JAMES F. BRINKLEY, M.D., Ph.D.

 

http://sig.biostr.washington.edu/~brinkley

                                                                             

Curriculum Vitae

                                                                             

September 8, 2009

 

EDUCATION

 

Amherst College, Amherst, Massachusetts, B.A. (Mathematics)

 

University of Washington, Seattle, Washington, M.D.

 

Stanford University, Palo Alto, California, Ph.D. (Medical Computer Engineering)

 

PRESENT POSITION

 

Professor, Department of Biological Structure, University of Washington, Seattle, Washington, 2007 – present.

 

Joint Professor, Department of Medical Education and Biomedical Informatics (Division of Biomedical and Health Informatics), University of Washington, 2007 – present.

 

Adjunct Professor, Department of Computer Science and Engineering, University of Washington, 2007 – present.

 

Director, University of Washington Structural Informatics Group, 1997-present.

http://sig.biostr.washington.edu.

 

PREVIOUS POSITIONS

 

Postdoctoral Fellow and Research Associate, University of Washington, Department of Bioengineering, Ultrasound Division, Seattle, Washington, 1974-1977

 

Research Assistant, Postdoctoral Fellow, and Interdisciplinary Ph.D. Graduate Student, Stanford University, Palo Alto, California, 1977-1984

 

Research Associate, Knowledge Systems Laboratory, Department of Computer Science, Stanford University, Palo Alto, California, 1984-1988

 

Research Assistant Professor, Department of Biological Structure, University of Washington, Seattle, Washington, October, 1988 - June, 1994

 

Adjunct Research Assistant Professor, Department of Computer Science, University of Washington, October, 1988 - June 1994

 

Research Associate Professor, Department of Biological Structure, University of Washington, Seattle, Washington, 1994-2000.

 

Adjunct Research Associate Professor, Department of Computer Science and Engineering, University of Washington, 1994-2000.

 

Adjunct Research Associate Professor, Division of Biomedical and Health Informatics, Department of Medical Education. University of Washington, 1997-2000.

 

Research Professor, Department of Biological Structure, University of Washington, Seattle, Washington, 2000 – 2007.

 

Adjunct Research  Professor, Department of Computer Science and Engineering, University of Washington, 2000 – 2007.

 

Joint Research  Professor, Department of Medical Education and Biomedical Informatics(Division of Biomedical Informatics), University of Washington, 2000 – 2007.

 

 

RESEARCH INTERESTS

 

Structural informatics, a branch of biomedical informatics dealing with methods for generating, storing, retrieving, analyzing and displaying information about the physical structure of the body. (Coined the term and defined the field of  "Structural Informatics" in 1991, see Refereed Publications #9). Primary focus  areas: biomedical information management, integration and visualization within a structural framework.

 

NATIONAL COMMITTEES, SERVICE AND HONORS

 

Fellow, American College of Medical Informatics (ACMI), elected summer 1999.

 

Editorial Board, Journal of Biomedical Informatics, January 2001 - present.

 

Editorial Board, Methods of Information in Medicine, 2003-present.

 

National Advisory Board, P41 Research Resources Grant, UCLA Laboratory of NeuroImaging, Arthur Toga, PI, 2000-present.

 

NIH Murine Atlas of Genitourinary  Development (GUDMAP) Consortium Advisory Board 2004-present.

 

Scientific Affairs Committee, American College of Medical Informatics (ACMI), 2003-2004.

 

Invited participant, National Library of Medicine workshop, Visible Human Project: Scope and Scale for the Future, Jan 16-17, 2007.

 

Invited participant, National Institute of Standards and Technology (NIST) workshop on ontology evaluation, Gaithersburg, Maryland, Oct 25-26, 2007.

 

Reviewer, American Medical Informatics Association Fall Symposium, 1989-present.

 

Editorial Board, Journal of the American Medical Informatics Association,  1999 - 2004.

 

Scientific Program Committee, International Medical Informatics Association (IMIA) Fall Symposium, 2004.

 

Scientific Program Committee, American Medical Informatics Association Fall 2000, Fall 2001 Symposia.

 

National Library of Medicine Board of Scientific Counselors, 1993-1997.

 

National advisory board, University of California at San Francisco, Medical Information Sciences Graduate Program, March 1999-2002.

 

American Association of Medical Colleges, Medical Education Software Resources Initiative, Task Force member, January 1996 - December 1996.

 

National Institutes of Health Special Study Sections

            Various, 1995-present

            Human Brain Project 1999-2006

                        Several from 1999-2002

                        Spring 2003, Winter 2004, Fall 2004, Winter 2005, Winter 2006

                       

            Biomedical Informatics Information Science Technology Initiative 2002-2003

                        Fall 2002, Winter 2003

            NIDDK RFA Murine Atlas of Genitourinary development – database

                        Summer 2004

            NIH Ad hoc study sections

                        NLM, Summer 2005 teleconference, chair

                        NLM, Summer 2006 teleconference

                        NLM, Spring 2008 teleconference

                        Spring 2009 teleconference

            P41 Site visit Ron Kikinis, Brigham and Women’s Hospital, Summer 2007

           

 

Washington State University Workshop, “Designing the future of Health Informatics Education and Discovery”, Sept 9-12, 2008. Invited participant.

 

PROFESSIONAL ORGANIZATIONS

 

ACM (Association for Computing Machinery)

AMIA (American Medical Informatics Association)

ACMI (American College of Medical Informatics)

Society for Neuroscience

 

 

ACTIVE GRANTS

 

NIH RO1 HL08770 “Realizing the Potential of Reference Ontologies for the Semantic Web”, in response to PA-05-063, Collaborations with National Centers for Biomedical Computing, 2/15/07-12/31/10, James F. Brinkley, Principal Investigator.  Query-based methods for creating simplified views of complex ontologies.

 

NIH NCRR 1 UL1 RR 025014, “Institute of Translational Health Sciences (ITHS)”, in response to RFA-RM-07-002, Institutional Clinical and Translational Science Award (CTSA), Mary L. Disis, Principal investigator. 9/1/07-5/31/12. Associate director of informatics core, with emphasis on data management and access to scientific data.

 

NIH RO1 AR051545, “Mechanisms of Tolerance to Renal Microchimerism”, Anne M Stevens, Principal Investigator,  Children’s Hospital and Regional Medical Center, 9/13/07-7/31/12. PI of  UW subcontract for informatics support: data management for observational clinical trials.

 

NIH P30NS055088, “NINDS Institutional center core grants  - Neuroproteomics P30, Richard Morrison, Principal Investigator, 8/1/08-7/31/13. PI of Core C: Bioinformatics: data management, integration and visualization for investigators.

 

RSNA-NIBIB RadLex Ontology Project, 9/30/2008-9/29/2009, Radiological Society of North America, PI of UW subcontract: creating the anatomy component of an ontology for structured reporting of radiology images.

 

 

PENDING GRANTS

 

NIH, “Ontology-based integration of human studies data”, Ida Sim, UCSF, PI, 7/1/09-6/30-12. PI of UW subcontract. Ontologies and ontology views for integrating clinical trials data.

 

Cardiovascular Image Informatics, with Harvard (Ron Kikinis, PI), 12/1/09-11/30/14,  PI of UW subcontract for ontology development for the cardiovascular informatics research grid (CVIRG).

 

Shape-Based Retrieval of 3D Craniofacial Data, (Linda Shapiro, PI), UW with Michael Cunningham, Children’s, 9/1/09-8/31/14. Co-investigator. Quantitative measures of craniofacial phenotypes.

 

PD-L1 as a Biomarker for SLE Disease Activity Versus Infection, (Anne Stevens, Childrens, PI), ARRA GO grant, 9/30/09-9/29/11. PI of UW subcontract.  Data management for clinical trials.

 

Intelligent Virtual Cadaver, with UW Institute for Simulation and Interprofessional Studies (ISIS), 6/1/10-5/30/12. Web-based 3-D system for virtual dissection.

 

The Center for Mushroom Research, (Leanna Standish, Bastyr, PI). PI of UW subcontract. Data management for clinical trials, 12/1/09-11/30/14.

 

Washington State Prematurity Research Network (Craig Reubens, Seattle Children’s PI), Life Sciences Discovery Fund Program Proposal. Co-investigator. Leadership committee, bioinformatics.

 

 

GRANTS IN PREPARATION

 

 

 

PREVIOUS GRANTS

 

NSF DBI-0543631, “Multimedia information retrieval for biological research”, Linda Shapiro, Principal Investigator, 7/1/06-6/30/09, $388,494 total cost/year.  Co-investigator. Content-based image retrieval.

 

National Institute on Deafness and Other Communication Disorders  RO1 DC/MH02310, "Structural Information Framework for Brain Mapping", a Human Brain Project grant, James F. Brinkley Principal investigator, 2/1/94-7/31/08. $250,000 average direct cost/year, $286,471 total cost/year.

 

 

UW General Clinical Research Center (GCRC) Pilot and feasibility grant application, “Beyond the spreadsheet: information management for GCRC investigators”, 3/1/06-6/30/07. $25,000 direct costs Principal investigator.

 

NIH SBIR R43 HG004295 with Yumetech, Inc., “Using visualization as an interface to heterogeneous gene expression data”, submitted in response to PA-05-003 Integration of heterogeneous data sources. 9/26-06-3/31/07, $100,000 total costs. Principal investigator of UW subcontract.

 

National Library of Medicine  P20 LM07714,  “Interdisciplinary Center for Structural Informatics”, a Biomedical Information Science Technology (BISTI) Center Planning Grant, James F. Brinkley Principal Investigator, 1/1/03-11/30/06. $420,000 average direct cost/year.

 

Defense Advanced Research Projects Agency (DARPA). Virtual Soldier Project. Co-investigator. Cornelius Rosse, Principle Investigator of UW component, 2004-2005.

National Library of Medicine RO1 LM 06822  "Foundational Model of Anatomy", Cornelius Rosse PI. Co-investigator,  6/1/99-5/30/03, $300,000 average direct cost.

 

National Library of Medicine  RO1 LM0316, "Structure-based Visual Access to Biomedical Information",  James F. Brinkley Principal Investigator, 5/1/97-4/30/03, $250,000 average direct cost/year.

 

University of Washington Initiatives Fund (UIF) to establish a degree program in Biomedical Informatics, with Ira Kalet (Principal Investigator). Co-investigator.

 

National Library of Medicine Contract  NO1 LM-0-3528 , "Anatomical knowledge sources enhancing UMLS applications",   Cornelius Rosse PI , Co-investigator, 5% effort, 9/30/2000-9/29/2001, $150,000 average direct cost.

Equipment grant from Intel Corporation, UW School of Medicine (SOM) subproject of a $5.9M gift to UW. With Sherrilynne Fuller, (Principal Investigator  for SOM subproject). 1997-1999. Co-Investigator and primary initiator of the  SOM  subproject. Thirty-two Intel computers received by the Department of Biological Structure).

 

University of Washington Initiatives Fund (UIF)  development grant to create an annotated image teaching database, Co-principal investigator, with John Clark and Kate Mulligan, 2000-2001.

 

National Library of Medicine Individual National Research Service Award for William Lober, M.D.,  "Knowledge-based Image Annotation", Sponsor.

 

National Library of Medicine RO1 LM06243, "Spatial-symbolic brain information management system", with Douglas Bowden, UW Primate Center (Principal Investigator). Co-investigator.

 

National Library of Medicine Contract  467-MZ-802300, "Adopting the NGI as a Tool for Healthcare and Information Access:  Assessment, Selection and Planning", with Brent K. Stewart (Principal Investigator), 1998-1999. Co-investigator.

 

Achievement Rewards for College Scientists, (ARCS) , $25,000 award for student training in the Digital Anatomist Program, $5000/year starting  1991. Principal Investigator.

 

National Cancer Institute 1R29 CA59070-01 FIRST award, "Medical Image Segmentation Using Knowledge of Anatomy", 7/1/92-6/30/97. Principal Investigator.

 

National Institute of Child Health and Human Development. "Ultrasonic Measurement of Fetal Volume and Weight", with W.D. McCallum (Principal Investigator), 7/1/79-6/30/81. Co-investigator.

 

Individual National Research Service Award (NIH Fellowship Grant), National Institute of General Medical Science.  "Ultrasonic Three-Dimensional Organ Modeling", 7/1/81 - 6/30/84, $56,388. Principal Investigator.

 

National Library of Medicine,  "Wide Area Client-Server Model for Accessing Structural Information, subcontract  to "Regional Medical Libraries Contract Enhancement Proposal N01-LM-1-3506,  Sherrilynne Fuller, Principal Investigator, 11/1/92-10/30/93.  Principal Investigator on subcontract.

 

National Library of Medicine grant number 1R01LM04925, "Image-based Knowledge System in Anatomy", with Cornelius Rosse, Principal  Investigator, 7/1/88-6/30/93. Co-Investigator.

 

National Science Foundation  IRI-9116809, "A Visual Database System for Computer Vision Research", with Linda Shapiro (Principal Investigator), 3/1/92-2/28/94. Co-Investigator.

 

Equipment grant from IBM: RS6000 workstation and X Terminal, 1992.

 

National Library of Medicine Individual National Research Service Award for Loyd Myers, F37 LM00017-01, "Structural Medical Image Segmentation", 10/1/92-9/30/95, Sponsor.

 

TEACHING ACTIVITIES

 

Currently supervised personnel

Graduate students

Hao Li, PhD student in Biomedical and Health Informatics, 2001-present (supervisor)

Wayne Warren, PhD student in Biomedical Informatics, 2003-present (supervisor)

Marianne Shaw , PhD student in Computer Science and Engineering, 2007-present (co-supervisor, with Dan Suciu)

Noah Benson, PhD student in Biomedical and Health Informatics, 2008-present (thesis committee)

Indriyati Atmosukarto, PhD student in Computer Science and Engineering, 2008-present (thesis committee)

Max Neal, PhD student in Biomedical and Health Informatics, 2008-present (thesis committee)

Andrew Simms, PhD student in Biomedical and Health Informatics, 2009-present (thesis committee)

Jiun-Hung Chen, PhD student in Computer Science and Engineering, 2009-present (thesis committee)

 

 

 

Undergraduate students

 

Postdoctoral fellows

 

Research staff

Todd Detweiler – Research Scientist

Joshua Franklin  - System Administrator/Programmer

Jose LV Mejino – Research Scientist

Ron Shaker – Programmer

Xenia Hertzenberg - Programmer

 

 

Previously supervised personnel  at UW

Graduate Students

Katarzyna Wilamowska, PhD student in Computer Science and Engineering, 2008-2009 (thesis committee)

Rosalia Tungaraza, PhD student in Computer Science and Engineering, 2008-2009 (thesis committee)

Terry Shen, PhD student in Biomedical and Health Informatics, 2007-2009 (thesis committee)

Melissa Clarkson, PhD student in Biomedical and Health Informatics, Fall 2008 lab rotation (supervisor)

Antoine Puget, MS student at KTH in Sweden, visiting scholar Winter, Spring 2008 (supervisor)

Mike Galdzicki, PhD student in Biomedical and Health Informatics, Winter 2008 lab rotation (supervisor)

Gary Yngve, PhD student in Computer Science and Engineering, 2006-2008 (co-supervisor, with Linda Shapiro)

Max Neal, PhD student in Biomedical and Health Informatics, 2006 (supervisor)

Wilmot Wei-mau Li, PhD student in CSE, 2004-2007 (co-supervisor, David Salesin chair)

Xiang Li, MS student in Biomedical Informatics, 2005-2006 (supervisor)

Chaitee Sengupta,  MS student in Speech and Hearing Sciences, 2006-present (supervisor for hourly work study)

Jill Lin, PhD student in Biomedical and Health Informatics, 2004-present (thesis committee, Linda Shapiro chair)

Jenny Thompson,  MS student in Speech and Hearing Sciences, 2004-present (co-supervisor, David Corina chair)

Sally Lee, PhD student in Biomedical Informatics, 2004-2005 (co-supervisor, Peter Tarczy-Hornoch, chair)

Hansang Cho, PhD student in EE, 2004-2005 (co-supervisor, Linda Shapiro chair)

Kelan Wang, MS student in Biomedical Informatics 2004-2005 (co-supervisor, Peter Tarczy-Hornoch, chair)

Veronica Smith, MS student in EE, 2003-2005 (co-supervisor, Linda Shapiro chair)

Christine Fong, MS student in Biomedical Informatics, 2003-2005 (supervisor)

Shobhit Mathur, PhD student in CSE, 2005 spring quartyer (co-supervisor, Dan Suciu chair)

Chris Re, PhD student in CSE, 2004-2005 (co-supervisor,  Dan Suciu chair)

Erin Gibson, MS student in Speech and Hearing Sciences, 2002-2004 (co-supervisor, David Corina chair)

Yana  Kadiyska, PhD student in CSE, summer 2002-December 2003 (co-supervisor, Dan Suciu chair)

Salvador Ruiz-Correa, PhD student in EE, summer 2002-2004 (co-supervisor, Linda Shapiro chair)

Vishrut Srivastava, MS student in Biomedical and Health Informatics, 2002 (supervisor)

Jessica Wilkinson, PhD student in Biomedical and Health Informatics, 2002 (supervisor)

Shawn Bonham, MS student in Computer Science, 2001-2002 (supervisor)

Karen Kinbar, MS student in Speech and Hearing Sciences, 2000-2002 (co-supervisor, David Corina chair)

Ravensara Travillian, MS student in Biomedical and Health Informatics, 2000-2001 (supervisor)

Zhenrong Qian , Phd student in Computer Science, 2001-present (quals committee, Linda Shapiro chair)

Kevin Hinshaw - Ph.D. -  student in Computer Science, 1992-2000 (supervisor).

Evan Albright  - M.S. student in Electrical Engineering, 1999-2000  (co-supervisor, Linda Shapiro chair).

Theresa Storheden – Visiting MS CS student from Sweden, supervisor for thesis project, 1999-2000

Jakob Skott – Visting MS CS student from Sweden, supervisor for thesis project, 1999-2000

Keith Steury -Ph.D. student in Cognitive Psychology, 1998-1999 (co-supervisor, with David Corina).

Rex Jakobovits - Ph.D. student in Computer Science, 1995-1999 (supervisor).

Jake Wegelin - Ph.D. student in Statistics, 1997-1999 (co-supervisor, with Paul Sampson).

Ken Thornton - PhD student in EE, 1993-1996 (thesis committee)

David Meyers - PhD student in CS, 1994 (grad faculty representative for PhD thesis).

James Ahrens - PhD student in EE, 1994-1996 (thesis committee)

Michael Geist, medical student, 1992-1993. (supervisor).

Teresa Lassek - MS student in Computer Science, 1992 (supervisor).

Andy Goodman, PhD student in EE, 1989-1990 (co-supervisor, with Bob Haralick).

Dan Benson PhD student in EE, 1990-1992. (co-supervisor, with Greg Zick).

Soohyung Kim MS student in EE, 1992 (co-supervisor, with  Linda Shapiro).

Masaharu Kobashi, MS student in CS, 1991-1992 (co-supervisor, with Linda Shapiro).

John Strupp, MS student in EE, 1990-1992 (co-supervisor, with  Bob Haralick).

Radhika Thekkath, Phd student in CS, 1992-1995 (grad faculty representative for PhD thesis).

Chun-Fe Yeung, PhD student in CS, 1989 (grad faculty representative for PhD thesis).

Gene Lee, medical student, 1989-1990.

Ken Gershing, medical student, 1989-1991.

 

Postdoctoral

Jeff Zavaleta, Anethesiology Fellow, 2007-2008, research mentor

Kate Mulligan – lecturer, 1998-2001 (supervisor for 10% time on brain grant).

Bill Lober, M.D, postdoctoral fellow, 1998-2001 (supervisor)

Jill Gardner - Research assistant professor  in Radiology (supervisor for 20% time on brain grant).

Andrew Poliakov, Ph.D. - postdoctoral fellow, 1998-2000 (supervisor)

Bharath Modayur, Ph.D.  - postdoctoral fellow, 1995-1997 (supervisor).

Loyd Myers - Postdoctoral fellow, 1992-1995 (sponsor).

Greg Heil - Postdoctoral fellow, January 1994-December 1995.

Janet E. Durik, MD - MS in Biological Structure, 1994

            joint Radiology/Biogical Structure MS program  (supervisory committee).

 

 

Undergraduates

J.E. Mejino, UW undergraduate, pre-CS major 2002-2007 (supervisor)

Peter Lincoln, UW senior undergraduate major, 2005-present (supervisor of senior honors project)

Nathan Bales, UW CSE undergraduate, 2004-2005(co-supervisor, with Dan Suciu)

Kelly Boccia, Biomedical Informatics Summer 2004 Undergraduate Research Program (supervisor)

Fraser Kitchell, Amherst College, 10 weeks summer 2004 (supervisor).

Xenia Guertsenberg, UW undergraduate in CSE, 2002-December, 2003 (supervisor)

Chris Grierson, UW undergrad in applied math  2001-2003 (supervisor)

Chevas Balloun, UW undergrad, 2002-present (supervisor)

J.J. Cheng,  undergrad in Computer Science, 2002-2002(supervisor)

Ho Joon “Felix” Lim,  undergrad in Computer Science, 2001-2002 (co-supervisor, with Linda Shapiro)

Eider Moore, Harvey Mudd undergrad in computer science, summer 2001-2002 (supervisor)

Greg Distelhorst, Yale undergraduate, summer 2002 (supervisor)

Kevin Yang, Amherst undergraduate, summer 2002 (supervisor)

Evgeny Roubinchtein – undergraduate student in Computer Science, 1999-2000 (supervisor).

Kuang Chen - undergraduate Computer Science major hopeful, 2000 (Gen Studies project)

Kelly Mayes - Undergraduate student in Computer Science, 1999 (co-supervisor for senior project).

Ben Wong --undergraduate in Computer science, 1997-1998 (supervisor).

Bibek Pandey - undergraduate student in Computer Science, 1997-1998(supervisor).

Deepa Dinendra - part-time student, 1996-1997 (supervisor)

Scott W. Bradley - undergraduate student in Computer Science, 1995-1997  (supervisor).

Bethany SaintClair - undergraduate student in Computer Science  1997 (supervisor for senior project)

Phil Shen - undergraduate in Computer Science, 1992-1993. CS Project.

Tanya Deriugin, premedical student, 1990-1992 (supervisor).

Steve Barney, pre-doctoral student , 1989-1990.

 

 

Staff

Andrew Poliakov – Research Scientist

Eider Moore - Programmer

Richard Martin – Research Scientist

Xenia Guertsenberg, Programmer

Kevin Hinshaw – Research Scientist

Scott Brockenbrough, Acting Instructor

Augusto Agoncillo – Research Scientist

Chris Grierson, System Administrator

 

Course Participation

MEBI 534, Biology and  Informatics, 1999-present, Course director  starting Fall 2002-present

MEBI 591B, Translational Informatics Research Seminar, Course director, Winter 2009

MEBI 591B/CSE590R, Virtual Human Research Seminar, Course director, 2005-2006.

MEBI 591C/CSE 590R, Structural Informatics Research Seminar, Course director, 1997-2005

MEBI 530, Introduction to Medical Informatics, 1999-2004

MEBI 532 , Java section for Introduction to Computing for Informaticists, 2001

MEBI 590, Special Topics in Biomedical and Health Informatics, 1995-present

MEBI 591, Biomedical and Health Informatics Research Colloquium, 2000-2005

MEBI 700, Independent study or research in biomedical informatics. 1999-present

CSE498, Senior Project, 1995-present

CSE520, Computer Science Colloquium, 1995

CSE590BR, Structural Informatics Research Seminar (course co-director), 1997-2006

CSE 600, Independent Study or Research, 1995-present

CSE 800, Doctoral Dissertation, 1995-present

 

Teaching Administration

Division of Biomedical and Health Informatics: Admissions committee, student quals committee

 

UNIVERSITY OF WASHINGTON  COMMITTEES AND SERVICE

 

Department of Biological Structure, Faculty Planning Committee, 2003-present.

 

Institute of Translational Health Sciences (ITHS), Small Grants Committee, 2008-2009.

 

School of Medicine Committee on Research and Graduate Education (CORGE), 2003-2006.

 

UW Faculty Senate, 2004-2006

 

Department of Biological Structure, Faculty Development Committee, 2002.

 

Division of Biomedical and Health Informatics: Faculty search committee, 2001.

 

Department of Computer Science and Engineering: Reviewer of faculty applicants, 2001-present.

 

Integrated Academic Medical Information Systems (IAIMS) Educational Systems advisory committee, 1994-1997.

 

Integrated Academic Medical Information Systems (IAIMS) Futures/Forecasting/Planning Group, 1994-1997.

 

Committee to  prepare a  University Initiative Fund (UIF) proposal for a graduate degree   in Medical Informatics, 1998-1999.

 

Department of Biological Structure, Departmental Web Server Committee, chair, March 1, 1995-1997.

 

Department of Biological Structure, Computer Graphics Committee, Oct 1989-1992.

 

University of Washington IAIMS Research Planning Committee, Jan 1991-Dec 1992.

 

NATIONAL INVITED TALKS

 

6/21/89                        National Library of Medicine Planning Panel on Electronic Imaging, Washington, D.C.

 

7/17/90                        National Cancer Institute Workshop on 3D Display and Analysis for Cancer Treatment Planning, Washington, D.C. "Knowledge-Based Medical Imaging".

 

2/12/91                        Stanford University Medical Informatics Research Colloquium, "The University of Washington Digital Anatomist Program".

 

10/15/92          NorthWestNet Annual Meeting, Portland, "The University of Washington Digital  Anatomist Program and its Application to Wide Area Structural Information Retrieval".

 

10/25/92          National Institute of Mental Health, The Human Brain Project, Anaheim, Ca.

 

2/21/94                        American Association for the Advancement of Science Annual meeting, San Francisco.The Digital Anatomist Program, In Imaging Systems for Health Education and Health Care, Michael Ackerman, organizer.

 

2/22/94                        National Network of Libraries of Medicine: Technology Awareness/Transfer Conference, University of California at San Francisco, Feb 22, 1994, "The Digital Anatomist Project".

 

4/16/94                        Iowa State University, "The Digital Anatomist Program".

 

5/24/94                        American Society for Information Science Mid Year Meeting, Portland, Oregon, "Empowering Medical Applications via the Network", panelist  with William Hersh and Robert Greenes.

 

11/6/94                        Tutorial:  Knowledge-based Medical  Image Representation, Analysis, and Management, with Casimir Kulikowski and Leiguang Gong, Eighteenth Symposium for Computer Applications  in Medical Care, November 5, 1994.

 

2/25/98                        National Institute of Dental Research workshop on the Virtual Head and Neck, Bethesda, “Building an anatomy information system”.

 

2/27/98                        National Insitutes of Health Bioengineering Symposium, Bethesda, “The Digital Anatomist Project”.

 

2/27/98                        National Insitutes of Health Bioengineering Symposium, Bethesda, “The UW Human Brain  Project”.

 

11/2/98                        Second Visible Human Project Conference, panelist. "Knowledge Representation and Structured Information in the Visible Human Project".

 

2/26/99                        Stanford University Medical Informatics Research Colloquim, "The Digital Anatomist Information System".

 

3/22/99                        National Institutes of Health Human Brain Project Workshop on Interoperability of Brain Project Databases.

 

6/26/00                        “Web-based experiment management and visualization for multimedia brain mapping data”, International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS ‘2000), Las Vegas, Nevada.

 

10/12/00          “Web-based integration and visualization of multimedia human cortical language map data”, Annual Fall Meeting of the Biomedical Engineering Society, Seattle.

 

11/3/01                        “Tool for Language Mapping”, Society for Neuroscience Satellite Symposium  on Neuroimaging databases and analytical tools, San Diego.

 

1/14/03                        National Institutes of Health, Biomedical Information Science Technology Initiative (BISTI) planning workshop, Washington, DC.

 

1/29/05                        “Towards Open Source, Standardized Resources for Digital Anatomy”, as part of a panel on “Use and Value of an Open 3D Standard for Medical Applications: Impact, Plans and Progress of the Medical Working Group of the Web3D Consortium”, presented at the 13th Annual Conference on Medicine Meets Virtual Reality, Long Beach, Jan 26-29, 2005.

 

12/11/06          Structure-based “in-between”  strategies for data integration: lessons from the Human Brain Project. Plenary talk at NIH Conference on Knowledge Environments in Biomedical Research

 

1/24/07                        “Managing, Integrating and Visualizing Biomedical Research Data: Lessons from the Human Brain Project”, Vanderbilt University informatics research seminar

 

6/1/07              “Realizing the potential of reference ontologies for the semantic web”, Web presentation to the Stanford National Center for Bioontology.

 

6/26/07                        Vanderbilt University conference on Frontiers in Imaging Science, “Imaging Informatics”.

 

4/21/08                        Western states collaboratory and INBRE PI meeting, Denver, Colorado, “The Institute for Translational Health Science”.

 

5/13/08                        “Ontology views: an update”, Web presentation to the Stanford National Center for Bioontology.

 

6/17/08                        “Data management, integration and visualization in a structural framework”, featured speaker at the business luncheon of the Medical Section, Biomedical and Life Sciences Division, Special Libraries Association Annual Conference, Seattle, WA.

 

3/17/09                        “Distributed XQuery-based Integration and Visualization of Multimodality Brain Mapping Data”, AMIA Summit on Translational Bioinformatics, San Francisco.

 

4/15/09                        “Ontology views: an update”, Web presentation to the Stanford National Center for Bioontology.

 

 

 

 

           

 

UNIVERSITY OF WASHINGTON  INVITED TALKS

 

12/6/88                        University of Washington Computer Science  Research Seminar  "Towards the Scientist's Workbench".

 

1/16/90                        University of Washington Computer Science Artificial Intelligence in Medicine Seminar, "Towards a Knowledge Base of Structural Biology".

 

11/14/90          University of Washington Scientific Visualization Seminar , "The University of Washington Digital Anatomist Program".

 

1/14/91                        University of Washington Imaging Research Seminar, "Interactive Medical Image Segmentation Using Knowledge of Anatomic Shape".

 

6/16/92                        University of Washington IAIMS site visit, "The University of Washington Digital Anatomist Program".

 

6/18/92                        IBM - University of Washington Research Workshop on Digital Radiology, "The University of Washington Digital Anatomist Program" and "Knowledge-Based Medical Image Segmentation".

 

4/12/93                        University of Washington Imaging Research Seminar, "Structural Informatics, the UW Digital Anatomist Program and Medical Imaging".

 

4/28/93                        University of Washington Health Information Sciences Lecture Series, "The UW Digital Anatomist Program and its Relationship to Structural Information and IAIMS".

 

3/30/94                        University of Washington Health Information Sciences Lecture Series, "Structural Informatics and the Digital Anatomist Program".

 

5/1/95              University of Washington Health Information Sciences  Lecture  Series, "The Human Brain Project: A Structural Information Framework for Brain Mapping"

 

1/23/96                        University of Washington Health Information Sciences  Lecture Series, "The Digital Anatomist on the World Wide Web", with Scott W. Bradley.

 

4/1/96              University of Washington Imaging Research Seminar, "Image-Based Systems in Anatomy".

 

4/1/97              University of Washington Health Information Sciences Lecture Series, "Structural Informatics Research in the Digital Anatomist Program".

 

5/27/97                        University of Washington Computer  Science Research Seminar, "Structural Informatics Research in Biological Structure".

 

8/29/01                        University of Washington Neurosurgery seminar, “UW Human Brain Project”.

 

10/29/01          University of Washington Imaging Research Seminar, “The UW Human Brain Project”.

 

2/12/02                        University of Washington, MedEd 590, Special Topics in Biomedical and Health Informatics, “The UW Structural Informatics Group”.

 

2/26/02                        University of Washington, MedEd 591, Biomedical and Health Informatics Research Colloquium,  “Discussion of the UW Human Brain Project renewal proposal and how it came about". 

 

1/28/03                        University of Washington, MedEd 591, Biomedical and Health Informatics Research Colloquium,  “BISTI planning proposal to create an Interdisciplinary Center for Structural Informatics".

 

5/3/03              Pacific Northwest Chapter, BioCommunications Association, Inc. Spring Meeting, University of Washington. “The Digital Anatomist Information System”. Keynote speaker.

 

10/23/03          University of Washington, Science in Medicine Lecture. “Structural informatics and its applications in medicine and biology”.

 

5/23/05                        University of Washington, Frontiers in Biomedical Research Symposium, Breakout session leader, “Beyond the spreadsheet: Informatics tools for management of local lab data, and integration of those data in large scale biomedical information networks”.

 

4/4/06              University of Washington, MEBI 591, Biomedical and Health Informatics Research Colloquium, “The Integrated Brain”.

 

12/5/06                        University of Washington, Biomedical Informatics Research Seminar (MEBI 590), “Managing, Integrating and Visualizing Biomedical Research Data”.

 

1/8/07              University of Washington, Neurobiology and Behavior Research Seminar, "Neuroinformatics for integrating and visualizing brain mapping data, with application to language processing"

 

10/30/07          University of Washington, Biomedical Informatics Research Seminar (MEBI 590), “Imaging Informatics and its Application in the UW Structural Informatics Group”.

 

4/24/08                        University of Washington, Translational Informatics Research Seminar, "Beyond the Spreadsheet: An Approach to Developing Information Management Tools for Small-scale Clinical Investigators", with Anne Stevens

 

5/21/08                        University of Washington, Dept of Computer Science and Engineering, Seminar on Artificial Intelligence in Biology (CSE 590A), “Ontology Views”.

 

11/4/08                        University of Washington, Biomedical Informatics Research Seminar (MEBI 590), “Towards a structural framework for managing, integrating and visualizing biomedical information: Current research in the UW Structural Informatics Group”.

 

12/5/08                        University of Washington, Guest lecture, Bioengineering 498C: Neural Engineering, Albert Folch, Course director, “The UW Human Brain Project”.

 


JAMES F. BRINKLEY

 

Refereed Publications

*invited

 

Refereed  Journal Papers

 

1.     Brinkley, J. F., Moritz, W. E. and Baker, D. W.  1978  Ultrasonic three-dimensional imaging and volume from a series of arbitrary sector scans.  Ultrasound Med. Biol. 4: 317-327.

 

2.     McCallum, W. D. and Brinkley, J. F.  1979  Estimation of fetal weight from ultrasonic measurements.  Amer. J. Obstet. Gynecol. 133(2): 195-200.

 

3.     Brinkley, J. F., Muramatsu, S. K., McCallum, W. D. and Popp, R. L.  1982  In vitro evaluation of an ultrasonic three-dimensional imaging and volume system.  Ultrasonic Imaging 4: 126-139.

 

4.     Brinkley, J. F., McCallum, W. D., Muramatsu, S. K. and Liu, D. Y.  1982  Fetal weight estimation from ultrasonic three-dimensional head and trunk reconstructions:  evaluation in vitro.  Amer. J. Obstet. Gynecol. 144(6): 715-721.

 

5.     Brinkley, J. F., McCallum, W. D., Muramatsu, S. K. and Liu, D. Y.  1984  Fetal weight estimation from lengths and volumes found by ultrasonic three-dimensional measurements.  J. Ultrasound Med. 3: 163-168.

 

6.     Brinkley, J. F.  1985  Knowledge-driven ultrasonic three-dimensional organ modelling.  IEEE Trans. Pattern Analysis and Machine Intelligence: PAMI-7(4): 431-441.

 

7.     Duncan, B., Buchanan, B., Hayes-Roth, B., Lichtarge, O., Altman, R., Brinkley, J., Hewett, M., Cornelius, C. and Jardetzky, O.  1987  PROTEAN:  A new method for deriving solution structures of proteins.  Bull. Mag. Res. 8(3/4): 111-119.

 

8.     Brinkley, J. F., Altman, R. B., Duncan, B. S., Buchanan, B. G. and Jardetzky, O.  1988  The heuristic refinement method for the derivation of protein solution structures:  Validation on cytochrome-b562.  J. Chem. Information and Computer Science   28(4): 194-210.   

 

9.     *Brinkley, J.F. 1991  Structural informatics and its applications in medicine and biology. Academic Medicine 66(10):589-591.

 

10.  Sundsten, J.W., Brinkley, J.F., Conley, D.M., Eno, K., Kastella, K.G. and Rosse, C.  1992 Three-dimensional computer graphics reconstructions of anatomy on videodisc. J. Audiovisual Media in Medicine 15:65-67.

 

11.  Brinkley, J.F. 1993 A flexible, generic model for anatomic shape: application to interactive two-dimensional medical image segmentation and matching. Computers and Biomedical Research 26:121-142.

 

12.  Brinkley, J.F., Eno, K. and  Sundsten, J.W. 1993 Knowledge-based client-server approach to structural information retrieval: the Digital Anatomist Browser. Computer Methods and Programs in Biomedicine 40:131-145.

 

13.  Dailey, D.J., and Brinkley, J.F. 1996  A metric for quantifying response time in a browser application. IEEE Trans. Systems, Man and Cybernetics, Part A (Systems and Humans 26(2):271-275.

 

14.  Brinkley, J.F. and Prothero, J.S. 1997   Slisp: A flexible software toolkit for hybrid, embedded and distributed applications. IEEE Software -- Practice and Experience 27(1):33-48.

 

15.  Jakobovits, R.M., Lewis, L.M., Ahrens, J.P., Shapiro, L.G., Tanimoto, S.L. and Brinkley, J.F. 1996 A visual database system for scientific research.  J. Visual Languages and Computing 7:361-365.

 

16.  *Brinkley, J.F. and Rosse, C. 1997 The Digital Anatomist distributed framework and its application to knowledge based medical imaging. J. American Medical Informatics Association 4(3):165-183. Selected for inclusion in the 1998 Yearbook of Medical Informatics.

 

17.  Brinkley, J.F., Bradley, S.W., Sundsten, J.W. and Rosse, C.  1997 The Digital Anatomist information system and its use in the generation and delivery of Web-based anatomy atlases. Computers and Biomedical Research 30: 472-503.

 

18.  *Rosse, C., Mejino, J.L., Modayur, B.R., Jakobovits, R.M., Hinshaw, K.P. and Brinkley, J.F. 1998 Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist symbolic knowledge base. J. American Medical Informatics Association 5(1):17-40.

 

19.  Modayur, B.R., Prothero, J.S., Ojemann, G.A., Maravilla, K. and Brinkley, J. 1997 Visualization-based mapping of language function in the brain. Neuroimage. 6:245-258.

 

20.  *Brinkley, J.F., Wong, B.A., Hinshaw, K.P. and Rosse, C. 1999 Design of an anatomy information system. IEEE Computer Graphics and Applications. 19(3):38-48.

 

21.  Corina, D.P., McBurney, S.L., Dodrill, C., Hinshaw, K., Brinkley, J. and Ojemann, G. 1999 Functional roles of Broca's Area and SMG: Evidence from cortical stimulation mapping in a deaf signer. Neuroimage. 10:570-581.

 

22.  Kim, S., Brinkley, J.F., and Rosse, C. 2003 A profile of on-line anatomy information resources: Design and instructional implications. Clinical Anatomy 16:55-71.

 

23.  Hinshaw, K.P., Poliakov, A.V., Moore, E.B., Martin, R.F., Shapiro, L.G. and Brinkley, J.F. 2002 Shape-based cortical surface segmentation  for visualization brain mapping. Neuroimage 16(2):295-316.

 

24.  Corina DP, Steury K, Poliakov AV, Martin RF, Mulligan KA, Maravilla K, Lettich E, Brinkley JF, Inuoe K, Ojemann G. A comparison of language function derived from cortical stimulation mapping and fMRI: data from object naming. Submitted 2001.

 

25.  Jakobovits, R.M., Rosse, C., Brinkley, J.F. 2002 WIRM: An open source toolkit for building biomedical web applications. JAMIA 9(6):557-590.

 

26.  Brinkley, J.F. and Rosse, C. 2002 Imaging informatics and the Human Brain Project: the Role of Structure. Haux, R. and Kulikowski, C (eds.), Yearbook of Medical Informatics, Stuttgart, Germany, Schattauer, pp. 111-128.

 

27. Brinkley, J.F. and Rosse, C. 2002. Imaging and the Human Brain Project: a review. Methods of Information in Medicine 41: 245-260.

 

28.  Corina DP, Gibson EK, Martin RF, Poliakov A, Brinkley JF, Ojemann  GA. Dissociation of action and object naming: evidence from cortical stimulation mapping. Human Brain Mapping 2005; 24(1):1-10.

 

29.  Mork P, Brinkley JF, Rosse C. OQAFMA Querying Agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to  large semantic networks. J. Biomedical Informatics 2003;36(6):501-517.

 

30.  Shapiro, L.G., Chung, E., Detwiler, L.T., Mejino, J.L.V., Agoncillo, A.V., Brinkley, J.F. and Rosse, C. 2005. Processes and problems in the formative evaluation of an interface to the foundational model of anatomy. J. American Medical Informatics Association  12:35-46.

 

31.  Poliakov AV, Albright E, Hinshaw KP, Corina DP, Ojemann G, Martin RF, Brinkley JF. Server-based approach to web visualization of integrated 3-D brain imaging data. Journal of the American Medical Informatics Association  2005;12(2):140-151.

 

32.  Poliakov A, Hertzenberrg X, Moore EB, Corina D, Ojemann GA, Brinkley JF. Unobtrusive integration of data management with fMRI analysis. Neuroinformatics  5(1):3-10, 2007.

 

33.  Anderson NR, Lee ES, Brockenbrough JS, Minie ME, Fuller S, Brinkley J, Tarczy-Hornoch P. Issues in biomedical research data management and analysis: needs and barriers. Journal of the American Medical Informatics Association, 14(4): 478-488, 2007.

 

34.  Moore, EB, Poliakov, AV, Lincoln, P, Brinkley, JF. MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. BMC Bioinformatics, 8:389-, 2007. http://www.biomedcentral.com/1471-2105/8/389.

 

35.  Yuen, J, Li, Y, Shapiro, LG, Clark, JI, Arnett, A, Sage, EH, Brinkley, JF 2008. Automated, computerized, feature-based phenotype analysis of slit lamp images of the mouse lens. Experimental Eye Research. 2008;86(4):562-575.

 

36.  Altman RB, Balling R, Brinkley JF, Coiera E, Consorti F, Dhansay MA, Geissbuhler A, Hersh W, Kwankam SY, Lorenzi NM, Martin-Sanchez F, Mihalas GI, Shahar Y, Takabayashi K, Wiederhold G. Commentaries on "Informatics and medicine: from molecules to populations". Methods Inf Med 2008;47(4):296-317.

 

37.  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/.

 

38.  Tungaraza, RF, Guan, J, Shapiro, LG, Brinkley, JF, Ojemann, J, and Franklin, JD. “A Similarity Retrieval Tool for Functional Magnetic Resonance Imaging (fMRI) Statistical Maps". Artificial Intelligence in Medicine. In Press 2009.

 

 

 

 

Refereed Proceedings Papers

 

39.  Brinkley, J. F., Moritz, W. E. and Baker, D. W.  1977  A technique for imaging three-dimensional structures and computing their volumes using non-parallel ultrasonic sector scans.  Proceedings of the 22nd Annual Conference, AIUM, Dallas, October, 1977, pp. 471-474.

 

40.  Brinkley, J. F. and McCallum, W. D.  1982  Organ volume determination by ultrasonic three-dimensional reconstruction.  Proceedings of the First AMIA Congress on Medical Informatics, American Medical Informatics Association, San Francisco, May, 1982, pp. 178-182.

 

41.  Hayes-Roth, B., Buchanan, B., Lichtarge, O., Hewett, M., Altman, R., Brinkley, J., Cornelius, C., Duncan, B. and Jardetzky, O.  1986  PROTEAN:  Deriving protein structure from constraints.  Proceedings of the Fifth National Conference on Artificial Intelligence, American Association for Artificial Intelligence, Philadelphia, Pennsylvania, August 11-15, 1986, pp. 904-909. 

 

42.  Brinkley, J. F.  1988  Representing biologic objects as geometric constraint networks.  Proceedings, 1988 Spring Symposium Series:  Artificial Intelligence in Medicine, American Association for Artificial Intelligence, Stanford University, March 22-24, pp. 7-8.

 

43.  Brinkley, J. and Prothero, J.  1989  Towards a knowledge-based system of structural biology.  Eng. Med. Biol. 11th Annual Conference, pp. 1841-1842.

 

44.  Brinkley, J. F., Prothero, J. S., Prothero, J. W. and Rosse, C.  1989  A framework for the design of knowledge-based systems in structural biology.  Proc. 13th Annual Symposium on Computer Application in Medical Care, pp. 61-65.

 

45.  Brinkley, J.F.  1990  Towards a knowledge base of structural biology.  Proceedings, 1990  Spring Symposium Series: Artificial Intelligence in Medicine, American Association for Artificial Intelligence, Stanford University, March 27-29, 1990, pp. 24-25.

 

46.  Brinkley, J.F.  1991  Semi-automatic  medical image segmentation using knowledge of anatomic shape.  Proceedings, SPIE Medical Imaging V: Image Processing, San Jose, California, February 27-March 1, 1991, pp 78-87.

 

47.  Brinkley, J.F.  1991  Spatial anatomic knowledge for 2-D interactive medical image segmentation and matching.   Proceedings, 15th Annual Symposium on Computer Applications in Medical Care, Washington, D.C., November 17-20, 1991, pp. 460-464.

 

48.  Eno, K., Sundsten, J.W. and Brinkley, J.F.  1991  A multimedia anatomy browser, incorporating a knowledge base and 3-D images. Proceedings, 15th Annual Symposium on Computer Applications in Medical Care, Washington, D.C., November 17-20, 1991, pp. 727-731.

 

49.  Brinkley, J.F.  1992 Hierarchical geometric constraint networks as a representation for spatial structural knowledge. Proceedings, 16th Annual Symposium on Computer Applications in Medical Care, Baltimore, M.D., November 8-11, 1992, pp. 140-144.

 

50.  Altman, R.B. and Brinkley, J.F. 1993 Probabilistic constraint satisfaction with structural models: application to organ modelling by radial contours. 17th Symposium on Computer Applications in Medical Care, Washington, DC, Oct 31-Nov 3, 1993, pp 492-497.

 

51.  Dailey, D.J., Eno, K., Zick, G.L. and Brinkley, J.F. 1993 A network model for wide area access to structural information. 17th Symposium on Computer Applications in Medical Care, Washington, DC, Oct 31-Nov 3, 1993, pp 497-501.

 

52.  Shapiro, L.G., Tanimoto, S.L., Brinkley, J.F., Ahrens, J.P., Jakobovits, R.M. and Lewis, L.M. 1994   A visual database system for data and experiment  management in model-based computer vision. Proceedings of the Second CAD-Based Vision Workshop, February, pp 64-72.

 

53.  Brinkley, J.F. 1994 A distributed, object-oriented framework for medical image management and analysis: application to evaluation of medical image segmentation techniques. Proceedings,  IEEE Workshop on Biomedical Image Analysis, Seattle, June 24-25, 1994. IEEE Computer Society Press pp 194-203.

 

54.  Dailey, D.J., Eno, K., and Brinkley, J.F. 1994 Performance evaluation of a distance learning program. Journal of the American Medical Informatics Association, Symposium Supplement, pp 76-80.

 

55.  Hinshaw, K.P., Altman, R.B. and Brinkley, J.F. 1995   Shape‑based models for interactive segmentation of medical images. SPIE Medical Imaging: Image Processing, San Diego, CA, Feb 26 ‑ Mar 2, 1995, pp 771-780.

 

56.  Myers, L.M. and Brinkley, J.F. 1995  Visualization of brain surface features using registered partially segmented MRI scans.  IEEE Medical Imaging: Image Display, San Diego, CA, Feb 26 ‑ Feb 28, 1995, pp 43-52.

 

57.  Bradley, S.W., Rosse, C. , and Brinkley, J.F. 1995 Web-based access to an online atlas of anatomy: the Digital Anatomist Common Gateway Interface. Journal of the American Medical Informatics Association, Symposium Supplement, pp 512-516. Nominated for best paper.

 

58.  Rosse, C., Ben Said, M., Eno, K.E., and Brinkley, J.F. 1995 Enhancements of anatomical information in UMLS knowledge sources. Journal of the American Medical Informatics Association, Symposium Supplement, pp 873-877. Nominated for best paper.

 

59.  Modayur, B.R., Prothero, J., Rosse, C., Jakobovits, R. and Brinkley, J.F. 1996 Visualization and mapping of neurosurgical functional data onto a 3-D MR-based model of the brain surface. Journal of the American Medical Informatics Association, Symposium Supplement, pp 304-308.

 

60.  Jakobovits, R.M., Modayur, B. and Brinkley, J.F. 1996 A Web-based repository manager for brain mapping data. Journal of the American Medical Informatics Association, Symposium Supplement, pp 309-313.

 

61.  Hinshaw, K.P. and Brinkley, J.F. 1997 Shape-based interactive three-dimensional medical image segmentation, in Hanson, K.M. (ed.),  SPIE Medical Imaging: Image Processing 3034:236-242.

 

62.  Modayur, B.R., Jakobovits, R.M., Maravilla, K., Ojemann, G.A. and Brinkley, J.F. 1997 Evaluation of a visualization-based approach to functional brain mapping. Journal of the American Medical Informatics Association, Symposium Supplement, pp 429-433.

 

63.  Jakobovits, R.M. and Brinkley, J.F. 1997 Managing medical research data with a Web-interfacing repository manager. Journal of the American Medical Informatics Association, Symposium Supplement, pp 454-458.

 

64.  Hinshaw, K.P. and Brinkley, J.F. 1997 Using 3-D shape models to guide segmentation of MR brain images. Journal of the American Medical Informatics Association, Symposium Supplement, pp 469-473.  Awarded second place, student paper competition.

 

65.  Brinkley, J.F. and Rosse, C. 1998 Requirements for  an  On-line Knowledge-based Anatomy Information system. Journal of the American Medical Informatics Association, Symposium Supplement, pp 892-896. Nominated for best paper.

 

66.  Hinshaw, K.P. and Brinkley, J.F. 1998 Incorporating constraint-based shape models into an interactive system for functional brain mapping. Journal of the American Medical Informatics Association, Symposium Supplement, pp 921-925.

 

67.  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.

 

68.  Kim, S.,  Brinkley, J.F. and Rosse, C.  1999 Design features of on-line anatomy information resources: a comparison with the Digital Anatomist. Journal of the American Medical Informatics Association, Symposium Supplement, pp. 560-564. Nominated for best paper.

 

69.  Poliakov, A.V.,  Hinshaw, K.P., Rosse, C. and Brinkley, J.F.  1999 Integration and visualization of multimodality brain data for language mapping. Journal of the American Medical Informatics Association, Symposium Supplement, pp. 349-353.

 

70.  Wong, B.A.,  Rosse, C. and Brinkley, J.F. 1999 Semi-automatic scene generation using the Digital Anatomist Foundational Model. Journal of the American Medical Informatics Association, Symposium Supplement, pp 637-641. Nominated for best paper.

 

71.  Kalet, I.J.,  Wu, J., Lease, M., Austin-Seymour, M.,  Brinkley, J.F. and Rosse, C. 1999 Anatomical information in radiation treatment planning. Journal of the American Medical Informatics Association, Symposium Supplement, pp. 291-295.

 

72.  Jakobovits, R., Soderland, S.G., Taira, R.K. and Brinkley, J.F. 2000 The Web-Interfacing Repository Manager: A framework for developing web-based multimedia applications for medical research. Proceedings, International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, June 26-29, 2000, pp 527-533.

 

73.  Jakobovits, R., Soderland, S., Taira, R.K. and Brinkley, J.F. 2000 Requirements of a web-based experiment management system. Journal of the American Medical Informatics Association, Symposium Supplement, pp 374-378.

 

74.  Martin, R.F., Poliakov, A.V., Mulligan, K.A., Corina, D.P., Ojemann, G.A. and Brinkley, J.F. 2000 Multi-patient mapping of language sites on 3-D brain models.  Proceedings, Sixth Annual Meeting of the Organization for Human Brain Mapping, June 12-16, San Antonio, Texas. Neuroimage 11(5), p. S534

 

75.  Campbell, B., Rosse, C. and Brinkley, J.F. 2001 The Virtual Anatomy Lab: A hands-on anatomy learning environment. Proceedings, Medicine Meets Virtual Reality 2001. Westwood, J.D., Hoffman, H.M., Mogel, G.T., Stredney, D. and Robb, R.A. (eds), Amsterdam, IOS Press, pp 85-87.

 

76.  Corina, D.P., Poliakov, A.V., Steury, K., Martin, R.F., Brinkley, J.F., Mulligan, K.A. and Ojemann, G.A. 2000 Correspondences between language cortex identified by cortical stimulation mapping and fMRI, Human Brain Mapping Annual Meeting, June 12-16, 2000, San Antonio, Texas. Neuroimage 11(5):S295.

 

77.  Poliakov, A.V.,  Jakobovits, R.M., Martin, R.F., Corina, D.P. and Brinkley, J.F. 2000 Software Tools for Visualization and Analysis of Human Brain Data for Language Mapping. Human Brain Mapping annual meeting, June 12-16, 2000, San Antonio, Texas. Neuroimage 11(5):S907.

 

78.  Poliakov, A.V., Albright, E., Corina, D., Ojemann, G., Martin, R.F. and Brinkley, J.F. 2001 Server-based approach to web visualization of integrated 3-D medical image data. Proc AMIA Symposium 2001, pp 533-537.

 

79.  Martin, R.F., Mejino, J.L.V., Bowden, D.M., Brinkley, J.F. and Rosse, C. 2001 Foundational model of neuroanatomy: implications for the Human Brain Project. Proc. AMIA Symposium 2001, pp 438-442.

 

80.  Jakobovits RM, Brinkley JF, Rosse C, Weinberger E. Enabling clinicians, researchers, and educators to build custom web-based biomedical information systems. In: Proc AMIA Annual Fall Symposium; 2001. p. 279-283.

 

81.  Lober WB, Trigg LJ, Bliss D, Brinkley JF. IML: An image markup language. In: Proc. AMIA Annual Symposium. Washington, DC; 2001. pp. 403-407.

 

82.  Distelhorst G, Srivastava V, Rosse C, Brinkley JF. A prototype natural language interface to a large complex knowledhge base, the Foundational Model of Anatomy. In: Proceedings, AMIA Fall Symposium.  pp 200-204, 2003.

 

83. Tang Z, Kadiyska Y, Li H, Suciu D, Brinkley JF. Dynamic XML-based exchange of relational data: application to the Human Brain Project. In: Proceedings, AMIA Fall Symposium. Pp 649-653; 2003.

 

84. Detwiler LT, Chung E, Li A, Mejino JLV, Agoncillo AV, Brinkley JF, Rosse C, Shapiro LG. A relation-centric query engine for the foundational model of anatomy. In: Proceedings, MEDINFO 2004, San Francisco, CA.;2004, pp 341-345.http://sigpubs.biostr.washington.edu/archive/00000152/.

 

85. Re, C., Brinkley,J., Hinshaw, K. and Suciu,D. Distributed XQuery. In: Proceedings of the Workshop on Information Integration on the Web (IIWeb), September 2004, pp 116-121.

 

86. Cho, H., Corina, D., Brinkley, J.F., Ojemann, G.A. and Shapiro, L.G. A new template matching method using variance estimation for spike sorting, In Proceedings, IEEE EMBS 2nd International Neural Conference on Engineering, March 16-19, 2005.

 

87.  Wang K, Tarczy-Hornoch P, Shaker R, Mork P, Brinkley JF. BioMediator Data Integration: Beyond Genomics to Neuroscience Data. In: Proceedings, AMIA Fall Symposium; 2005. p. 779-783.

 

88.  Bales N, Brinkley J, Lee ES, Mathur S, Re C, Suciu D. A framework for XML-based integration of data, visualization and analysis in a biomedical domain. In: Proceedings, Third International XML Database Symposium (XSym 2005). Trondheim, Norway; 2005. p. 207-221. http://sigpubs.biostr.washington.edu/archive/00000178/.

 

89.  Warren W, Brinkley JF. Knowledge-based, interactive, custom anatomical scene creation for medical education: the Biolucida system. In: Proceedings, AMIA Fall Symposium. Washington, D.C.; 2005. p. 789-793. http://sigpubs.biostr.washington.edu/archive/00000181/

 

90.  Smith VS, Shapiro LG, Hanlon D, Martin RF, Brinkley JF, Poliakov AV, Ojemann GA, Corina DP. Evaluating spatial normalization methods for the human brain. In: Proceedings, 27th Annual Conference of the IEEE Engineering in Medicine and Biology Society (EMBS). Shanghai, China; 2005. p. 5331-5334.

 

91.  Brinkley, JF, Suciu, D, Detwiler, LT, Gennari, JH, and Rosse, C. A framework for using reference ontologies as a foundation for the semantic web. In: Proceedings AMIA Fall Symposium; 2006, p. 96-100. http://sigpubs.biostr.washington.edu/archive/00000188/

 

92.  Li, H., Gennari, JH, Brinkley, JF. Model-driven laboratory information management systems. In: Proceedings AMIA Fall Symposium; 2006, pp 484-488. http://sigpubs.biostr.washington.edu/archive/00000189/.

 

93.  Li, X., Gennari, JH, Brinkley, JF. XGI: A graphical interface for XQuery creation. In: Proceedings AMIA Fall Symposium; 2007, pp 453-457.

 

94.  Yngve, G., Brinkley, JF, Cook, D, Shapiro, LG. A model browser for biosimulation. In: Proceedings AMIA Fall Symposium; 2007, pp 836-840.

 

95.  Yang, S., Franklin, J., Brinkley, J.F., Suciu, D., Shapiro, L.G., “A model of multimodal fusion for medical applications”, SPIE Medical Imaging, 2008.

 

96.  Mejino JL, Rubin DL, Brinkley J. FMA-RadLex: An application ontology of radiological anatomy derived from the Foundational Model of Anatomy reference ontology. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2008, pp 465-469.

 

97.   Shaw M, Detwiler LT, Brinkley JF, Suciu D. Generating application ontologies from reference ontologies. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2008, pp 672-676.

 

98.   Detwiler LT, Suciu D, Brinkley JF. Regular paths in SparQL: Querying the NCI thesaurus. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2008, pp 161-165.

 

 

 

 

Book Chapters

 

 

 1.        Hayes-Roth, B., Buchanan, B., Lichtarge, O., Hewett, M., Altman, R., Brinkley, J., Cornelius, C., Duncan, B. and Jardetzky, O.  1988  Elucidating protein structure from constraints in PROTEAN.  In:  Blackboard Systems.  Engelmore, R. and Morgan, A., eds., Addison-Wesley, Menlo Park, CA, London, pp. 417-431.

 

2.         Wiederhold, G., Brinkley, J., Samadani, R., and Clauer, C. 1989  Model-driven image analysis to augment databases.  In: Visual Databases, Kunii, T. ed., Springer-Verlag, pp. 159-180.

 

3.         Jardetzky, O., Lichtarg, O., Brinkley, J., and Madrid, M.  1989  The structure of proteins and their binding sites:  NMR and artificial intelligence.  In: Computer-Assisted Modeling of Receptor-Ligand Interactions, Alan R. Liss, Inc., pp. 145-156.

 

4.         Greenes, R. G. and Brinkley, J. F.  1990  Chapter 11.  Radiology applications.  In: An Introduction to Medical Computer Science.  Shortliffe, E. H., Fagan, L. and Wiederhold, G., eds., Menlo Park, Addison Wesley. 

 

5.         Brinkley, J.F. 1993  Chapter 5. The potential for  three-dimensional ultrasound. In:Ultrasound in Obstetrics and Gynecology. Chervenak, F.A., Isaacson, G.C. and Campbell, S., eds., Boston, Little, Brown and Company, pp 61-72.

 

            6.         Brinkley, J.F. 1994 Educational Systems, Synopsis. In: Yearbook of Medical Informatics. Van Bemmel, J.H. and McCray, A.T., eds., The Netherlands, International Medical Informatics Association, pp. 465-467.

 

7.         Brinkley, J.F., Myers, L.M., Prothero, J.S., Heil, G.H., Tsuruda, J.S.,Maravilla, K.R., Ojemann, G.A. and Rosse, C. 1997 A structural information framework for brain mapping. In: Neuroinformatics: An Overview of the Human Brain Project. Koslow, S.H. and Huerta, M.F., eds., Lawrence Erlbaum, Mahwah, New Jersey, pp. 309-334.

 

8.         Greenes, R. G. and Brinkley, J.F. 1997 Imaging Systems. In: Medical Informatics: Computer Applications in Health Care (2nd edition). Shortliffe, E.H., Perreault, L.E., Wiederhold, G. and Fagan, L.M. eds., Chapter 14, pp 485-538.

 

9.         Brinkley, J.F. 1998 The use of anatomical knowledge in medical imaging: an overview of the University of Washington Structural Informatics Group. In: Medical Image Databases. Wong, S. (ed.), Boston, Kluwer Academic Press., pp 89-116.

 

10.       Brinkley, J.F. and Greenes, R.G. 2006 Imaging and Structural Informatics. In: Biomedical Informatics: Computer Applications in Health Care and Biomedicine (3rd edition). Shortliffe, E.H. and Cimino, J.J.. eds., Chapter 9, pp 344-378.

 

11.       Greenes, R. G. and Brinkley, J.F. 2006 Imaging Systems in Radiology. In: Biomedical Informatics: Computer Applications in Health Care and Biomedicine (3rd edition). Shortliffe, E.H. and Cimino, J.J.. eds., Chapter 18, pp 626-659.

 

 

Technical Reports

 

1.         Brinkley, J. F.  1984  Ultrasonic three-dimensional organ modelling.  Tech. report STAN-CS-84-1001, Department of Computer Science, Stanford University, March, 1984, Ph.D. Dissertation.

 

2.         Buchanan, B., Hayes-Roth, B., Lichtarge, O., Altman, R., Brinkley, J., Hewett, M., Cornelius, C., Duncan, B. and Jardetzky, O.  1985  The heuristic refinement method for deriving solution structures of proteins.  Tech. report KSL-85-41, Stanford University.

 

3.         Brinkley, J., Cornelius, C., Altman, R., Hayes-Roth, B., Lichtarge, O., Duncan, B., Buchanan, B. and Jardetzky, O.  1986  Application of constraint satisfaction techniques to the determination of protein tertiary structure.  Tech. report KSL-86-28, Stanford University, March, 1986.

 

4.         Brinkley, J. F., Buchanan, B. G., Altman, R. T., Duncan, B. S. and Cornelius, C. W.  1987  A heuristic refinement method for spatial constraint satisfaction problems.  Tech. report STAN-CS-87-1142, KSL-87-05, Stanford University, January, 1987.

 

5          Re, C., Brinkley, J., Suciu, D. 2006 A performant XQuery to SQL translator. Technical Report 2006-06-02. Dept. Computer Science and Engineering, University of Washington. http://silkroute.cs.washington.edu/SilkRouteII_TR.pdf.

 

 

 

                                                                             


                                          Abstracts and  Non-Refereed Publications

 

 

1.     McCallum, W. D. and Brinkley, J. F.  1977  Fetal weight estimation from single and multiple ultrasonic measurements.  Abstract, 22nd Annual Conference of the American Institute of Ultrasound in Medicine, Dallas, October, 1977.

 

2.     Brinkley, J. F., McCallum, W. D. and Daigle, R. E.  1979  A distributed computer system for fetal weight  determination.  Proceedings of the 24th Annual Conference, AIUM, Montreal, August, 1979, pp. 113.

 

3.     Brinkley, J. F., McCallum, W. D. and Muramatsu, S. K.  1980  Three-dimensional display of fetus, placenta and uterus using an ultrasonic computer modelling system.  Proceedings of the 25th Annual Conference, AIUM, New Orleans, September, 1980, p. 98.

 

4.     Brinkley, J. F., McCallum, W. D., Muramatsu, S. K. and Liu, D. K.  1982  The use of ultrasonic three-dimensional volume measurements in the estimation of fetal weight.  Proceedings of the 29th Annual Meeting, Society for Gynecologic Investigation, Dallas, Texas, March, 1982, p. 6.

 

5.     Brinkley, J. F., McCallum, W. D. and Popp, R. L.  1982  Ultrasonic three-dimensional imaging and volume:  an in vitro evaluation.  Am. J. Cardiol. 49: 897.  (Abstract presented at the 31st Annual Scientific Session, American College of Cardiology, Atlanta, Georgia, April 25-29, 1982).

 

6.     Brinkley, J. F.  1983  Artificial intelligence and ultrasonic imaging:  the use of learned shape knowledge to analyze 3D data.  Proceedings, 28th Annual Meeting, AIUM, New York, October, 1983, p. 71.

 

7.     Brinkley, J. F.  1983  Learned shape knowledge in ultrasonic three-dimensional organ modelling.  Student paper competition, Symposium on Computer Applications in Medical Care, Baltimore, Maryland, October 23-26, 1983. Awarded second place.

 

8.     Eik-Nes, S. H. and Brinkley, J. F.  1983  Tredimensjonal framstilling av foster in utero ved hjelp av ultralyd og moderne datateknologi.  Abstract, Annual Meeting, Norwegian Society of Ultrasound Diagnosis, Roeros, Norway, 1983, p. 40.

 

9.     Altman, R., Duncan, B., Brinkley, J., Buchanan, B. and Jardetzky, O.  1988  Determination of the spatial distribution of protein structure using solution data.  In: Proceedings of Alfred Benzon Symposium 26:  NMR Spectroscopy in Research, Copenhagen, pp. 209-232.

 

10.   Rosse, C., Brinkley, J.F. and Prothero, J.   1990  Structural informatics:  the representation of anatomical knowledge in computer readable form.  American Medical Informatics Association, 1st Annual Educational and Research Conference, Snowbird, UT, June 20-23, pp 37-38.

 

11.   Sundsten, J.W., J.F. Brinkley, K. Eno, R.M. Harris and K.G. Kastella 1991  Interactive use of videodisc animations of computer-reconstructed human brain. Annual Meeting, Society for Neuroscience, New Orleans, November 10-15.

 

 

 

12.   Sundsten, J.W., Brinkley, J.F. and Eno, K. 1993 Digital Anatomist Browser: teaching neuroanatomy with the use of digital and video-disc images accessed by computer. Proc. American Association of Anatomists Annual Meeting, San Diego, March 1993.

 

13.   Conley, D.M., Brinkley, J.F., Rauschning, W. and Rosse, C. A multimedia approach to the study of the mediastinum utilizing a computer-generated three-dimensional model. Proc. American Association of Anatomists Annual Meeting, San Diego, March 1993.

 

14.   Shapiro, L.G., Tanimoto, S.L. and Brinkley, J.F. 1993  Design of a visual database system for computer vision research. Proc. Workshop on Advances in Data Management for the Scientist and Engineer. Chu, W.,  Cardenas, A., and Taira, R. (eds), Boston, February, 1993.

 

15.   Brinkley, J.F. 1994  The Digital Anatomist Project, Proc. American Association for the Advancement of Science, Annual Meeting, San Francisco, Feb 18-23, 1994, p. 6.

 

16.   Brinkley, J.F., Eno, K.R., Sundsten, J.W., Conley, D.M., and Rosse, C. 1995 A distributed framework for distance learning in anatomy: the Digital Anatomist Interactive Atlas. 19th Symposium on Computer Applications in Medical Care, New Orleans, Oct 30-Nov 1, 1995, p 972.

 

17.   Myers, L.M., Prothero, J.S. and Brinkley, J.F. 1995 Volume rendering of multi-spectral MR data for brain language site mapping. Proc. Advanced Visual Systems User Conference, Boston, April 19-21, pp 471-480.

 

18.   Graney, D., Conley, D., Sundsten, J.W., Ratiu, P., Rauschning, W., Brinkley, J.F. and Rosse, C. 1995 Digital Anatomist interactive atlases. Abstracts, 3rd European Congress of the European Association of Clinical Anatomy. In Journal of Clinical Anatomy 17(3):213.

 

19.   Modayur, B., Ojemann, G., Lettich, E, Jakobovits, R., Sundsten, J. and Brinkley, J. 1997 Information system for mapping and studying cortical language localization.  Abstracts, Society for Neuroscience Annual Meeting, Oct 25-30, 23:2228.

 

20.   Wong, B.A. and Brinkley, J.F. 1998 Dynamic 3-D Scene Navigation in Web-based Anatomy Atlases. Journal of the American Medical Informatics Association, Symposium Supplement, p 1100. Nominated for best poster.

 

21.   Jakobovits, R.M. and Brinkley, J.F. 1998  Query-by-context: a framework for modelling and navigating multimedia research data. Journal of the American Medical Informatics Association, Symposium Supplement, p 1021.

 

22.   Corina, D.P., McBurney, S.L., Hinshaw, K., Brinkley, J., Lettich, E. and Ojemann, G.A. 1998 Left hemisphere specialization for American Sign Language: a cortical stimulation study. Abstracts, Society for Neuroscience annual Meeting, Nov 7-12, 15.4.

 

23.   Bowden, D.M., Robertson, J.E., Martin, R.F., Dubach, M.F., Wu, J.S., McLean, M.R. and Brinkley, J.F. 1999 Web-tools for neuroscience based on NeuroNames, a template brain atlas, edgewarp and geographic information systems software. Fifth international conference on functional mapping of the human brain, Heinrich-Heine University, Dusseldorf, Germany.

 

24.   Lober, W.B.  and  Brinkley, J.F. 1999 A portable image annotation tool for web-based anatomy atlases. Journal of the American Medical Informatics Association, Symposium Supplement, p. 1108.

 

25.   Hahn, J.S.,  Burnside, E., Brinkley, J.F., Rosse, C. and Musen, M.A. 1999 Representing the Digital Anatomist Foundational Model as a Protege ontology. Journal of the American Medical Informatics Association, Symposium Supplement, p. 1070.

 

26.   Poliakov, A.V., Hinshaw, K.P., Corina, D.P., Steury, K.R., Maravilla, K.R., Ojemann, G.A., Mulligan, K.A. and Brinkley, J.F. 1999 Integration and visualization of multimodality brain data for language mapping. Abstracts, Society for Neuroscience Annual Meeting, Miami, Oct 23-29, 654.1.

 

27.   Corina, D.P., Steury, K.R., Mulligan, K.A., Hinshaw, K.P., Poliakov, A.P., Brinkley, J.F., Maravilla, K.R. and Ojemann, G.A. 1999 A comparison of language cortex indentified by cortical stimulation mapping and fMRI techniques. Abstracts, Society for Neuroscience Annual Meeting, Miami, Oct 23-29, 654.2.

 

28.   Bowden, D.M., Robertson, J.E., Martin, R.F., Dubach, M.F., Wu, J.S., McLean, M.R. and Brinkley, J.F. 1999 BrainInfo: A primate brain atlas & neuroanatomic resource based on geographic information systems (GIS) software. Abstracts, Society for Neuroscience Annual Meeting, Miami, Oct 23-29, 47.23.

 

29.   Lober, W. B. and Brinkley, J. F., 2000 "A personal annotated image server," in JAMIA Supplement, Fall 2000 Annual Symposium. Los Angeles, p. 1068.

 

30.   Martin, R.F., Poliakov, A.V., Mulligan, K.A., Kinbar, K., Corina, D.P., Maravilla, K., Lettich, E., Ojemann, G.A. and Brinkley, J.F. 2000 Multi-patient mapping of language sites on 3-D brain models. 30th Annual Meeting, Society for Neuroscience, New Orleans, Nov 4-9, 464.20.

 

31.   Brinkley JF, Albright EM, Kim S, Mejino JLV, Shapiro LG, Rosse C. Visible Human, Construct Thyself: The Digital Anatomist Dynamic Scene Generator. In: The Third Visible Human Project Conference Proceedings. Bethesda: NLM, 2000;27-28.

 

32.   Rosse C, Mejino JLV, Shapiro LG, Brinkley JF. Visible Human, Know Thyself: The Digital Anatomist Structural Abstraction. In: The Third Visible Human Project Conference Proceedings. Bethesda: NLM, 2000;85-86.

 

33.   Kinbar, K., Martin, R., Hill, J., Mulligan, K., Poliakov, A, Brinkley, J.F., Ojemann, G.A., Corina, D.P. 2001 Naming deficits during cortical stimulation mapping: functional specificity reconsidered. Proceedings, Eighth Annual. Meeting Cognitive Neuroscience Society (CNS), New York , March 25-27, p. 126.

 

34.   Poliakov, A.V., Albright, E., Corina, D.P., Ojemann, G.A., Martin, R.F. and Brinkley, J.F. 2001 Server-based approach to web visualization of integrated 3-D brain mapping data. 31st Annual Meeting, Society for Neuroscience, San Diego, Nov 10-15, 529.1.

 

35.   Martin, R.F., Mejino, J.L.V., Bowden, D.M., Brinkley, J.F., Mulligan, K. and Rosse, C. 2001 A next-generation knowledge source: foundational model of neuroanatomy. 31st Annual Meeting, Society for Neuroscience, San Diego, Nov 10-15. 23.48.

 

36.  Brinkley JF, Jakobovits R, Rosse C. 2002 An online image management system for anatomy teaching. In: Proceedings of the  AMIA 2002 Annual Symposium, San Antonio, Nov 9-13, p 983.

 

37.  Mork P, Suciu D, Brinkley J, Rosse C. 2002 A declarative query interface for large semantic networks. In: Proceedings of the  AMIA 2002 Annual Symposium, San Antonio, Nov 9-13, p 1110.

 

38.  Detwiler LT, Mejino JLV, Rosse C, Brinkley JF. Efficient web-based navigation of the Foundational Model of Anatomy. In: Proceedings AMIA Fall Symposium. P 829; 2003.

 

39.  Martin RF, Rickard K, Mejino JLV, Agoncillo AV, Brinkley JF, Rosse C. The evolving neuroanatomical component of the Foundational Model of Anatomy. In: Proceedings AMIA Fall Symposium. P 927; 2003.

 

40.   Poliakov AV, Moore E, Corina DP, Brinkley JF. Software tools for visualization of multimodality brain data for language mapping. In: Proceedings, Society for Neuroscience. New Orleans; 2003. p. 428.16.

 

41.  Tarczy-Hornoch P, Brinkley J, Shaker R, Mork P, Donelson L, Barrier M, Gennari J, Rosse C, Rossini A, Suciu D, Halevy A. Bio-PDMS: A structural ontology driven peer data management system (PDMS) for biology. In: Biomedical Information Science and Technology Initiative (BISTI) Symposium. Washington, DC; 2003.

 

42.  Distelhorst GM, Hinshaw KP, Rosse C, Brinkley JF. An improved natural language interface to a complex anatomical knowledge base. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004, p. 1575. http://sigpubs.biostr.washington.edu/archive/00000143/.

 

43.  Fong C, Rosse C, Clark JI, Shapiro L, Brinkley JF. An ontology-based image repository for a biomedical research lab. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004, p. 1598. http://sigpubs.biostr.washington.edu/archive/00000144/.

 

44.  Hertzenberg X, Poliakov AV, Brinkley JF. Unobtrusive integration of data management with fMRI analysis. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004, p 1639. http://sigpubs.biostr.washington.edu/archive/00000153/.

 

45.  Li H, Brinkley  JF, Gennari J. Semi-automatic database design for neuroscience experiment management systems. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004, p. 1717. http://sigpubs.biostr.washington.edu/archive/00000145/.

 

46.  Moore EB, Poliakov AV, Brinkley JF. Brain visualization in Java3D. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004. p. 1761. http://sigpubs.biostr.washington.edu/archive/00000151/. Best Poster Award (out of over 400 posters).

 

47.  Poliakov AV, Moore EB, Brinkley JF. Use of remote surface based tools for visualizing integrated brain imaging data. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004, p. 1814. http://sigpubs.biostr.washington.edu/archive/00000150/.

 

48.   Tang Z, Kadiyska Y, Suciu D, Brinkley JF. Results visualization in the XBrain XML interface to a relational database. In: Proceedings, MEDINFO 2004. San Francisco, CA.; 2004, p. 1878. http://sigpubs.biostr.washington.edu/archive/00000146/.

49.   Martin RF, Brinkley JF, Hertzenberg X, Poliakov A, Corina D, Ojemann GA. Anatomical parcellation of cortical language sites. In: MEDINFO 2004. San Francisco, CA.; 2004, p. 1742. http://sigpubs.biostr.washington.edu/archive/00000156/.

 

50.   Brinkley, JF, Jakobovits RM, Poliakov, AV, Martin, RF, Gibson, ER,  Corina, DM, and Ojemann GA, An experiment management system for cortical stimulation mapping data. In: Society for Neuroscience Annual Meeting. San Diego, CA; 2004, 1032.12.

 

51.   Smith, VS, Hanlon, D., Martin, RF, Poliakov, AV, Brinkley, JF, Shapiro, LS, Van Essen, D., Ojemann, GA, Corina, DM. Evaluating anatomical normalization methods. In: Society for Neuroscience Annual Meeting. San Diego, CA; 2004, 12.11.

 

52.   Hertzenberg, X, Poliakov, AV, Corina, DM, Ojemann, GA, Brinkley, JF. X-Batch: Embedded data management for fMRI analysis. In: Society for Neuroscience Annual Meeting. San Diego, CA; 2004, 694.21.

 

53.   Lee, E.S., Suciu, D. and Brinkley, J.F. Automatic XQuery Generation and Generalized Visualization for an XML Interface to a Relational Database. In: Proceedings Fall AMIA Symposium, 2005, p 1019.

 

54.   Moore EB, Poliakov A, Brinkley JF. Web-enabled 3D multimodality brain visualization in Java. In: Society for Neuroscience Annual Meeting; 2005. p. 570.2.

 

55.   Ojemann GA, Schoenfield-McNeill, Lettich E, Oskin N, Zanos S, Panagiotides H, Zamora L, Sengupta C, Cho H, Corina D, Poliakov A, Martin RF, Brinkley JF. The relationship between fMR, single neuronal activity, and local field potentials in human association cortex. In: Proceedings, Society for Neuroscience Annual Meeting; 2005. p. 814.9.

 

56.   Jeng S, Wang K, Barbero J, Brinkley J, Tarczy-Hornoch P. A pilot bridging data integration and analytics: BioMediator and R. In: Proceedings American Medical Informatics Fall Symposium; 2005. p. 995.

 

57.   Fong, CT, Arnett, EE, Brinkley, JF and Clark, JI. Image Management System for Correlation of Temporal and Spatial Variation in Mouse Lens Phenotype, Invest. Ophthalmol. Vis. Sci. 2005 46: E-Abstract 2910.

 

58.   Poliakov AV, Moore EB, Brinkley JF. Software tools for batch processing, management and visualization of functional MRI data. In: Proceedings, 14th Annual Meeting of the International Society for Magnetic Resonance in Medicine. Seattle; 2006. p. 620.

 

59.   Detwiler, LT, Brinkley, JF. Custom views of reference ontologies. In: Proceedings AMIA Fall Symposium; 2006, p. 909. http://sigpubs.biostr.washington.edu/archive/00000187.

 

60.   Warren, W, Agoncillo, A, Franklin, J, Brinkley, J. Intelligent web-based whole body visualization for anatomy education. In: Proceedings AMIA Fall Symposium; 2006, p 1136.

 

61.   Fong, C, Brinkley, J. Customizable electronic laboratory online (CELO): A web-based data management system builder for biomedical research laboratories. In: Proceedings AMIA Fall Symposium; 2006, p. 922. http://sigpubs.biostr.washington.edu/archive/00000191.

 

62.   Brinkley JF, Poliakov AV, Moore EB, Detwiler LT, Franklin JD, Corina DP, Ojemann GA. Lightweight XML-based query, integration and visualization of distributed, multimodality brain imaging data. In: Proceedings, Annual Meeting of the Society for Neuroscience; 2006. p. 100.13.

 

63.   Mejino JL, Martin RF, Detwiler LT, Brinkley JF: Challenges in reconciling different views of neuroanatomy in a reference ontology of anatomy. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2007, p 1046. Nominated for distinguished poster award. http://sigpubs.biostr.washington.edu/archive/00000214/.

 

64.   Detwiler LT, Brinkley JF: Querying non-materialized ontology views. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2007, p 934. http://sigpubs.biostr.washington.edu/archive/00000213/.

 

65.   Brinkley, JF, Ach, D, Franklin, JF, Anderson, N, Stevens, A, Tarczy-Hornoch, P: Tools for clinical trials management: handling the norm and the outliers. In Abstracts, Clinical Research Informatics Expo, Fall Symposium of the American Medical Informatics Association, 2007, http://www.amia.org/mbrcenter/wg/cri/docs/cri_expo_2007.pdf, p 5.

 

66.   I. Atmosukarto, R. S. Travillian, J. D. Franklin, L. G. Shapiro, J. F. Brinkley, D. Suciu, J. I. Clark, M. L. Cunningham, “A Unifying Framework for Combining Content-Based Image Retrieval with Relational Database Queries for Biomedical Applications,”  Society of Imaging Informatics in Medicine Annual Symposium, 2008.

 

67.   Franklin JD, Mejino JL, Detwiler LT, Rubin DL, Brinkley JF. Web service access to semantic web ontologies for data annotation. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2008, p 946.

 

68.   Guidry A, Brinkley JF, Anderson NR, Tarczy-Hornoch P. Concept mapping to develop a framework for characterizing electronic data capture (EDC) systems. In: Proceedings, Fall Symposium of the American Medical Informatics Association. 2008, p. 960.

 

69.   Detwiler LT, Shaw MS, Cook DL, Gennari JH, Brinkley JF. Post-coordinating orthogonal ontologies for data annotation. In: Proceedings, Fall Symposium of the American Medical Informatics Association. In Press; 2009.

 

70.   Franklin JD, Detwiler LT, Brinkley JF. Lightweight distributed XML-based integration of translational data. In: Proceedings, Fall Symposium of the American Medical Informatics Association. In Press; 2009.