework.

 Representative Publications:

  • Devine EB, Lau B, Overby CL, Wirtz HS. Use of a clinical decision support tool in the ambulatory setting to improve adherence to national monitoring guidelines for medication-laboratory tests. Appl Clin Inf 2013; 4:_-_http://dx.doi.org/10.4338/ACI-2013-06-RA-0041
  • Devine EB, Van Eaton E, Capurro D, Alfonso-Cristancho R, Devlin A, Yanez ND, Yetisgen-Yildiz M,  Flum DR, , Tarczy-Hornoch P, for the SCOAP CERTAIN Corporate Authorship. Preparing Electronic Clinical Data for Quality Improvement and Comparative Effectiveness Research: The CERTAIN Automation and Validation Project. Generating Evidence & Methods to improve patient outcomes (eGEMS) 2013; September in press
  • Devine EB, Edwards T, Patrick DL, Alfonso-Cristancho R, Yanez ND, Devlin A, Symons R, Flum DR, for the SCOAP CERTAIN Corporate Authorship. A Model for Incorporating Patient and Stakeholder Voices in a Learning Healthcare Network: Washington State’s Comparative Effectiveness Research Translation Network (CERTAIN). J Clin Epi 2013;66:S122e-S129
  • Overby CL, Tarczy-Hornoch P, Kalet IJ, Thummel KE, Smith JW, Del Fiol G, Fenstermacher D, Devine EB. Developing a prototype system for integrating pharmacogenomics findings into clinical practice. J Pers Med 2012;2:241-56
  • Cheng MM, Blough DK, Goulart B, Veenstra DL, Devine EB. A mixed treatment comparison of therapies for symptomatic, previously untreated chronic lymphocytic leukemia. Cancer Treat R 2012 38:1004-11

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Website 1, Website 2

Sherrilynne Fuller, PhD
Emeritus Professor, Biomedical Informatics and Medical Education
Joint Professor, Information School
Adjunct Professor, Health Services
Fellow, American College of Medical Informatics
Senior Advisor, Dean, University Libraries University of Washington

Background:  She received her BA (Biology) and MLS (information Science) degrees from Indiana University, Bloomington, Indiana, USA and her PhD (Information Science) from the University of Southern California, Los Angeles California, USA.   Fuller served as the founding head of the Division of Biomedical and Health Informatics, School of Medicine, UW and has led several large-scale campus and regional research and development projects in the areas of biomedical and health informatics, telemedicine and information technology.    One of the first web-based medical record systems in the world (Mindscape), which still in use at UW Medical Center and Harborview Medical Center, was a product of her IAIMS (Integrated Academic Information Management System) program leadership for the UW Academic Health Sciences Center.   As Director, Health Sciences Libraries, University of Washington for over twenty years she led the development of state of art library and information systems with particular emphasis on  linking library resources to clinical information systems in the UW Medical Centers and development of knowledge mining and mapping systems.  As Co-Director, Center for Public Health Informatics Fuller has led the development of innovative computing and information systems projects to improve public health practice nationally and internationally with a particular focus on open source decision support tools and  knowledge management  systems and was a contributor to the development of EpiVue, an open source data visualization tool for public health.  

Fuller has lectured, led training programs and consulted throughout the world on the development of interoperable health information systems for low resource environments and on the creation of education and research  programs in biomedical and health informatics.  Examples of international courses and workshops she has led in recent years include:  Introduction to Public Health Informatics Principles in Health Information Systems Development Within the Vietnam Health System  (Hanoi School of Public Health, Hanoi, Vietnam);  Improving Health Outcomes through Interoperability (Ministry of Health leaders and university faculty from throughout the Mekong Basin region countries  and beyond);  Health Informatics for HIV/AIDS Data Management Fellowship Program (University of Nairobi, Kenya); Biomedical and Health Informatics Resources, Tools and Technologies (multiple courses over past ten years in collaboration with Cayetano-Heredia University, Lima, Peru).  She currently leads a UW group that is part of a larger team to contribute to Strengthening HIV Strategic Health Management Information Systems in Tanzania with particular responsibility for supporting the development of the Enterprise Architecture and e-health strategy. See web page for further information including funded research.

Representative Publications:
Peer Reviewed Articles:

  • Fuller S: From Intervention Informatics to Prevention Informatics. [Invited] Bulletin of the American Society for Information Science and Technology 2011 (in press).
  • Fuller S: Tracking the Global Express: New Tools Addressing Disease Threats Across the World. [Invited] Epidemiology 2010;21(6):1-2.
  • Corbell C, Katjitae I, Mengistu A, Kalemeera F, Sagwa E, Mairizi D, Lates J, Nwokike J, Fuller S, Stergachis S. A records linkage of electronic databases for the assessment of adverse effects of antiretroviral therapy in Namibia. Pharmacoepidemiology and Drug Safety 2011 (in press).
  • Turner K, Fuller S. Patient-Held Maternal and/or Child Health Records: Meeting the Informational Needs of Patients and Healthcare Providers in Developing Countries: Online Journal of Public Health Informatics 2011 (in press).
  • Curioso WH, Fuller S, Garcia PJ, Holmes KK, Kimball AM. Ten Years of International Collaboration in Biomedical Informatics and Beyond: The AMAUTA Program in Peru. J Am Med Inform Assoc 2010;17(4):477-480.
  • Revere D, Turner A, Madhavan A, Rambo N, Bugni PF, Kimball AM, Fuller S. Understanding the information needs of public health practitioners: a literature review to inform design of an interactive digital knowledge management system. Journal of Biomedical Informatics 2007;40(4):410-421 Special Issue on Public Health Informatics.
  • Fuller S, Revere D, Bugni P, Martin G. A knowledgebase system to enhance scientific discovery: Telemakus: Biomedical Digital Libraries 2004;1:2-15.


  • Chen HC, Fuller S, Friedman C, Hersh W (co-editors). Medical Informatics: Knowledge Management and Data Mining in Biomedicine. New York, Springer, 2005.
  • Norris TE, Fuller S, Tarczy-Hornoch P, Goldberg H (co-editors). Informatics in Primary Care. New York, Springer-Verlag, 2002.

Book Chapters:

  • Revere D, Bugni PF, Dahlstrom L, Fuller S myPublicHealth: Utilizing Knowledge Management to Improve Public Health Practice and Decision Making. In: Liebowitz J, Schieber RA, Andreadis JD. Knowledge Management in Public Health. CRC Press, 2010.
  • Revere D, Fuller S. Characterizing biomedical concept relationships: Concept relationships as a pathway for knowledge creation and discovery. In: Chen HC, Fuller SS, Friedman C, Hersh W. Medical Informatics: Knowledge Management and Data Mining in Biomedicine. New York, Springer, 2005.
  • Fuller S, Masuda D, Gorman PN, Lindberg DAB. Medical Informatics and Information Access. In: Geyman JP, Hart G, Norris T (eds). Textbook of Rural Health Care. New York, McGraw-Hill, 2001.

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Rex Gantenbein, PhD
Professor, Medical Education and Public Health, University of Wyoming
Adjunct Professor, Department of Computer Science, University of Wyoming
Affiliate Professor, Biomedical and Health Informatics, University of Washington

Background: 26 years research in reliability, security, and privacy for networked computer systems; 15 years experience in telehealth/telemedicine networks and health informatics. Education: B.S. (mathematics) Iowa State University, M.S. and Ph.D. (computer science) University of Iowa. Director, University of Wyoming Center for Rural Health Research and Education. Senior member, Association for Computing Machinery, IEEE, International Society for Computers and Their Applications; member, American Telemedicine Association, Sigma Xi/ The Scientific Research Society. Current major projects: Wyoming Network for Telehealth (WyNETTE), Wyoming Telehealth Trauma Treatment Center.

Representative Publications:

  • M. Gray, C. Hassija, R. Gantenbein, R. Wolverton, T. James, and B. Robinson, “Utilization of distal technologies to meet the needs of rural survivors of domestic violence and sexual assault,” Community Psychology: New Developments. Hauppauge, NY: Nova Science Publishers (in press).
  • S.Y. Shin, R. Gantenbein, T.-W. Kuo, and J. Hong (eds.), Reliable and Autonomous Computational Science. Basel, Switzerland: Springer Basel AG (January 2011).
  • A.W. Wallace and R.E. Gantenbein, “A Framework for Structured Search of Distributed Research Resources,” Proc. 22nd Int. Conf. on Computers and Their Applications in Industry and Engineering (CAINE) (Nov. 2009), 151-156.
  • R.E. Gantenbein, “The Cowboy State Corrals Providers into a Telehealth Network,” Behavioral Healthcare 28,4 (April 2008).
  • R.E. Gantenbein and B.J. Robinson, “Decoding CODECs,” J. Telemedicine and Telecare 14 (2008), 59-61

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John Gennari, PhD
Associate Professor, Biomedical Informatics and Medical Education

Background: PhD (Computer Science) UC-Irvine. Experience: Protege developer at Stanford Medical Informatics.

Current projects: Primary focus on semantic web, knowledge representation and ontology development.  See web pages for other interests: synthetic biology, physics-based biosimulation, health-care guidelines / protocols, and cellular signaling pathways.

Currently accepting new MS students and new PhD students.

Representative Publications:

  • Galdzicki M, Rodriguez C, Chandran C, Sauro HM, Gennari JH. (2001). Standard Biological Parts Knowledgebase. PLoS ONE 6(2):e17005.
  • Gennari JH, Neal ML, Galdzicki M, and Cook DL. (2011). Multiple Ontologies in Action: Composite Annotations for Biosimulation Models. Journal of Biomedical Informatics 44(1):146-154.
  • Gennari JH, Neal ML, Carlson B, Cook DL. (2008). Integration of Multi-Scale Biosimulation Models Via Light-Weight Semantics. Proceedings of the Pacific Symposium on Biocomputing, pp. 414-425, 2008.
  • Weng C, McDonald DW, Sparks D, McCoy J, and Gennari JH (2007). Participatory design of a colloborative clinical trial protocol writing system. The International Journal of Medical Informatics 76(S1), 245-251.
  • Gennari JH, Musen MA, Fergerson RW, Grosso WE, Cruzbezy M, Eriksson H, Noy NF, and Tu SW (2003). The Evoluation of Protege: An Environment for Knowledge-Based Systems Development. International Journal of Human-Computer Studies, 58, 89-123.

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Amanda (Mandi) Hall
Affiliate Assistant Professor, Biomedical Informatics and Medical Education

Background: Dr. Halls’ research interests stem from working in home healthcare, patient care, and using and evaluating health information systems. She graduated with her PhD in 2013 from the University of Florida (UF) with a research background in Health Education and Behavior and worked with the Center for Digital Health and Wellness. During her graduate work she was awarded the Finger Fellowship in Sustainable Health from the Methodist Hospital Research Institute in Houston Texas to test a new telemonitoring device and worked on a grant conducting research on games for health. Dr. Hall was a National Library of Medicine Postdoctoral Fellow in biomedical and health informatics in the Department of Biomedical Informatics and Medical Education at the University of Washington School of Medicine from 2013-2015. Her research focuses on the evaluation and usability of consumer health information technologies, including mobile health applications, wearable sensor devices, healthcare robotics, and patient portals to effectively disseminate health information to improve medical decision-making and promote health behavior change of older adults. Currently Dr. Hall is a Sr. Human Factors Design Engineer at Physio-Control Dev. Co. LLC in Redmond Washington.

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Kenric Hammond, MD
Clinical Associate Professor, Pyschiatry and Behavior Sciences
Joint Clinical Associate Professor, Biomedical Informatics and Medical Education

Background: 11 yrs clinical information systems research. Dr. Hammond is the director, VA Puget Sound Health Care System Postdoctoral Fellowship In Medical Informatics.

Research: a) impact on cost/quality/outcomes of electronic medical record systems, b) natural language analysis of patient records.

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David Heckerman, MD, PhD
Distinguished Scientist at Microsoft Research
Affiliate Professor, Biomedical Informatics and Medical Education

Background: Since 1992, he has been a Senior Researcher at Microsoft, where he has created applications including the first machine-learning spam filter, data-mining tools in SQL Server and Commerce Server, handwriting recognition in the Tablet PC, text mining software in Sharepoint Portal Server, troubleshooters in Windows, and the Answer Wizard in Office.  Most recently, he has been applying methods from statistics and machine learning to problems in health, such as the design of a vaccine for HIV.

Representative Publications: 

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Eric Horvitz, MD, PhD
Affiliate Professor, Biomedical Informatics and Medical Education

Background:  I'm interested in computational foundations of intelligent sensing, reasoning, and action--with a particular focus on methods for grappling with uncertainty about environments or situations. I'm also interested in models of human cognition, and in developing computational systems that leverage insights about cognition to help people to achieve their goals. Much of my work makes use of probability and decision theory, decision analysis, and, in particular, Bayesian and decision-theoretic principles. My research spans both theoretical issues and concrete, real-world applications. I'm interested in information triage and alerting that takes human attention into consideration, spanning work on notification systems, multitasking, and psychological studies of interruption and recovery.

Other interests include principles of mixed-initiative interaction that can support fluid, efficient collaborations between people and computing systems, methods for guiding computer actions in accordance with the preferences of people, search and information retrieval, and collaboration. I've also been long interested in offline and real-time optimization of the expected value of computational systems under limited and varying resources. Areas of concentration in this realm include flexible or anytime computation, ideal metareasoning for guiding computation, compilation for reducing real-time deliberation, ongoing, continual computation, and the construction of bounded-optimal reasoning systems--systems that maximize the expected utility of the people they serve, given the expected costs of reasoning, the problems encountered over time, and assertions about a system's constitution. Research in this arena includes tackling hard reasoning problems with learning and decision making methods. I'm serving as President-Elect of the American Association for Artificial Intelligence. See the AAAI web pages for more information on research and events in the AI community.

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Ann Marie Kimball, MD
Professor Emeritus, Epidemiology
Professor Emeritus, Biomedical Informatics and Medical Education

Background: epidemiology, medicine. Other: Director UW MPH Program, NIH and IOM review panel member.

Funded research: the nexus between emerging infectious diseases, international trade, and climate change with a focus on international epidemiologic applications of informatics.

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Eugene Kolker, PhD

Chief Data Officer, Seattle Children's Hospital
Director, Bioinformatics & High-throughput Analysis Lab, Seattle Children's Research Institute
Executive and Founding Editor of OMICS: A Journal of Integrative Biology & Big Data journals
Affiliate Professor, Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington

Adjunct Professor, Departments of Chemistry and Chemical Biology, Northeastern University, Boston, MA

Address: Seattle Children's Research Institute, JMB-9, 1900 9th Avenue. Seattle, WA 98101
Telephone: (206) 884-7170

Background: Eugene Kolker is the Chief Data Officer at Seattle Children’s -- Hospital, Research Institute, and Foundation. Eugene has over 25 years of experience in multi-disciplinary data analysis, predictive analytics, and modeling and over 15 years of experience in management, business, and community development. At Seattle Children’s, Eugene heads the CDO Analytics team (cdoanalytics.org), which focuses on leveraging large and complex data to improve outcomes and safety, reduce costs, broaden access, and drive innovation. In addition to his hospital work, he is also the Director of the Bioinformatics & High-throughput Analysis Laboratory (kolkerlab.org) at the Research Institute. Previously, Eugene Kolker was the Founder and President of BIATECH Biotechnology Innovation Center, which was acquired by Seattle Children’s. Currently, Dr. Kolker is an Adjunct Professor at Northeastern University College of Science, Boston and an Affiliate Professor at University of Washington School of Medicine, Seattle. He has 130 publications in 40 different journals and also serves as the Executive Editor of the journals “OMICS: A Journal of Integrative Biology” and “Big Data.” In 2015, Eugene was nominated by the HIMSS (Healthcare Information and Management Systems Society) members to be one of the top three "Innovators" in their annual HIT Awards. He was also named one of the “top 16 data-driven geeks to watch” by HIMSS.

Research: Data Analysis, Predictive Analytics, Big Data, Data Mining, Machine Learning, Optimization, Statistical and Algorithmic Development, Bioinformatics, Omics, Community Development, Proteomics, Systems Analysis, Systems Biology, Autism, Heart Diseases.


Representative Publications:

1. Keller, Nesvizhskii, Kolker, Aebersold, Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search, Analytical Chemistry, 2002, 74 (20): 5383-5392.

2. Kolker et al., Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations, PNAS USA, 2005, 102 (6): 2099-2104.

3. Taylor… Kolker et al., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology, 2008, 26 (8): 889-896.

4. Field… Kolker et al., Megascience. ‘Omics data sharing, Science, 2009, 326 (5950): 234-236.

5. Chain… Kolker et al., Genome project standards in a new era of sequencing. Science, 2009, 326 (5950): 236-237.

6. Hather… Kolker, The United States of America and scientific research, PLOS ONE, 2010, 5 (8): e12203.

7. Kolker… Kolker, Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins, OMICS JIB, 2011, 15 (7-8): 513-521.

8. Higdon… Kolker, Predictive analytics in healthcare: Medications as a predictor of medical complexity. Big Data, 2013, 1 (4), 237-244.

9. Kolker, Kolker, Healthcare analytics: Creating a prioritized improvement system with performance benchmarking. Big Data, 2014, 2 (1), 50-54.

10. Montague… Kolker, Beyond protein expression, MOPED goes multi-omics. Nucleic Acid Research, 2015, 43 (D1): 1145-1151.

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Tao Sheng Kwan-Gett, MD MPH

Director, Northwest Center for Public Health Practice
Senior Lecturer, Health Services
Adjunct Senior Lecturer, Biomedical and Health Informatics

Background: Tao Sheng Kwan-Gett became Director of the Northwest Center for Public Health Practice in March 2013. Before that he worked for 6 years as a medical epidemiologist in the communicable disease program at Public Health - Seattle & King County, where he helped oversee the day to day work of the disease investigation team. He also has several years’ experience working as a primary care pediatrician at Virginia Mason, during which he made annual volunteer trips to the Thai Burma border working with refugees and migrant workers from Burma. He served on the Public Health Informatics Institute workgroup, Redesigning Surveillance for an e-Health World.

Research Interests:
Public health practice; communicable disease epidemiology; health informatics

Representative Publications:

  1. Kwan-Gett TS, Baer A, Duchin JS. Spring 2009 H1N1 influenza outbreak in King County, Washington. Disaster Med Public Health Prep. 2009 Dec;3 Suppl 2:S109-16.
  2. Pina J, Turner A, Kwan-Gett T, Duchin J. Task analysis in action: the role of  information systems in communicable disease reporting. AMIA Annu Symp Proc. 2009 Nov 14;2009:531-5.
  3. Taylor JA, Kwan-Gett TS, McMahon EM Jr. Effectiveness of a parental educational intervention in reducing antibiotic use in children: a randomized controlled trial. Pediatr Infect Dis J. 2005 Jun;24(6):489-93.
  4. Taylor JA, Kwan-Gett TS, McMahon EM Jr. Effectiveness of an educational intervention in modifying parental attitudes about antibiotic usage in children.  Pediatrics. 2003 May;111(5 Pt 1):e548-54.
  5. Kwan-Gett TS, Lozano P, Mullin K, Marcuse EK. One-year experience with an inpatient asthma clinical pathway. Arch Pediatr Adolesc Med. 1997 Jul;151(7):684-9.
  6. Tarczy-Hornoch P, Kwan-Gett TS, Fouche L, Hoath J, Fuller S, Ibrahim KN, Ketchell DS, LoGerfo JP, Goldberg HI. Meeting clinician information needs by integrating access to the medical record and knowledge resources via the Web. Proc AMIA Annu Fall Symp. 1997:809-13.

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Michael Leu, MD, MS, MHS

Research Interests: Translating innovations into practice in ways that improve patient care and clinical outcomes, while respecting clinical practice patterns. Using technology to efficiently disseminate the best clinical care so that it is practiced throughout the WWAMI region.

Representative publications:

Leu MG, Cheung M, Webster TR, Curry L, Bradley EH, Fifield J, Burstin H. Centers Speak Up: The Clinical Context for Health Information Technology in the Ambulatory Care Setting. Journal of General Internal Medicine. 2008; 23: 372-378.

Council on Clinical Information Technology. Policy Statement: Using Personal Health Records to Improve the Quality of Health Care for Children. Pediatrics. 2009; 124: 403-409.

Avansino J, Leu MG. Effects of CPOE on provider cognitive workload: a randomized crossover trial. Pediatrics. 2012; 130(3) e547-52.

Leu MG, O’Connor K, Marshall R, Price DT, Klein JD. Pediatricians’ Use of Health Information Technology: A National Survey. Pediatrics. 2012;130(6) e1441-6.

Leu MG, Morelli SA, Chung O, Radford SM. Systematic Update of Computerized Physician Order Entry (CPOE) Ordersets to Improve Quality of Care: A Case Study. Pediatrics. 2013;131 Suppl 1:S60-7.

Thompson KL, Leu MG, Drummond KL, Popalisky J, Spencer SM, Lenssen PM. Nutrition Interventions to Optimize Pediatric Wound Healing: An Evidence-Based Clinical Pathway. Nutr Clin Pract. 2014; 29(4):473-482.

Koves l, Leu MG, Spencer S, Popalisky J, Drummond K, Beardsley E, Klee K, Zimmerman J. Improving care for pediatric diabetic ketoacidosis. Pediatrics. 2014; 134(3):e848-56.

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Bill Lober, MD
Professor, Biobehavioral Nursing and Health Systems
Joint Professor, Biomedical Informatics and Medical Education
Joint Professor, Global Health
Adjunct Professor, Health Services

Background: 10 years in computer industry. His research focuses on the development, integration, and evaluation of information systems to support individual and population health. His academic interests include informatin system-based surveillance; web-based information systems; support of population based research in public health and biomedical research; computer supported collaborative work; and privacy and security. His research employs heterogeneous data integration, web infrastructures, distributed security models, and usability assessment. Specific research includes 1) facility level systems and architecture (EMR, Lab systems, interoperability) to support health care in low and middle income countries, 2) systems and architectures to support public health information exchange, 3) architecture, algorithms, and visualization strategies for integrated surveillance, 4) population-based systems to support biomedical research in HIV/AIDS, and 5) Patient Reported Outcomes and Measures (PROs) in HIV and Oncology practice and research.

Other: Director of the UW Clinical Informatics Research Group, Director of Informatics for the International Training and Education Center for Health (I-TECH), co-Director of the UW Center for Public Health informatics. 

Representative Publications:

  • Olson DR, Paladini M, Lober WB, Buckeridge DL, Working Group ID. Applying a New Model for Sharing Population Health Data to National Syndromic Influenza Surveillance: DiSTRIBuTE Project Proof of Concept, 2006 to 2009. PLoS Curr 2011;Aug 2;3:RRN1251. PubMed PMID 21894257; PubMed Central PMCID: PMC3148528.
  • Lober WB, Flowers JL. Consumer empowerment in health care amid the internet and social media. Semin Oncol Nurs 2011;Aug 27(3):169-82. doi: 10.1016/j.soncn.2011.04.002. PubMed PMID: 21783008.
  • Reeder B, Revere D, Olson DR, Lober WB. Perceived usefulness of a distributed community-based syndromic surveillance system: a pilot qualitative evaluation study. BMC Res Notes 2011;Jun 14(4):187. PubMed PMID: 21672242; PubMed Central PMCID: PMC3146436.
  • Berry DL, Blumenstein BA, Halpenny B, Wolpin S. Fann JR, Austin-Seymour M, Bush N, Karras BT, Lober WB, McCorkle R. Enhancing patient-provider communication with the electronic self-report assessment for cancer: a randomized trial. J Clin Oncol 2011;Mar 10;29(8):1029-35. Epub 2011 Jan 31. PubMed PMID: 21282548; PubMed Central PMCID: PMC3068053.
  • Kim EH, Coumar A, Lober WB, Kim Y. Addressing mental health epidemic among university students via web-based, self-screening, and referral system: a preliminary study. IEEE Trans Inf Technol Biomed 2011;Mar 15(2):301-7. Epub 2011 Jan 20. PubMed PMID: 21257386.
  • Berry DL, Halpenny B, Wolpin S, Davison BJ, Ellis WJ, Lober WB, McReynolds J, Wulff J. Development and evaluation of the personal patient profile-prostate (P3P), a Web-based decision support system for men newly diagnosed with localized prostate cancer. J Med Internet Res 2010;Dec 17;12(4):e67. PubMed PMID: 21169159; PubMed Central PMCID: PMC3056527.
  • Lober WB, Revere D, Hills R. A Lab-EMR interoperability profile as an eHealth architecture component for resource-constrained settings. Stud Health Technol Inform 2020;160(Pt 1):257-61. PubMed PMID: 20841689.
  • Van Eaton EG, McDonough K, Lober WB, Johnson EA, Pellegrini CA, Horvath KD. Safety of using a computerized rounding and sign-out system to reduce resident duty hours. Acad Med 2010;Jul 85(7):1189-95. PubMed PMID: 20592514.
  • Wolpin S, Berry DL, Kurth A, Lober WB. Improving health literacy: a Web application for evaluating text-to-speech engines. Comput Inform Nurs 2010;Jul-Aug 28(4):198-204. PubMed PMID: 20571370.
  • Kim EH, Stolyar A, Lober WB, Herbaugh AL, Shinstrom SE, Zierler BK, Soh CB, Kim Y. Challenges to using an electronic personal health record by a low-income elderly population. J 19861298; PubMed Central PMCID: PMC2802566.

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David Masuda, MD
Lecturer, Biomedical Informatics and Medical Education, Adjunct lecturer, Health Services, School of Public Health

Background: 14 years clinical experience in diagnostic radiology, 8 years experience in clinical executive leadership, 10 years experience in clinical informatics teaching.

Current interest areas: Applied informatics educational program development with a focus on leadership in health information technology and clinical informatics.

Peer-reviewed Publications:

  • “Integrating knowledge resources at the point of care: opportunities for librarians”., Fuller SS; Ketchell DS; Tarczy-Hornoch P; D. Masuda, Bull Med Libr Assoc 1999 Oct;87(4):393-403
  • “Low-bandwidth, low-cost telemedicine consultations in rural family practice.”;  Norris TE, Hart GL, Larson EH, Tarczy-Hornoch P, Masuda DL, Fuller SS, House PJ, Dyck SM.;  J Am Board Fam Pract. 2002 Mar-Apr;15(2):123-7. J Am Board Fam Pract. 2002 Mar-Apr;15(2):123-7.
  • “Development and Evaluation of Public Health Informatics at the University of Washington”;  Karras B; O’Carrol P; Oberle M; Masuda D; Lober W; Robins L; Schaad D; Scott C; Journal of Public Health Management and Practice; Vol. 8, No.3; May 2002
  • “Teaching Technology with Technology: Learning Management Systems and Anchored Modular Inquiry in Graduate Health Administration Education”; Journal of Health Administration Education; in preparation

Other Publications:

  • “Evaluation Strategies and Findings from a Regional Integrated Telemedicine Testbed”; Fuller, S, Tarczy-Hornoch, P, Masuda, D, Cannava, T, Hard, G, Larson, E, Johnson, C, Dyck, S, Kramer, W, Norris, T. " Telemedicine & Telecommunications: Options for the New Century, Proceedings, 93-94, 2001
  • “Hospital Quality Outcomes: The results of a pilot study performed to define risk adjustment and Internet report specifications”, Meyer K; Posse C; Masuda D; AMIA 2001 Poster
  • “Using a Large Group Interactive Audience Response System to Enhance Medical Student’s Understanding of Risk Information”; Wolf FM, Masuda D, Pinsky LP; May 3; Pacific Grove, CA.; 2006. OpenURL


  • “Medical Informatics and Information Access.”, Fuller SS; Masuda D; Gorman P; Lindberg DA, Chapter 15, Textbook of Rural Medicine, Geyman J; Norris T; Hart G, Editors, McGraw-Hill, 2001
  • “Telecommunications in Primary Care”; Masuda D.; Chapter 15; Primary Care Informatics, Norris T, Editor; 2002
  • Medical Informatics for Physician Executives, ACPE, 2003
  • “Careers in Clinical Computing and Medical Informatics”; Masuda D; Chapter 15; in Practical Guide to Clinical Computing Systems: Design, Operations, and Infrastructure; Elsevier; Thomas Payne, Editor; 2008
  • “Project Management for Health Information Technology”; Coplan Sand Masuda D; McGraw-Hill; 2011

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Daniel Masys, MD
Affiliate Professor, Biomedical Informatics and Medical Education
Fellow, American College of Medical Informatics

Background:  Dr. Daniel R. Masys is Affiliate (volunteer) Professor, Biomedical and Heath Informatics, joining the Department of Biomedical Infomatics and Medical Education after retiring as Professor and Chair of the Department of Biomedical Informatics and Professor of Medicine at the Vanderbilt University School of Medicine in 2011.  An honors graduate of Princeton University and the Ohio State University College of Medicine, he completed postgraduate training in Internal Medicine, Hematology and Medical Oncology at the University of California, San Diego, and the Naval Regional Medical Center, San Diego.  He served as Chief of the International Cancer Research Data Bank of the National Cancer Institute, National Institutes of Health, and was also Director of the Lister Hill National Center for Biomedical Communications, which is a computer research and development division of the National Library of Medicine.  He also served as Director of Biomedical Informatics at the University of California, San Diego School of Medicine, Director of the UCSD Human Research Protections Program, and Professor of Medicine.

Dr. Masys is an elected member of the Institute of Medicine of the National Academy of Sciences.  He is a Diplomate of the American Board of Internal Medicine in Medicine, Hematology, and Medical Oncology.  He is a Fellow of the American College of Physicians, and Fellow and Past President of the American College of Medical Informatics.  

Research: Dr. Masys' professional interests include development of informatics infrastructure for conducting clinical and translational research, genome-phenome correlation using phenotype data derived from electronic medical records data, and approaches to incorporating genomic data effectively into clinical systems.

Dr. Masys is not accepting new Masters or PhD students at this time.

Representative Publications:

  • Denny JC, Bastarache L, Ritchie MD, Carroll RJ, Zink R, Mosley JD, Field JR, Pulley JM, Ramirez AH, Bowton E, Basford MA, Carrell DS, Peissig PL, Kho AN, Pacheco JA, Rasmussen LV, Crosslin DR, Crane PK, Pathak J, Bielinski SJ, Pendergrass SA, Xu H, Hindorff LA, Li R, Manolio TA, Chute CG, Chisholm RL, Larson EB, Jarvik GP, Brilliant MH, McCarty CA, Kullo IJ, Haines JL, Crawford DC, Masys DR, Roden DM. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol. 2013 Nov 24;31(12):1102-1111.
  • Ding K, de Andrade M, Manolio TA, Crawford DC, Rasmussen-Torvik LJ, Ritchie MD, Denny JC, Masys DR, Jouni H, Pachecho JA, Kho AN, Roden DM, Chisholm R, Kullo IJ. Genetic Variants That Confer Resistance to Malaria Are Associated with Red Blood Cell Traits in African-Americans: An Electronic Medical Record-based Genome-Wide Association Study.  G3 (Bethesda). 2013 Jul 8;3(7):1061-8.
  • Oetjens MT, Denny JC, Ritchie MD, Gillani NB, Richardson DM, Restrepo NA, Pulley JM, Dilks HH, Basford MA, Bowton E, Masys DR, Wilke RA, Roden DM, Crawford DC. Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records.  Pharmacogenomics. 2013 May;14(7):735-44.
  • Ritchie MD, Denny JC, Zuvich RL, Crawford DC, Schildcrout JS, Bastarache L, Ramirez AH, Mosely JD, Pulley JM, Basford MA, Bradford Y, Rasmussen LV, Pathak J, Chute CG, Kullo IJ, McCarty CA, Chisholm RL, Kho AN, Carlson CS, Larson EB, Jarvik GP, Sotoodehnia N, Manolio TA, Li R, Masys DR, Haines JL, Roden DM. Genome- and Phenome-Wide Analysis of Cardiac Conduction Identifies Markers of Arrhythmia Risk.  Circulation. 2013 Mar 5.
  • Masys DR, Harris PA, Fearn PA, Kohane IS, Designing a public square for research computing. Sci. Transl.  Med. 4, 149fs32 (August 2012).
  • Masys DR, Jarvik GP, Abernethy NF, Anderson NR, Papanicolaou GJ, Paltoo DN, Hoffman MA, Kohane IS, Levy HP.  Technical desiderata for the integration of genomic data into Electronic Health Records. J Biomed Inform. 2011 Dec 27.

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Sean D. Mooney, PhD
Professor, Biomedical Informatics and Medical Education
Chief Research Information Officer (CRIO) of UW Medicine

Research Interests: Professor Mooney has spent his career managing the development of collaborative electronic systems supporting biomedical research. His interests focus on leading the next generation informatics tools for biomedical research and in understanding the underlying molecular causes of inherited genetic diseases and cancer.

Background: Previous to his CRIO role, he was an Associate Professor and Director of Bioinformatics at the Buck Institute for Research on Aging. As an Assistant Professor, he was appointed in Medical and Molecular Genetics at Indiana University School of Medicine and was founder and director of the Indiana University School of Medicine Bioinformatics Core. In 1997, he received his B.S. with Distinction in Biochemistry and Molecular Biology from the University of Wisconsin at Madison. Then receiving a Ph.D. in 2001 at the University of California in San Francisco, and then an American Cancer Society John Peter Hoffman Fellowship at Stanford University.

His group is funded by the National Library of Medicine and other NIH Institutes, mostly in the area of data science and translational medicine. He also has experience leading the construction of communities; he was co-founder of one of the largest nonprofits focusing on biomedical entrepreneurship in the SF Bay Area, BioE2E, and the Indiana Biomedical Entrepreneur Network. He was part of the team that won the $150k 2000 Garage.com Student Business Plan Competition, where the proposed plan focused on web-based tools for drug discovery research.

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Peter J. Myler, PhD
Member, Seattle Biomedical Research Institute
Affiliate Professor, Global Health
Affiliate Professor, Biomedical Informatics and Medical Education

Background: B.Sc.(Hons.), and Ph.D. in Biochemistry from the University of Queensland.  25 years experience in molecular parasitology, genomics and bioinformatics.

Research interests:
1. Structural genomics (high throughput protein structure determination) of biodefense and emerging infectious disease organisms -- funding through NIAID contract
2. RNAP II-mediated transcription in Leishmania - funded, renewal pending
3. Genome-wide and bioinformatics approaches to studying differentiation between insect and mammalian lifecycle stages of Leishmania -- minimal funding
4. Drug and diagnostic development for African trypanosomes and Leishmania -- funded through collaborations
5. Annotation and curation of trypanosomatid sequence and functional genomics databases -- currently funded

Informatics projects include development of sequence, functional genomics and process management databases, analytical software tools and web-based interfaces for analysis of sequence, mRNA expression and proteomics data.

Currently accepting new MS students only if funded. Potentially may have one slot for new PhD student, but check with Dr. Myler.

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Websites:  Seattle BioMed; School of Public Health; Global Health

William Stafford Noble, PhD
Professor, Department of Genome Sciences
Adjunct Professor, Department of Computer Science and Engineering
Adjunct Professor, Department of Biomedical Informatics and Medical Education
Adjunct Professor, Department of Medicine

Background: William Stafford Noble (formerly William Noble Grundy) received the Ph.D. in computer science and cognitive science from UC San Diego in 1998.  After a one-year postdoc with David Haussler at UC Santa Cruz, he became an Assistant Professor in the Department of Computer Science at Columbia University.  In 2002, he joined the faculty of the Department of Genome Sciences at the University of Washington.  His research group develops and applies statistical and machine learning techniques for modeling and understanding biological processes at the molecular level.  Noble is the recipient of an NSF CAREER award and is a Sloan Research Fellow.

Current research: Research in the Noble lab focuses on the development and application of maching learning and statistical methods for interpreting complex biological data sets.  The lab tends to work on research problems that involve fundamental problems in biology while also pushing the state of the art in machine learning.  Currently, the lab's research can be roughly divided into two areas.

  • Chromatin and gene regulation. We use motif-based hidden Markov models to characterize collections of transcription factor binding sites in genomic DNA.  We also develop models that predict properties of chromatin from genomic DNA.
  • Analysis of mass spectrometry data.  In collaboration with Michael MacCoss's lab, we have developed a series of machine learning and statistical methods for the analysis of shotgun proteomics data.  In this field, we continue to work on protein identification and quantification, targeted proteomics, and biomarker discovery.

Representative Publications:

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Mark Oberle, MD
Associate Dean and Professor, Health Services
Professor, Epidemiology
Adjunct Professor, Biomedical Informatics and Medical Education

Background: 32 yrs in public health informatics, practice, & epidemiology research. Associate Dean for Public Health Practice, UW. Funded research: a) distance learning applications (PI on HRSA Public Health Training Center grant), b) informatics applications in advanced public health surveillance, especially related to bioterrorism preparedness (co-PI on CDC Preparedness Center grant). Co-director UW Center for Public Health Informatics.

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Patrick O'Carroll, MD
Affiliate Professor, Epidemiology
Affiliate Professor, Health Services
Affiliate Professor, Biomedical Informatics and Medical Education
Fellow, American College of Medical Informatics
Fellow, American College of Preventive Medicine

Background: 19 years medical epidemiologist, 20 years public health informatics. Dr. O'Carroll is a Rear Admiral and Assistant Surgeon General, US Public Health Service (USPHS), serving as the Regional Health Administrator, USPHS Region X, US Dept of Health and Human Services. Research: public health information systems projects. 

Representative Publications:

  • O'Carroll PW, Yasnoff WA, Ward E, Ripp L, Martin E.  Public Health Informatics and Information Systems.  New York: Springer-Verlag New York, Inc. 2002; 790 pp.
  • O'Carroll PW, Yasnoff WA.  Development of curriculum and competencies for public health informatics.  In: Proceedings of the Health and Medical Informatics Education Working Group Meeting (April 23-25 2003) of the International Association of Medical Informatics (IMIA): Teach Globally, Learn Locally: Innovations in Health and Biomedical Informatics Education in the 21st Century.  Available on CD-ROM, www.imia.org
  • O'Carroll PW, Halverson P, Baker EL.  The Health Alert Network in action Northwest Public Health Spring/Summer 2002;14-15.
  • Yasnoff WA, O'Carroll PW, Koo D, Linkins RW, Kilbourne E.  Public Health Informatics: Improving and transforming public health in the information age.  Journal of Public Health Management and Practice 2000;6(6):67-75.
  • O'Carroll PW, Yasnoff WA, Wilhoite W.  Public Health Informatics: a CDC course for public health program managers.  Proceedings of the 1998 AMIA Annual Fall Symposium (formerly SCAMC); 1998;472-476.

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Tom Payne, MD
Associate Professor, Medicine
Adjunct Associate Professor, Health Services
Adjunct Associate Professor, Biomedical Informatics and Medical Education
Fellow, American College of Medical Informatics

Background: Medicine & 24 yrs medical informatics. Dr. Payne is the Medical Director, Information Technology Services, UW Medicine. Under his leadership VA Puget Sound received a 2000 Nicholas E. Davies CPR Recognition Award of Excellence.

UW research: Use and evaluation of computer-based medical records in patient care clinical research, and quality improvement with current focus on electronic documentation, computerized practitioner order entry, and natural language processing

Representative Publications:

  • Payne TH, Detmer DE, Wyatt JC, Buchan IE.National-scale clinical information exchange in the United Kingdom: lessons for the United States.  J Am Med Inform Assoc. 2011;18(1):91-8.
  • Payne TH, Bates DW, Berner ES, et al. Healthcare information technology and economics.  J Am Med Inform Assoc 2012 (in press).
  • Payne TH. Improving clinical documentation in an EMR world. Healthcare Finance Magazine. 2010 Feb;. 70-74.
  • Payne TH, tenBroek AE, Fletcher GS, Labuguen MC.  Transition from paper to electronic  inpatient physician notes.  J Am Med Inform Assoc, 2010;17:108-111.
  • Payne TH and Ash M. Use of natural language processing to extract encoded information from notes in a commercial electronic medical record system. AMIA Annu Symp Proc., 2009:1127-1129.
  • Lin CP, Payne TH, Nichol, WP, Hoey PJ, Anderson CL, Gennari JH.  Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates in the Department of Veterans Affairs’ Computerized Patient Record System.  J Am Med Inform Assoc. 2008 Sep-Oct;15(5):620-6.

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Mark H. Phillips, PhD
Professor of Radiation Oncology and Neurological Surgery
Adjunct Professor, Biomedical Informatics and Medical Education

Background:  B.A. in physics from Oberlin College; Ph.D. in atomic physics from University of Wisconsin-Madison.  Post-doctoral fellow in radiation biophysics, UC-Berkeley.  Staff scientist in the heavy charged particle clinical medicine program at Lawrence Berkeley Laboratory.  On the UW faculty since 1991.

Research Interests: Multiobjective optimization, utility measurements, probabilistic modeling of clinical outcomes in radiation oncology, decision modeling in oncology.

Representative publications:

  • Holdsworth CH, Corwin D, Stewart RD, Rockne R, Trister AD, Swanson KR,  Phillips M.  Adaptive IMRT using a mulitobjective evolutionary algorithm integrated with a diffusion-invasion model of glioblastoma.   Phys Med Biol, 57: 8271-8283, 2012.
  • Kim M, Ghate A,  Phillips M. A Stochastic Control Formalism for Dynamic Biologically Conformal  Radiation Therapy,  European Journal of Operations  Research, 219: 541-556, 2012.
  • Holdsworth C, Stewart R, Kim M, Liao J,  Phillips M. Investigation of  effective decision criteria for multiobjective optimization in IMRT,  Med Phys, 38: 2964-2974, 2011.
  • Phillips M, Smith W, Parvathaneni U, Laramore G. The Role of PET in the treatment of occult disease in head and neck cancer: a Modeling Approach.  Int J Radiat Oncol Biol Phys, 79: 1089-1095, 2011.
  • Holdsworth C, Kim M, Liao J,  Phillips MH. A Hierarchical Evolutionary Algorithm for Multiobjective   Optimization in IMRT. Med Phys, 37: 4986-4997, 2010.
  • Kim M, Ghate A,  Phillips M. A Markov Decision Process Approach to Temporal Modulation of Dose Fractions in Radiation Therapy Planning.  Phys Med Biol, 54: 4455-4476, 2009.
  • Smith WP, Doctor J, Meyer J, Kalet IJ,   Phillips MH. A decision aid for IMRT plan selection in prostate cancer based on a prognostic Bayesian network and a Markov model.  Artif Intell Med, 46(2): 119-130, 2009.

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Wanda Pratt, PhD
Professor, Information School
Adjunct Professor, Biomedical Informatics and Medical Education
Fellow, American College of Medical Informatics

Background:  developed medical expert systems for NASA, led a team of people representing common sense knowledge for the Cyc Project Education - PhD in Medical Informatics from Stanford University, and MS in Computer Science from the University of Texas.

Research Interests:  Wanda Pratt's research is motivated by the problems patients face in finding, using, and managing information.  Her research includes studying patient's work to understand their problems, developing new types of technology to address those problems, and evaluating the technology with patients.  She is also interested in using technology to improve patient-physician communication and collaboration.

Affiliations:  UW: joint appointment in the Information School, member of DuB – an alliance of faculty and students across UW exploring human computer interaction

Currently accepting new PhD students.  Not accepting MS students at this time. 

Representative Publications:

  • Klasnja P, Hartzler A, Powell C, Phan G, Pratt W. HealthWeaver Mobile Designing a Mobile Tool for Managing Personal Health Information during Cancer Care. Proceedings of the American Medical Informatics Association Fall symposium (AMIA '10). Nov 2010, Washington DC.
  • Unruh KT, Skeels M, Civan-Hartzler A, Pratt W. Transforming Clinic Environments into Informatin Workspaces for Patients. http://faculty.washington.edu/wpratt/Publications/pap1428-UnruhCamera.pdf Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI '10). April 2010, Atlanta, GA.
  • Skeels M, Unruh KT, Powell C, Pratt W. Catalyzing Social Support for Breast Cancer Patients http://faculty.washington.edu/wpratt/Publications/pap1135-Skeels.pdf Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CH '10). April 2010, Atlanta, GA.
  • Unruh K, Pratt W. Patients as actors: The patient's role in detecting, preventing, and recovering from medical errors. http://faculty.washington.edu/wpratt/Publications/unruh-pratt-IJMI.pdf International Journal of Medical Informatics 2005;v76:236-244.
  • Pratt W, Unruh K, Civen A, Skeels M. Managing health information in your life http://faculty.washington.edu/wpratt/Publications/CACMp51-pratt.pdf Communications of the Association for Computing Machinery (CACM) 2006;49(1):51-55.
  • Patel R, Hartzler A, Czerwinski M, Pratt W, Back A, Roseway A.  Visual Feedback on Nonverbal Communication: A Design Exploration with Healthcare Professionals. 7th International Conference on Pervasive Computing Technologies for Healthcare (PervasiveHealth 2013). Venice, Italy.
  • Klasnja P, Pratt W. (2012) Healthcare in the Pocket: Mapping the Space of Mobile-Phone Health Interventions. Journal of Biomedical Informatics. 2012;45(1):184–198.

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James D. Ralston, MD, MPH
Associate Scientific Investigator, Group Health Research Institute
Affiliate Associate Professor, Health Services, University of Washington School of Public Health
Affiliate Associate Professor, Biomedical Informatics and Medical Education, University of Washington School of Medicine
Consultative Internal Medicine, Group Health Permanente

Background:  B.A. Classics (Stanford University); M.D. (University of Washington); MPH (University of Washington)

Research:  Dr. Ralston is a Health Services and Health Informatics researcher with a focus in web-based and mobile support for patients with chronic medical conditions.  Dr. Ralston also practices Internal Medicine at Group Health Cooperative.

Representative Publications:

  • Lyles CR, Harris LT, Le T, Flowers J, Tufano J, Britt D, Hoath J, Hirsch I, Goldberg HI, Ralston JD.  Qualitative Evaluation of  Mobile Phone and Web-Based Collaborative Care Intervention for Patients with Type 2 Diabetes.  Diabetes Technol Ther 2011 May;13(5):563-569.
  • Simon GE, Ralston JD, Savarino J, Pabniak C, Wentzel C, Operskalski BH.  Randomized trial of depression follow-up care by online messaging.  J Gen Intern Med 2011 Jul;26(7):698-704 PMCID: PMC3138593.
  • Harris LT, Tufano J, Le T, Rees C, Lewis GA, Evert AB, Flowers J, Collins C, Hoath J, Hirsch IB, Goldberg HI, Ralston JD.  Designing mobile support for glycemic control.  J Biomed Inform 2010;43(5):S37-40.
  • Ralston JD, Hirsch IB, Hoath J, Mullen M, Cheadle A, Goldberg HI.  Web-based collaborative care for type 2 diabetes: a pilot randomized trial.  Diabetes Care 2009;32(2):234-239.  PMCID: PMC2628685.
  • Green BB, Cook AJ, Ralston JD, Fishman PA, Catz SL, Carlson J, Carrell D, Tyll L, Larson E, Thompson RS.  Effectiveness of home blood pressure monitoring, web communication, and pharmacist care on hypertension Control.  JAMA 2008 Jun 25;299(24):2857-2867.  PMCID: PMC2715866.
  • Ralston JD, Revere D, Robins LS, Goldberg HI.  Patient experience with a diabetes support program based on an interactive electronic medical record: qualitative study.  BMJ 2004;328(7449):1159.  PMCID: PMC411089.

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Eric Rose, MD
Clinical Assistant Professor, Biomedical Informatics and Medical Education
Clinical Assistant Professor, Family Medicine

Clinical Background: Currently employed as Director of Clinical Terminology, Intelligent Medical Objects.  Prior to that, 7 years of product management of clinical information systems (Microsoft, McKesson, etc.) and 7 years EHR management in a multi-specialty ambulatory care network (University of Washington Physicians Network).

Research interests: Electronic Medical Record design and implementation, Evidence-Based Medicine, Terminology Systems, Automated Decision-Support

Representative Publications:

  • Leviss J., ed. H.I.T. or Miss: Lessons Learned from Health Information Technology Implementations.
    AHIMA Press: Chicago, 2010. [served as Associate Editor and Contributor]
  • Rose E. Preparing for ICD-10-CM. Journal of AHIMA, July 2009.
  • Bae S., Khouangsathiene S., Morey C., O’Connor C., Rose E., and Shakil A. Implementation of a Web-Based Incident-Reporting System at Legendary Health System. In Lorenzi NM, Ash JS, Einbinder J et al. eds. Transforming Health Care Through Information, 2nd ed. Springer: New York, 2005.

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Brian K. Ross, PhD, MD
Professor, Anesthesiology
Adjunct Professor, Medical Education and Bioinformatics
Executive Director, Institute for Surgical and Interventional Simulation (ISIS)

Background:  Brian K. Ross, M.D., Ph.D., UW Medicine professor of anesthesiology, received his Ph.D. in physiology/pharmacology from the University of North Dakota in 1975. He completed postdoctoral research in respiratory diseases at the University of Washington in 1979, where he also received his M.D. in 1983. In 1984, he completed an internship in UW School of Medicine. In 1986, Dr. Ross completed a fellowship in Obstetrical Anesthesia from the University of California at San Francisco. In 1987, he completed a residency in anesthesiology, also at the University of Washington. 

Dr. Ross has been on the UW School of Medicine faculty since 1987. In 2003, he was appointed full professor status. Dr Ross has been involved in medical simulation at the UW since 1996, when he developed the initial curriculum for the Department of Anesthesiology. Since then, he has developed 20 courses for medical students, residents, and nurses. To promote careers in health care, he performs outreach to local high schools, conducting full-scale virtual operating room scenarios using the human patient simulator. Dr. Ross is the energy behind the advancement of medical simulation within the Department of Anesthesiology, reaching throughout the UW schools of medicine, nursing, and dentistry. He identified equipment and designed the labs that became the cornerstone of the Institute for Surgical and Interventional Simulation (ISIS). Based on his vision and expertise in medical simulation, Dr. Ross was appointed by the dean of the School of Medicine to serve as the first executive director of ISIS in November 2005.He will take ISIS into its next phase, as it expands into its new offices and labs in the UW Medical Center Surgery Pavilion, and as ISIS establishes itself as the medical simulation resource for the UW, community, industry, and the five-state WWAMI region (Washington, Wyoming, Alaska, Montana, and Idaho).

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Anthony Rossini, ScD
Affiliate Associate Professor, Biomedical Informatics and Medical Education

Background: Statistics, biostatistics, and biomedical informatics, with over 25 years experience in software and information technology systems.

Research interests:  My interests lie in the intersection of statistics and informatics, especially with respect to the commoditization of technology for data analysis. Past work has included simple parallel computing, the use of virtual reality for common statistical analyses, as well as support for projects which drive interactive data analysis modalities (http://ess.r-project.org/ | http://www.bioconductor.org/). Past statistical methodology research focused on estimation for semiparametric regression models for interval censored data and drug development program design. Current research interests focus on the design of model specification languages for statistics based on Common Lisp.

I am currently Head of Biostatistics and Bioinformatics for the Novartis Pharma AG Molecular Diagnostics business unit, based Basel, Switzerland, which does R&D and commercialization of diagnostic devices to drive personalized medicine.

My current activities range from complex statistical modelling to the design and specification of informatics technologies to support reuseable, knowledge-containing statistical and mathematical models. This latter work can be thought of as data-integration for data-analytic methods (both classes and instances) along with associated metadata.

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Doug Schaad, PhD
Professor, Biomedical Informatics and Medical Education

Research: Career trajectories in the medical profession; Health outcomes associated with new orthopaedic techniques and materials; Compassion, empathy and cynicism in the professional development of physicians; Interprofessional teams and learning outcomes; Curriculum enhancement and associated performance assessment.

Background: BS degrees in Zoology and Psychology; M.Ed in Counseling and Ph.D in Measurement and Evaluation all from the University of Washington.  Hired as a graduate research assistant in the Office of Research in Medical Education in 1974.  Continuously employed within the Department of Biomedical Informatics and Medical Education since that time.  Currently, Professor and Division Head of Medical Education and Evaluation; Chairman of the First Year Curriculum committee; Senior member of the Student Progress Committee; Member of the Council on University Relations and Member of the Faculty Senate.

Other Interests: Chairman Conservation Committee of the Washington FlyFishing Club; Advisor to Washington Department of Fish and Wildlife for Steelhead and Cutthroat Management; Owner/Operator of a vineyard in the Chehalem AVA of Oregon; Executive Director of the Whitewater Creek Conservation Association.

Representative Publications:

  • King JC, Manner PA, Stamper DL, Schaad DC, Leopold SS.  Is minimally invasive total knee arthroplasty aoosciated with lower costs than traditional TKA.  Clinical Orthopaedics and Related Research 2011;469(6):1716-20.
  • Norris TE, Schaad DC, DeWitt D, Ogur B, Hunt DD.  Longitudinal integrated clerkships for medical students: An innovation adopted by Australia, Canada, South Africa, and the United States.  Acad Med 2009;Jul 84(7):902-7.
  • King J, Stamper DL, Schaad DC, Leopold SS.  Minimally invasive total knee arthroplasty compared with traditional total knee arthoplasty.  Assessment of the learning curve and the postoperative recuperative period.  J Bone Joint Surg Am 2007;July 89(7):1497-1503.
  • Mitchell PH, Belza B, Schaad DC, Robins LS, Gianola FJ, Odegard PS, Kartin D, Ballweg RA.  Working across the boundaries of health professions disciplines in education, research and service: Lessions from the University of Washington Experience.  Acad Med 2006;Oct 81(10):891-896.
  • Mouradian WE, Reeves A, Kim S, Evans R, Schaad DC, Marshall SG, Slayton R.  An oral health curriculum for medical students at the University of Washington.  Acad Med 2005;May 80(5):434-442.

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Craig Scott, PhD
Professor, Biomedical Informatics and Medical Education
Director, NW Consortium for Clinical Assessment

Research Interests: His interests include clinical skills development and assessment, medical school admissions, mind/body medicine and stress management for medical students and faculty, performance-based teaching and evaluation (including TBL, PBL, flipped classrooms, objectively-structured clinical examinations and standardized patients), international medical education and assessment of outcomes of National Science Foundation research centers. He recently produced and directed a video for the National Science Foundation entitled "Catalysts for Innovation" (http://www.nsf.gov/eng/iip/iucrc/iucrc_video.jsp) and is completing work on the 5th edition of the NSF's Compendium of Industry-Nominated Technological Breakthroughs of NSF Research Centers (http://faculty.washington.edu/scottcs/NSF/2012/nsf2012.html.

Representative Publications:

  • Finkelstein C, Lan YL, Brownstein A, Scott CS.  Anxiety/Stress Reduction in Medical Education: An Intervention. Med Educ 2007;Mar 41(3):258-64.
  • Scott CS (Ed). Industry-Nominated Technological Breakthroughs of National Science Foundations Industry/University Cooperative Research Centers (2012). National Science Foundation, Industry-University Cooperative Research Program. Arlington, Virginia.
  • Losh D, Ambrozy D, Cunningham M, Struijk J, Scott C, Adding value to OSCEs by providing real-time clinician feedback. Medical Educator. (In press).
  • Booth-LaForce C, Scott CS, Heitkemper MM, Cornman BJ, Lan MC.  CAM Attitudes and Competencies of Nursing Students and Faculty: Results of Integrating CAM into the Nursing Curriculum.  J Prof Nsg 2010;Sept-Oct 26(5):293-300.
  • Scott CS, Nagasawa PR, Abernethy NF, Ramsey BW, Martin PJ, Hacker BM, Schwartz HD, Brock DM, Robins LS, Wolf FM, Disis ML. Expanding Assessments of Translational Research Programs: Supplementing Metrics with Value Judgments. Evaluation in the Health Professions (in press).

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Linda Shapiro, PhD
Professor, Computer Science and Engineering
Adjunct Professor, Biomedical Informatics and Medical Education
Joint: Electrical Engineering

Background: 38 yrs computer science. Funded research: a) object and pattern recognition b) medical imaging c) multimedia information retrieval for medical applications d) biomedical informatics information systems e) craniofacial image analysis

Currently accepting new MS students and new PhD students only if they have their own funding.

Representative Publications:

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Kari A. Stephens, PhD
Assistant Professor, Psychiatry & Behavioral Sciences

Adjunct Assistant Professor, Biomedical Informatics and Medical Education

Background: BS in Psychology (with distinction, UW), MS in Clinical Psychology (UW), PhD in Clinical Psychology (UW). Academic Medical Center industry experience working as data design architect and developer for the centralized institutional clinical data repository, data interface development, data analytics, and data quality management in support of research, clinical, and operational needs, including software and security development for a web-based proprietary medical record system (“MINDscape”) and post hoc query application (“MAP”).

Current Primary Interests: Development and sustainability of data sharing architectures for health data, primarily focused in primary care and mental health settings; utility of data sharing tools for promotion and execution of clinical research using shared data systems; development and use of behavioral health intervention based electronic applications, particularly supporting integrated team based medical care settings.

Current Research: Currently leading Data QUEST, a project and set of tools incorporating data sharing architecture into Practice Based Research Networks in collaboration with the WWAMI Practice-Based Research Network (WPRN) and an American Indian / Alaska Native research network supported by the UW Institute for Translational Health Sciences (ITHS). Data QUEST intersects with multiple research projects and groups including the DARTNet Institute and Northwest-Alaska Pharmacogenomics Research Network (NWA-PGRN).

Representative Publications:

  • Goldberg, H. I., Tarczy Hornoch, P., Stephens, K. A., Larson, E. B., & LoGerfo, J. P. (1998). Internet access to patients' records [with comment]. Lancet, 351(9118), 1811. PMID: 9635973
  • Sinanan, M. N., Wicks, K., Peccoud, M., Canfield, J., Poser, L., Sailer, L., Stephens, K. A., & Edwards, D. (2000). Formula for surgical practice resuscitation in an academic medical center. The American Journal of Surgery, 179, 417-421. PMID: 10930493
  • Lin, C., Black, R. A., LaPlante, J., Keppel, G. A., Tuzzio, L., Berg, A. O., Whitener, R. J., Buchwald, D. S., Baldwin, L., Fishman, P. A., Greene, S. M., Gennari, J. H., & Tarczy-Hornoch, P., Stephens, K. A. (2010). Facilitating health data sharing across diverse practices and communities, AMIA Summits Translational Science Proceedings, Mar 1, 2010, 16-20. PMCID: PMC3041543
  • Lin, C., Stephens, K. A., Keppel, G., Baldwin, L., Pace, W., & Green, L. (2010, June). Strategies for Facilitating Data Sharing in PBRNs. Abstract and panel presentation for 2010 AHRQ Annual PBRN Research Conference, Bethesda, MD.
  • Stephens, K. A., Anderson, N., & Lin, C. (2010, November). Developing best practices for evaluating federated data sharing: Approaches from academic hospital and primary care clinic networks. Abstract and poster presented at the annual meeting of the American Medical Informatics Association, Washington, DC.
  • Stephens, K. A., Baldwin, L., Lin, C., & Keppel, G. (2010, November). Facilitating data sharing in a Practice Based Research Network. Abstract and panel presentation for the annual meeting of the North American Primary Care Research Group, Seattle, WA.
  • Stephens, K. A., Lin, C., Baldwin, L., Echo-Hawk, A., & Keppel, G. (2011, October). A web-based tool for cataloging primary care electronic medical record federated data: FindIT. Abstract and poster presented at CTSA 2011 Informatics Annual Meeting, Bethesda, MD.
  • Stephens, K. A., Lin, C., Baldwin, L., Echo-Hawk, A., Keppel, G. A., Buchwald, D., Whitener, R., Korngiebel, D., Berg, A. O., Black, R. A., & Tarczy-Hornoch, P. (2012). LC Data QUEST: A technical architecture for federated data sharing across community primary care practices. AMIA Summits Translational Science Proceedings, Mar 19, 2012, 57-62. PMCID: PMC3392065

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Peter Tarczy-Hornoch, MD
Chair and Professor, Biomedical Informatics and Medical Education
Professor, Pediatrics (Division of Neonatology)
Adjunct Professor, Computer Science and Engineering
Fellow, American College of Medical Informatics

Background: 30 years software development (biomedical instrumentation, bioinformatics, clinical informatics), 20 years clinical medicine (pediatrics, neonatology). 

Other: Head - Division of Biomedical and Health Informatics, Director and PI of UW NLM funded Biomedical and Health Informatics Research Training Program, Deputy Director - Biomedical and Health Informatics Graduate Program, Advisory Committee for Harvard NCBC i2b2 (Informatics for Integrating Biology and the Bedside, http://www.i2b2.org/), Advisory Committee for University of California NCBC iDASH (Integrating Data for Analysis, Anonymization and Sharing, http://idash.ucsd.edu/) Advisory Committee for University of Utah CTSA (http://www.ccts.utah.edu/), Associate Editor for Translational Bioinformatics for the Journal of Biomedical Informatics, Editorial board for the Journal of the American Medical Informatics Association (jamia.bmj.com). 

Current Research: a) Foundational and applied research in the context of biomedical informatics support for translational and clinical research as part of the Institute of Translational Health Sciences (www.iths.org), b) facilitation of biospecimen acquisition and subject recruitment as part of two Life Sciences Discovery Fund grants (Washington Phenotyped Biospecimen Resource and the Cancer Biospecimen Resource), c) extraction of phenotype from the electronic medical record and pharmacogenomic decision support as part of the Northwest Institute of Genetic Medicine (www.nwigm.org), d) integration of whole exome data into the electronic medical record as part of the NEXT U01 Clinical Sequencing Exploratory Research grant (Jarvik, PI), e) data integration and clinical data repositories as part of the UW Medicine clinical computing leadership group, f) leveraging electronic medical records for comparative effectiveness research as part of the SCOAP CERTN (www.scoap.org),  g) past research on a database of available genetic testing and on the application of genetic testing (GeneTests - http://www.genetests.org/, co-PI 1995-2004, consultant 2004-6) and general purpose data integration systems (2000-2010) (http://www.biomediator.org). Other past research descriptions available at home page.

Currently accepting new MS students and new PhD students.

 Representative Publications:

  • Overby C, Tarczy-Hornoch P, Hoath J, Kalet I, Veenstra D. Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support. Accepted for AMIA Translational Bioinformatics Summit 2010, as one of best papers. BMC Bioinformatics 2010;Oct 28;11 Suppl 9:S10.
  • Cadag E, Tarczy-Hornoch P. Supporting Retrieval of Diverse Biomedical Data using Evidence-aware Queries. J Biomed Inform 2010;Dec;43(6):873-82.
  •  Sarkar, IN, Butte, AJ, Lussier, YA, Tarczy-Hornoch, P, Ohno-Machado, L. “Translational Bioinformatics: A Macroscopic Approach to Bridge the Biological and Clinical Divide”.  J Am Med Inform Assoc. 2011 Jul-Aug;18(4):354-7. Epub 2011 May 10 (2011)
  • Sittig DF, Hazlehurst BL, Brown J, Murphy S, Rosenman M, Tarczy-Hornoch P, Wilcox A.  A survey of informatics platforms that enable distributed comparative research using multiinstitutional heterogeneous clinical data.  Accepted April 2012 by Medical Care.
  • Overby CL, Devine EB, Tarczy-Hornoch P, Kalet I.  Deriving rules and assertions from pharmacogenomic knowledge resources in support of patient drug exposure predictions.  J Am Med Inform Assoc 2012 Apr 26 [Epub ahead of print] 2012.

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Anne Turner, MD, MLIS, MPH
Assistant Professor, Department of Health Services, School of Public Health 
Associate Professor, Biomedical Informatics and Medical Education
Dr. Anne M. Turner, MD (Dartmouth-Brown), MPH (University of Washington) and MLIS (University of Washington).

Background:  public health informatics research (>10 years); library and information science research (>15 years); and clinical pediatrics (>20 years).

Research interests:  the use of natural language processing and machine translation to improve access to public health information; health  information needs and workflow;  task analysis; use of GIS for preparedness planning and targeting interventions; evaluation of public health information systems; public health grey literature.

Other: Faculty at the UW Northwest Center for Public Health Practice (NWCPHP - http://www.nwcphp.org/) and the UW Center for Public Health Informatics (CPHI -http://www.cphi.washington.edu/.

Representative Publications:

  • Turner AM, Liddy ED, Bradley J, Wheatley J. Modeling public health interventions for improved access to the public health grey literature. J Med Libr Assoc 2005;93(4):487-94.
  • Revere D, Turner AM, Madhaven AM, Rambo N, Bugni P, Kimbal A, Fuller S. Understanding the information needs of publich health professionals: A literature review to inform design of an interactive digital knowledge management system. J Biomed Inform 2007;40(4):410-421.
  • Turner, A.M., Kirchhoff, K. and Capurro, D.  Using crowdsourcing technology for testing multilingual public health promotion materials. Jour Med Internet Res. 2012; 14(3):e79.
  • Turner AM, Ramey J, Lee S. Connecting public health IT systems with enacted work: Report of an ethnographic study. AMIA Annu Symp Proc 2008;Nov 6:737-41.
  • Kirchhoff K, Turner AM, Axelrod A, Saavedra F. Statistical Machine Translation of Public Health Information: A Feasibility Study. JAMIA 2011;18(4):473-478. 

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Erik G. Van Eaton, MD, FACS
Associate Professor, Department of Surgery, Division of Harborview Trauma and Burns.
Adjunct Associate Professor, Department of Biomedical Informatics and Medical Education, Division of Biomedical and Health Informatics.

Background: An Alaskan commercial fisherman who obtained an M.D. from the University of Washington in 2001. During residency training in General Surgery in 2002, started working on applied clinical informatics projects for inpatient care. Completed an NLM Biomedical Informatics fellowship in 2005. Began clinical practice in trauma surgery, emergency general surgery, and surgical critical care in 2009 at the University of Washington Medical Center and Harborview Medical Center.

Other: Assistant Medical Director for Surgical Critical Care, University of Washington Medical Center. Service Director of the Surgical Intensive Care Unit at the University of Washington Medical Center. Member of the American College of Surgeons Committee on Informatics. Clinical Design Strategist for TransformativeMed Inc, a medical software spin-out company that is commercializing licensed biomedical informatics technology developed at the University of Washington.

Current Research : a) Co-PI for UW-funded project to develop clinical informatics system for better capture of near misses and adverse events by clinical teams, b) Co-investigator on AHRQ-funded project to leverage electronic medical records for comparative effectiveness research as part of the SCOAP CERTN (www.scoap.org) project, c) NLM (NN/LM Regional Medical Libraries) funded project to explore mobile computing library resources for clinician teams at the bedside.

 Representative Publications:

  • Van Eaton EG, Tarpley JL, Solorzano CC, Cho CS, Weber SM, Termuhlen PM. Resident Education in 2011: Three Key Challenges on the Road Ahead. Surgery 2011;149(4):465-73. PMID:21295811.
  • Van Eaton EG, McDonough KA, Lober WB, Johnson EA, Pellegrini CA, Horvath KD. Safety of Using a Computerized Rounding and Sign-out System to Reduce Resident Workhours. Acad Med 2010;85(7):1189-95. PMID:20592514.
  • Sarkar U, Carter JT, Omachi TA, Vidyarthi AR, Cucina R, Bokser S, Van Eaton E, Blum M. SynopSIS: integrating physician sign-out with the electronic medical record. J Hosp Med 2007; 2(5):336-42. PMID:17935249
  • Williams RG, Silverman R, Schwind C, Fortune JB, Sutyak J, Horvath KD, Van Eaton EG, et al. Surgeon Information Transfer and Communication: Factors Affecting Quality and Efficiency of Inpatient Care. Ann Surg 2007; 245(2):159-169. PMID:17245166.
  • Van Eaton EG, Lober WB, Pellegrini CA, Horvath KD. User-driven design of a Computerized Rounding and Sign-out application. AMIA Annu Symp Proc. 2005:1145. PMID:16779431.
  • Van Eaton EG, Horvath KD, Lober WB, Rossini AJ, Pellegrini CA. A randomized, controlled trial evaluating the impact of a computerized rounding and sign-out system on continuity of care and resident work hours. J Am Coll Surg 2005; 200(4):538-45. PMID:15804467.

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Lucy Vanderwende, PhD
Senior Researcher, Microsoft Research
Affiliate Associate Professor, Biomedical Informatics and Medical Education

Background: Since 1992, senior researcher at Microsoft Research in Natural Language Processing group.  Contributed to the Word Grammar Checker, which has been shipping since 1997.  PhD in Computational Linguistics (Georgetown University), MSc in Theoretical Linguistics (Georgetown University), BA in English Language and Literature (University of Leiden, NL)

Research interests: I am broadly interested in knowledge acquisition from naturally occurring text.  Earlier, I worked on extracting lexico-semantic information from dictionaries, which we extended to encyclopedic text and eventually to general domain text; this project is known as MindNet.  Currently, I am interested in knowledge acquisition from biomedical text, including both clinical texts, written in the course of patient care, as well as basic research literature. For the latter, it is our goal to extract and then visualize information in such a way that scientists will be able to review existing literature more broadly than is possible today; this project spans both knowledge extraction as well as summarization.  I am currently collaborating with Meliha Yetisgen-Yildiz and others on several projects that focus on extracting medical information (e.g., phenotypes) from clinical data such as radiology reports and ICU reports, using both structured and unstructured data.

Representative Publications:

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Thomas Wetter, PhD
Prof. of Medical Informatics, Heidelberg University, Germany
Affiliate Professor, Biomedical Informatics and Medical Education

Background: Masters degree (diploma) in Mathematics from Aachen Technical University (Germany), working on mathematical models of the human circulation. Doctoral research in biostatistics, biomedical modeling, and clinical decision support systems. 1984 PhD from Aachen Technical University on the modal logic of clinical decision support.

Research on expert systems, natural language processing, human computer interaction, speech recognition, and software quality at the IBM Germany Scientific Center. Assignments to the several national and international projects. 1992 external "Habilitation" (postdoctoral degree) from Kaiserslautern University (Germany) on formal foundations of knowledge modeling.

Current research and teaching: Since 1997 Prof. in the School of Medicine of Heidelberg University (Germany). In charge of the medical informatics curriculum for students of medicine. Teaching in BSc and MSc curricula in a joint curriculum with Heilbronn University (Germany). IPHIE (International Partnership for Health Informatics Education) liaison for Heidelberg University.

Research interests include clinical software  (challenges under 3rd world conditions, new software design paradigms), the scientometrics and dynamics of scientific discovery, and more recently consumer health informatics and clinical decision support in fields such as breast cancer or leukemia.

Representative publications:

  • Wetter, Th; To decay is system: The challenges of keeping a health information system alive; Int. J. Med. Inform. 76 (2007) (S1), pp. 252–260
  • Weires MB, Tausch B, Haug PJ, Edwards CQ, Wetter T, Cannon-Albright LA. Familiality of Diabetes Mellitus. Exp Clin Endocrinol Diabetes 115,  634-40  (2007)
  • Ndira, SP, Rosenberger KD, Wetter Th. Assessment of data quality of and staff satisfaction with an electronic health records system in a developing country (Uganda): a qualitative and quantitative comparative study. Meth Inf Med 47(6) 489-98 (2008)
  • Chou H_L, Yao C-T, Su S-L, Lee C-Y, Hu K-Y, Terng H-J, Shih Y-W, Chang Y-T, Lu Y-F,  Chang C-W, Wahlqvist ML, Wetter T and Chu C-M. Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees. BMC Bioinformatics 2013, 14:100 
  • Chen YC, Yeh HY, Wu JC, Haschler I, Chen TJ, Wetter T. Taiwan's national health insurance research database: administrative health care database as study object in bibliometrics. Scientometrics 86 365-80 (2011). [SCI][SSCI] (online DOI)
  • Wicht A, Wetter T, Klein U. (2013): A web-based system for clinical decision support and knowledge maintenance for deterioration monitoring of hematooncological patients. Computer Methods and Programs in Biomedicine,111(1):26-32,2013

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Mark Whipple, MD, MS, FACS
Associate Professor, Dept. of Otolaryngology-Head & Neck Surgery
Associate Professor, Dept. of Biomedical Informatics and Medical Education
Chief of Oto/HNS, Harborview Medical Center
Head, Big Sky College, University of Washington School of Medicine

Background: Dr. Whipple received his BS degree in Biological Sciences from Stanford University and his MD degree from the University of Washington School of Medicine.  He completed his residency training in Otolaryngology-Head & Neck Surgery at the University of Illinois and his MS degree in Medical Informatics from the Harvard-MIT program.  He practices Otolaryngology-Head & Neck surgery and serves as the chief of service at Harborview Medical Center.  He served as co-director of the Biocommons Computing Center.  Dr. Whipple has been a faculty member of the UW School of Medicine Colleges since their inception and has served as the Head of Big Sky College since 2009.  His past research activities have included developing algorithms for analysis of genomic data of head and neck cancer.

Current Research:  Developing  predictive models of head and neck tumor metastasis from sparse data sources using formal anatomic knowledge representations.  Genomics of head and neck tumors (squamous cell carcinoma, infantile hemangiomas, lymphatic malformations.)

 Representative Publications:

  • Kalet IJ, Whipple M, Pessah S, Barker J, Austin-Seymour MM, Shapiro LG. A rule based model for local and regional tumor spread. Proc AMIA Symp. 2002: 360-4.
  • Kuo WP, Mendez E, Chen C, Whipple ME, Farwell DG, Agoff N, Park PJ. Functional relationship between gene pairs in oral squamous cell carcinoma. Proc AMIA Symp. 2003; 371-5.
  • Whipple ME, Mendez E, Farwell DG, Chen C. A log likelihood predictor for genomic classification of oral cancer using principal component analysis for feature selection. MedInfo 2004;2004: 823-8.
  • Benson N, Whipple M, Kalet IJ. A markov model approach to predicting regional tumor spread in the lymphatic system of the head and neck. AMIA Annu Symp Proc. 2006:31-5.
  • Mendez E, Fan W, Choi P, Agoff SN, Whipple M, Farwell DG, Futran N, Weymuller EA, Zhao LP, Chen C. Tumor-specific genetic expression profiles of metastatic oral squamous cell carcinoma. Head Neck. 2007 Sep;29(9):803-14.
  • Hasina R, Whipple ME, Martin LE, Kuo WP, Ohno-Machado L, Lingen MW. Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications. Lab Invest. 2008 Apr;88(4):342-53.
  • Kalet IJ, Mejino JL, Wang, V, Whipple M, Brinkley JF. Content-specific auditing of a large scale anatomy ontology. J Biomed Inform. 2009 Jun;42(3):540-9.

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Adam Wilcox, PhD
Professor, Biomedical Informatics and Medical Education
Chief Analytics Officer (CAO) of UW Medicine

Background:  Dr. Wilcox completed a double major in 1995 in Physics and Mathematics at the University of Utah. He then obtained his PhD in 2000 in Medical Informatics at Columbia University (Advisor George Hripcsak). Dr. Wilcox worked with the informatics group at Intermountain Healthcare under Paul Clayton from 2001-2006, where he led the development and implementation of primary care and emergency medicine systems, while also researching the effectiveness of care managers in an advanced practice model that was a precursor to the patient-centered medical home. While at Intermountain, he was also faculty at the University of Utah, where he taught courses and lectures in research design and decision support. He was on the faculty of Columbia University from 2006-2013, where he directed the legacy clinical information system, clinical data repository and data warehouse, and was also principal investigator of the Washington Heights/Inwood Informatics Infrastructure for Comparative Effectiveness Research (WICER) project, one of the country's first population health research databases, funded by AHRQ.

Dr. Wilcox arrives most recently from Intermountain Healthcare where he led Intermountain’s clinical decision support efforts and directed its analytic health repository. In 2015, Dr. Wilcox was appointed a member of the PCORI Methodology Committee. He is an elected fellow of the American College of Medical Informatics, is a senior editor for eGEMs, and serves on the Clinical Informatics Subcommittee for the American Board of Preventive Medicine, which administers the board examination for the clinical informatics subspecialty.

Research interests: Electronic health records, quality improvement, patient-centered outcomes, methodology, health care transformation.

Representative Publications:

1. Wilcox A, Randhawa G, Embi P, Cao H, Kuperman G. Sustainability Considerations for Health Research and Analytic Data Infrastructures. EGEMs Gener Evid Methods Improve Patient Outcomes [Internet]. 2014 Sep 17;2(2). Available from: http://repository.academyhealth.org/egems/vol2/iss2/8
(This was my primary paper that the discussion of which during the inception of the design led to a special issue in eGEMS on sustainability.  This was picked up in the health technology press.)

2. Wilcox A, Gallagher K, Bakken S. Security Approaches in Using Tablet Computers for Primary Data Collection in Clinical Research. EGEMs Gener Evid Methods Improve Patient Outcomes [Internet]. 2013 Feb 13;1(1). Available from: http://repository.academyhealth.org/egems/vol1/iss1/7

3. Wilcox AB, Shen S, Dorr DA, Hripcsak G, Heermann L, Narus SP. Improving Access to Longitudinal Patient Health Information within an Emergency Department. Applied Clinical Informatics 2012, 3: 290-300.

4. Wilcox AB, Chen YH, Hripcsak G. Minimizing electronic health record patient-note mismatches. J Am Med Inform Assoc. 2011 Jul-Aug;18(4):511-4.

5. Dorr DA, Wilcox AB, Brunker CP, Burdon RE, Donnelly SM. The effect of technology-supported, multidisease care management on the mortality and hospitalization of seniors. J Am Geriatr Soc. 2008 Dec;56(12):2195-202.

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Fred Wolf, PhD
Professor, Biomedical Informatics and Medical Education
Adjunct Professor, Health Services, Epidemiology
Fellow, American College of Medical Informatics

Background: My own research over the past 30 years has focused on the study of 1) clinical reasoning, decision making, and judgment under uncertainty, 2) dissemination and evaluation of new technology, including decision support systems, 3) evidence-based medicine, systematic reviews and meta-analysis of educational and healthcare interventions, including comparative effectiveness research and training, and 4) evaluation of clinical and translational research interventions and training. This work dates back to the mid-1980s with the publication in JAMA of my research on diagnostic reasoning and heuristics and biases, and the publication of Meta-analysis: Quantitative Methods for Research Synthesis in the Sage Series on Quantitative Applications in the Social Sciences (Vol. 59).  The JAMA article is cited in Jerome Groopman’s best-selling book on How Doctor’s Think as one of two articles to read “For those interested in the Bayesian approach” to decision making and led to my first NIH R01-supported research program, while my work in meta-analysis has led to my collaboration and co-authorship of many systematic evidence reviews as part of the International Cochrane Collaboration. Formerly, I was professor of postgraduate medicine and health professions education, and director of the Learning Resource Center and the Laboratory for Computing and Cognition (LC3), at the University of Michigan Medical School and a Visiting Scholar at the UK Cochrane Centre and Green College, University of Oxford. I served as Co-Principal Investigator and Program Director for a new NIH Administrative Supplement for Comparative Effectiveness Research (CER) Workforce Development: The ITHS Institute for CER Training and Web-based Toolkit.

Representative Publications:

  • Park, M., Katon, W.J. & Wolf, F.M. (2013). Depression and risk of mortality in individuals with diabetes: a meta-analysis and systemic review. General Hospital Psychiatry. 2013;35 (3):217-225. PMID: 23415577.
  • Chilana, P. K., Fishman, E., Geraghty, E., Tarczy-Hornoch, P., & Wolf, F. M., Anderson, N. R. (2011). Characterizing data discovery and end-user computing needs in clinical translational science. Journal of Organization and End User Computing (JOEUC), 23 (4): 17-30.
  • LaVallie, D. L., Wolf, F. M., Jacobsen C., D., Sprague, D., & Buchwald, D. S. (2012). Health numeracy and understanding of risk among older American Indians and Alaska Natives. Journal of Health Communication, 17(3):294-302. PMID: 22188207
  • Emerson W, Brand RA, Heckman JD, Warme WJ, Wolf FM, Leopold SS (2010). Testing for the presence of positive-outcome bias in peer review: A randomized controlled trial. Archives of Internal Medicine 170 (21):1934-1939
  • Sprague D, LaVallie DL, Wolf FM, Jacobsen C, Sayson K, Buchwald D (2011). Influence of graphic format on comprehension of risk information among American Indians. Medical Decision Making 31(3):437-43

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Fei Xia, PhD
Associate Professor, Linguistics Department
Adjunct Associate Professor, Biomedical Informatics and Medical Education

Background: B.S. in Computer Science (Peking University), M.S. and Ph.D. in Computer Science (University of Pennsylvania), Research Staff Member at the IBM T. J. Watson Research Center at Yorktown Heights, NY before joining UW in 2005.

Research interests: Her research area is natural language processing (NLP), and her research covers a wide range of NLP tasks including morphological analysis, grammar extraction and grammar generation, treebank development, machine translation, and creating resources for low-density languages. She is especially interested in bio-NLP -- that is, using NLP techniques to process biomedical data. She is currently collaborating with Meliha Yetisgen-Yildiz and others on several projects that focus on extracting medical information (e.g., critical results, recommendation, and phenotypes) from clinical data such as radiology reports and ICU reports.

Representative publications:

  • Cuijun Wu, Fei Xia, Louise Deleqer, and Imre Solti, 2011. “Statistical Machine Translation for Biomedical Text: Are We There Yet?” In the Proc. of the AMIA 2011 Annual Symposium, Washington DC, Oct 22-26, 2011.
  • Meliha Yetisgen-Yildiz, Martin Gunn, Fei Xia, and Tom Payne, 2011. “Automatic Identification of Critical Follow-Up Recommendation Sentences in Radiology Reports”. In the Proc. of the AMIA 2011 Annual Symposium, Washington DC, Oct 22-26, 2011.
  • Meliha Yetisgen-Yildiz, Bradford Glavan, Fei Xia, Lucy Vanderwende, and Mark Wurfel, 2011. “Identifying Patients with Pneumonia from Free-Text Intensive Care Unit Reports”. In Proc. of the ICML workshop on Learning from Unstructured Clinical Text, Bellevue, WA, July 2, 2011.
  • Scott Russell Halgrim, Fei Xia, Imre Solti, Eithon Cadag, Ozlem Uzuner, 2011. “A cascade of MaxEnt classifiers applied to extracting medication information from discharge summaries”, Journal of Biomedical Semantics 2011,  2 (Suppl 3):S2.
  • Ozlem Uzuner, Imre Solti, Fei Xia, and Eithon Cadag, 2010. “Community Annotation Experiment for Ground Truth Generation for the i2b2 Medication Challenge”,  Journal of the American Medical Informatics Association (JAMIA),  17:519-523. 

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Meliha Yetisgen, PhD
Assistant Professor, Biomedical Informatics and Medical Education
Adjunct Assistant Professor, Linguistics Department
Background: PhD in Information Science (University of Washington), MSc in Computer Engineering (Middle East Technical University), BSc in Computer Engineering (Bilkent University).
Research Areas: Statistical natural language processing, bio-medical text mining and information retrieval.

Currently accepting new MS students and new PhD students.

Representative Publications:

  • Yetisgen-Yildiz M, Glavan BJ, Xia F, Vanderwende L, Wurfel MM. Identifying patients with pneumonia from Free Text Intensive Care Unit Reports. In Proceedings of Learning from Unstructured Clinical Text Workshop of ICML '2011. Bellevue, WA, July, 2011.
  • Yetisgen-Yildiz M, Gunn ML, Xia F, Payne TH.  Automatic Identification of Critical Fellows Up Recommendation Sentences in Radiology Reports. In Proceedings of the American Medical Informatics Association Fall Symposium (AMIA'11). Washington  DC, October, 2011.
  • Luo Z, Yetisgen-Yildiz M, Weng C. Dynamic Categorizatiion of Clinical Research Eligibility Criteria by Hierarchical Clustering. Journal of Biomedical Informatics, 2011 (Accepted).
  • Yetisgen-Yildiz M, Solti I, Xia F, Halgrim SR. Preliminary experiments with Amazon's Mechanical Turk for Annotating Medical Named Entities. Proceedings of Creating Speech and Language Data with Amazon's Mechanical Turk Workshop of NAACL'2010, 2010.
  • Yetisgen-Yildiz M, Pratt W. A New Evaluation Methodology for Literature Based Discovery. Journal of Biomedical Informatics. 2009, Vol. 42, No. 4, pp 633-643.

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Brenda Zierler, PhD, RN, FAAN
Professor, Biobehavioral Nursing and Health System
Co-Director, Center for Health Sciences Interprofessional Education, Practice and Research
Associate Director, Institute for Simulation and Interprofessional Studies
Adjunct Professor, Department of Surgery, Vascular Division, School of Medicine;
Adjunct Professor, Department of Health Services, School of Public Health
Adjunct Professor, Biomedical Informatics and Medical Education

Representative Publications:

  • Demiris G, Zierler B. (2010) Integrating problem-based learning in a nursing informatics curriculum. Nurse Education Today; 30:175–179.
  • Zierler B, Ross B, Liner D. (2010) The Macy Interprofessional Collaborative Project, The University of Washington. Journal of Allied Health; 39(3):e131-132.
  • Lee JA, Zierler BK, Liu CF, Chapko M. (2011) Cost-effective diagnostic strategies in patients with a high, intermediate, or low clinical probability of pulmonary embolism. Vascular and Endovascular Surgery; 45(2) 113-121.
  • Wolpin SE, Lee J, Glenny R, Wolf F, Zierler B. (2011) Evaluation of Online Training on the Prevention of Venous Thromboembolism. Vascular and Endovascular Surgery; 45(2):146-156.
  • Jaff MR, McMurtry MS, Archer SL, Cushman M, Goldenberg N, Goldhaber SZ, Jenkins JS, Kline JA, Michaels AD, Thistlethwaite P, Vedantham S, White RJ, Zierler BK; American Heart Association Council on Cardiopulmonary, Critical Care, Perioperative and Resuscitation; American Heart Association Council on Peripheral Vascular Disease; American Heart Association Council on Arteriosclerosis, Thrombosis and Vascular Biology. (2011) Management of massive and submassive pulmonary embolism, iliofemoral deep vein thrombosis, and chronic thromboembolic pulmonary hypertension: a scientific statement from the American Heart Association. Circulation; 123(16):1788-1830.
  • Nguyen D, Nguyen H, Zierler BK. (2011) A Survey of Nursing Faculty Needs for Training in Use of New Technologies for Education and Practice. Journal of Nursing Education; 50(4):181-189.
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Email:  brendaz
Website  http://collaborate.uw.edu/