PART I: General Information
| Date Prepared: | January 2, 2007 |
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| Name: | Griffin M Weber |
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| Office Address: | Harvard Medical School
Information Technology
107 Avenue Louis Pasteur
Boston, MA 02115 |
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| E-Mail: | weber@ fas.harvard.edu |
Education:
| 2000 | S.B. | Harvard University (Biomedical Sciences and Engineering) |
| 2004 | S.M. | Harvard University (Computer Science) |
| 2005 | Harvard/MIT Health Sciences and Technology (Medical Engineering and Medical Physics, Bioinformatics and Integrative Genomics Training Program) |
| 2005 | Ph.D. | Harvard University (Computer Science, Biomedical Informatics & Artificial Intelligence) |
| 2007 | M.D. | Harvard/MIT Health Sciences and Technology (Medical Scientist Training Program) |
Research Assistant Positions:
| 1997 | Center for Pediatric Research, Eastern Virginia Medical School, Children's Hospital of The King's Daughters
Converted archival laboratory data to a clinical care database with a web-based graphical user interface. This was one of the first web-based electronic medical records ever created. |
| 1998 - 1999 | Institute of Genetic Medicine, The Johns Hopkins University School of Medicine
Developed unique algorithms and computer software to perform automated pattern recognition to score aneuploidy in human cells. |
| 1998 - 1999 | Harvard Biomedical Engineering Laboratory
Designed "fall-safe" flooring to prevent hip injuries in nursing homes. |
| 1999 | Children's Hospital of The King's Daughters
Developed a computerized system to automate the process of administering audiologic evaluations. |
| 1999 - 2004 | Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School
Created computer simulation models of breast cancer growth using data from the Breast Imaging Division at the Massachusetts General Hospital and used these to determine optimal mammography screening schedules. |
| 2000 - 2001 | New England Medical Center
Developed a web-based Markov simulation of competing health risk models to be used in the analysis of treatment options and in the generation of life expectancy predictions; designed and implemented an interactive web site for the "Living a Healthy Life After Breast Cancer" project. |
| 2001 - 2002 | Center for Excellence in Vascular Biology & Decision Systems Group, Harvard Medical School, Brigham and Women's Hospital
Invented efficient search algorithms to rapidly analyze genetic data obtained using microarrays. |
| 2001 - 2003 | Dana-Farber Cancer Institute, Harvard Medical School, Brigham and Women's Hospital
Identified candidate infectious agents using computational sequence filtering, and applied novel clustering algorithms to mRNA expression levels from the tissue of human lung carcinomas. |
| 2001 - 2005 | Decision Systems Group, Harvard Medical School, Brigham and Women's Hospital
Developed techniques using logistic regression and "fuzzy logic" algorithms for multivariate selection of genetic markers in diagnositic classification, and created software that uses these methods to analyze microarray databases. |
| 2002 - 2004 | Division of Women's Health, Brigham and Women's Hospital
Created novel algorithms for medical decision analysis using Markov processes, and invented techniques for extrapolating disease risk models beyond their intended time intervals. |
| 2003 - 2005 | Division of Engineering and Applied Sciences, Harvard University
Developed stochastic search algorithms for phylogenetic tree reconstruction and invented a method for rapidly determing the Hamming distance between sequences. |
Academic and Hospital Appointments:
| 2007- | Instructor in Medicine, Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School |
Professional Positions:
| 2001 - 2003 | Lead Web Developer, Program in Medical Education, Educational Computing, Harvard Medical School.
Inventor and lead programmer of Harvard Medical School's MyCourses student web portal, the first leading-edge eLearning tool that supports the full education curriculum of a medical school; developed the Virtual Patient, a web-based application used to create online cases that include multimedia, interactive history and physical exam modules, and tools to evaluate student performance; and created and managed the Academy at Harvard Medical School internet web site. The Virtual Patient was featured in Boston Globe Magazine, and a public version of it is now a central component of the Association of American Medical Colleges' MedEdPortal initiative. |
| 2003 - 2005 | Database Developer and Programmer, StreamSage, Inc.
Invented algorithms for performing efficient queries on multiple gigabytes of indexes of multimedia files; developed techniques for searching file-based and segment-based meta-data of multimedia files; and designed an efficient database schema for storing and retrieving word co-occurrence information. |
| 2003- | Director, Brigham and Women's Hospital Research Informatics Core (BRIC), Brigham and Women's Hospital
Provided informatics services to support research at Brigham and Women's Hospital. The services covered a range of tasks, from creating a basic lab web site to advanced data analysis and web application development. Specific projects included constructing software tools to assist clinical trial management, creating clustering and data visualization tools for microarray and SAGE databases, and building clinical-research databases with web-based interfaces. |
| 2003 - 2006 | Lead Software Architect, Information Technology Department, Harvard Medical School
Developed the public web sites and content authoring tools for Harvard Medical School and many of its departments and organizations, and designed and implemented Harvard Medical School's eCommons intranet web portal, which combines the electronic administrative, research, and educational tools available at the medical school into one application used by 20,000 faculty, staff, and students more than 30,000 times a day. The Dean of Faculty at HMS listed eCommons as a highlight of his past ten years at the school. |
| 2004- | Chief Technology Officer, Strategic Health Decisions, Inc.
Invented award-winning algorithms for determining optimal medical treatment strategies using Markov-based simulations and multicriteria decision analysis. Strategic Health Decisions is a software company that builds applications using these algorithms to help patients and their physicians make complex medical decisions. |
| 2007- | Director, Biomedical Research Informatics Core (BRIC), Beth Israel Deaconess Medical Center
Lead a team of informaticians with backgrounds in computer science, engineering and biostatistics to facilitate research at BIDMC by providing a high level of service and experience in informatics, developing informatics infrastructure, and fostering collaboration among life scientists and quantitative scientists. |
| 2007- | Chief Technology Officer, Harvard Medical School
Oversee research and development of new IT initiatives by designing an architecture plan for the future of HMS, evaluating new technologies, implementing enterprise-wide solutions, and initiating collaborative projects with the IT departments of Harvard affiliated hospitals and institutions. |
Professional Societies:
| 2000 - 2002 | American Medical Informatics Association, Member |
| 2003 - 2004 | Society Medical Decision Making, Member |
Community Service:
| 1999 - 2002 | Webmaster, Shamrock Sportsfest
Created and maintained the internet website for Shamrock Sportsfest, an annual leukemia fundraising marathon race. |
Editorial Boards:
| 2002 | Ad Hoc Reviewer, International Journal of Medical Informatics |
| 2005 | Ad Hoc Reviewer, Journal of the American Medical Informatics Association |
| 2005 | Ad Hoc Reviewer, Journal of Biomedical Informatics |
| 2005 | Ad Hoc Reviewer, Data Science Journal |
Awards and Honors:
| 1994 | First Grand Award, Medicine and Health, International Science and Engineering Fair |
| 1995 | USA Today, All U.S.A. Academic First Team |
| 1995 | Westinghouse Science Talent Search Finalist / One of ten top award winners. |
| 1997 | Harvard Detur prize recipient for academic excellence |
| 1997 | First Prize, Physiology, Eastern Colleges Science Conference |
| 1997 | John Harvard Scholarship in recognition of Group I academic record (1996-97) |
| 1998 | John Harvard Scholarship in recognition of Group I academic record (1997-98) |
| 1999 | New York Post of the Society of American Military Engineers award (Presented to the top undergraduate in Engineering at Harvard University) |
| 2000 | Best Undergraduate Thesis in Engineering (Awarded by Harvard faculty) |
| 2000 | Clemens Herschel Prize for practical hydraulics (Awarded by Harvard faculty) |
| 2000 | Harvard Hoopes Prize recipient for undergraduate thesis |
| 2000 | Elected to Phi Beta Kappa, Alpha Iota of Massachusetts at Harvard University |
| 2002 | Finalist in the Student Paper Competition of the American Medical Informatics Association Annual Symposium |
| 2003 | Lee B. Lusted Student Prize, Society of Medical Decision Making |
| 2006 | Elected to The Aesculapian Club of Harvard Medical School (Awarded by Harvard Faculty) |
| 2007 | Massachusetts Medical Society Medical Technology Award
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PART II: Research and Teaching
Narrative Report
With backgrounds in biomedical engineering, computer science, and medicine, my research interests focus on exploring various ways in which biomedical informatics can be used to improve medical education, research, and patient care. Biomedical informatics is very much an applied science, and most of the theoretical research I conduct is aimed towards developing computer algorithms to solve specific real-world problems. As a result, I've had the opportunity to collaborate with dozens of biologists and clinical research scientists on a vast range of research projects. Many of these projects involve developing techniques for efficiently encoding, searching, or processing large datasets. I have used these algorithms to build enterprise-wide intranet web portals, electronic medical records systems, and software tools for analyzing sequence and microarray databases. Other studies require designing machine learning models using logistic regression, neural networks, and dimension reduction, or creating computer simulations using Markov models, Monte Carlo methods, and finite element analysis. Below are descriptions of three of my research projects.
Division of General Internal Medicine, Rhode Island Hospital, Brown Medical School
Hormone therapy (HT) provides the most effective relief of menopausal symptoms. This therapy is associated with a decreased risk of osteoporosis and colorectal cancer but increased risks of cardiovascular disease, venous thrombosis, and breast cancer. In order to identify which women should benefit from HT, I invented a new modeling technique, which builds upon traditional Markov methods, to simulate the effect of short-term (2 years) estrogen and progestin HT on life expectancy and quality-adjusted life expectancy. The findings were published in Archives of Internal Medicine. The modeling technique was honored by the Society for Medical Decision Making and can be applied to many other complex medical decision applications.
Division of Engineering and Applied Sciences, Harvard University
Phylogenetic tree reconstruction is a process in which the ancestral relationships among a group of organisms are inferred from their DNA sequences. For all but trivial sized data sets, finding the optimal tree is computationally intractable. Many heuristic algorithms exist. The most popular method begins with an initial tree constructed using a “greedy” stepwise addition technique and attempts to improve it by swapping branches and evaluating the new tree. I developed a novel stochastic search algorithm, which improves stepwise addition by changing the order in which taxa are processed. When followed by branch-swapping, this can produce better trees for a given total amount of time.
Information Technology Department, Harvard Medical School
The MyCourses and eCommons internet web portals and content management systems, which I invented, have revolutionized the way information is shared among members of the Harvard Medical School community. The MyCourses portal serves students by providing a single home for all course events, announcements, and online resources; enhancing the educational experience through interactive multimedia tools and Virtual Patients; improving scores on exams; and enabling students to search for medical concepts in more than 65,000 electronic resources posted by faculty across 500 courses. The eCommons portal addresses the needs of administrators, faculty, and researchers through an expansive suite of web-based tools for communication and collaboration. Over 350 departments and organizations at HMS use eCommons to share documents through secure internal networks, push targeted news and surveys to selected groups of people, and publish content to public internet websites. Researchers use eCommons to register for conferences and talks, access thousands of electronic journals through the Digital Library, and even analyze DNA sequences directly from a BLAST module on the portal home page. Together, the portals receive over 30,000 page hits per day, and the Dean of Faculty at HMS regards them as a highlight of his past ten years at the school. A number of research projects grew out of the development of these portals: I invented a new method for encoding set-valued fields in relational database table, which is used in eCommons to determine the members of organizations; I created a natural language processing algorithm, which allows students to “talk” to the Virtual Patients; and I designed a more efficient version of a voice recognition algorithm, which is used to by students to find lecture videos posted to MyCourses by searching for words that the instructor spoke during class.
Report of Teaching
| 2003 | Harvard Medical School
Genetics 224, Genomics and Computational Biology
Teaching Fellow
20 Undergraduate and Graduate Students
150 hours |
| 2004 | Harvard University, Division of Engineering and Applied Sciences
Computer Science 165, Information Management
Guest Lecturer
15 Undergraduate Students
10 hours |
PART III: Bibliography
Original Articles
- Weber G, Weber G. "Pizza Combinatorics." The College Mathematics Journal. 1995 March; 26(2):141-3.
- Michaelson JS, Satija S, Moore R, Weber G, Halpern E, Garland A, Kopans DB. "Observations on Invasive Breast Cancer Diagnosed in a Service Screening and Diagnostic Breast Imaging Program." Journal of Women's Imaging. 2001 3:99-104
- Comander J, Weber G, Gimbrone MA Jr, Garcia-Cardena G. "Argus--a new database system for Web-based analysis of multiple microarray data sets." Genome Research. 2001 Sep;11(9):1603-10.
- Bhattacharjee A, Richards W, Staunton J, Cheng L, Stefano M, Vasa P, Ladd E, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark E, Lander E, Wong W, Johnson B, Golub T, Sugarbaker D, Meyerson M. "Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses." Proc. Natl. Acad. Sci. USA 2001 Nov 20;98(24):13790-5
- Michaelson JS, Satija S, Moore R, Weber G, Garland G, Phuri D, Kopans DB. "The Pattern of Breast Cancer Screening Utilization and its Consequences." Cancer. 2002 Jan 1;94(1):37-43.
- Weber G, Shendure J, Tanenbaum DM, Church G, Meyerson M. "Identification of candidate infectious agents by transcript sequence filtering." Nature Genetics. 2002 Feb;30(2):141-142.
- Col NF, Fortin JM, Weber G. "Using the Web to Promote Smoking Cessation and Health for College-Aged Women. Educational Resources Information Center." Clearinghouse Number JC020766: 2002.
- Ohno-Machado L, Vinterbo S, Weber G. "Classification of Gene Expression Data Using Fuzzy Logic." Journal of Intelligent and Fuzzy Systems. 2002;12(1):19-24
- Michaelson JS, Silverstein M, Wyatt J, Weber G, Moore R, Halpern E, Kopans DB, Hughes K. "Predicting the survival of patients with breast carcinoma using tumor size." Cancer. 2002 Aug 15;95(4):713-23.
- Michaelson JS, Satija S, Moore R, Weber G, Halpern E, Garland A, Kopans DB. "Estimates of the Sizes at Which Breast Cancers Become Detectable on Mammographic and Clinical Grounds." Journal of Women's Imaging. 2003 Feb 5(1):3-10
- Michaelson JS, Satija S, Moore R, Weber G, Halpern E, Garland A, Kopans DB. "Estimates of Breast Cancer Growth Rate and Sojourn Time from Screening Database Information." Journal of Women's Imaging. 2003 Feb 5(1):11-19
- Xu Y, Stange-Thomann N, Weber G, Bo R, Dodge S, David RG, Foley K, Beheshti J, Harris NL, Birren B, Lander ES, Meyerson M. "Pathogen discovery from human tissue by sequence-based computational subtraction." Genomics. 2003 Mar;81(3):329-35.
- Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL. "Genomic Analysis of Mouse Retinal Development." PLoS Biology. 2004 Jun 29.
- Weber G, Vinterbo S, Ohno-Machado L. "Multivariate selection of genetic markers in diagnostic classification." Artificial Intelligence in Medicine Journal. 2004 Jun;31(2):155-67.
- Col N, Weber G, Stiggelbout A, Chuo J, D'Agostino R, Corso P. "Short-term Menopausal Hormone Therapy for Symptom Relief: An Updated Decision Model." Archives of Internal Medicine. 2004 Aug 9-23;164(15):1634-40.
- Weber G, Weber G. "Pizza Combinatorics Revisited." The College Mathematics Journal. 2006 Jan; 37(1):43-4.
- Weber G, Ohno-Machado L, Shieber S. "Representation in stochastic search for phylogenetic tree reconstruction." Journal of Biomedical Informatics. 2006 Feb; 39(1):43-50.
Proceedings of Meetings
- Weber G, Vinterbo S, Ohno-Machado L. "Building an asynchronous web-based tool for machine learning classification." Proc AMIA Symp. 2002:869-73.
Thesis
- Weber G. "Using Tactile Images to Differentiate Breast Cancer Types." Undergraduate Thesis in Engineering at Harvard University. April 2000.
- Weber G. "Data Representation and Algorithms for Biomedical Informatics Applications." PhD thesis, Harvard University, Cambridge, MA, 2005.
Patent
- Weber GM, Col NF. Methods for Optimizing Treatment Strategies: A Patient-Specific Rating System. US60/604,768, assigned to SHD, Inc.
Abstracts
- Koeppen PM, Weber G, Buescher ES. "Human Milk and Colostrum Exposures Modify Locomotive Responses of Polymorphonuclear Leukocytes." Abstract presented at the 1998 Pediatric Academic Societies Meeting of the Society for Pediatric Research.
- Weber G, Col N. "The 'Deale' Revisited: A Practical Method for Partitioning Causes of Death." Abstract in the Proceedings of the 23rd Annual Meeting of the Society for Medical Decision Making.
- Col N, Weber G, Corso P, Chuo J, D'Agostino R, Wong J, Stiggelbout A. "Short-term Menopausal Hormone Therapy for Symptom Relief: An Updated Decision Model." Abstract in the Proceedings of the 25th Annual Meeting of the Society for Medical Decision Making. 2003 Oct.
- Weber G, Col N. "Methods for Extrapolating Risk Equations beyond Their Valid Intervals." Abstract in the Proceedings of the 25th Annual Meeting of the Society for Medical Decision Making. 2003 Oct.
- Weber G, Col N. "Enter the Matrix: Improved Software for Modeling the Effects of Treatments on Multiple Comorbidities Using Markov Processes." Abstract in the Proceedings of the 25th Annual Meeting of the Society for Medical Decision Making. 2003 Oct.
- Weber G, Fortin J, Landau C, Cyr M, Col N. "Measuring how patients use internet-based decision aids." Abstract in the Proceedings of the 26th Annual Meeting of the Society for Medical Decision Making. 2004 Oct.
Computer Software and Websites
- Weber G. The Asthma Wheel: Asthma and allergy severity prediction software. 1994.
- Weber G. ECGCompression: Electrocardiogram data compression software. 1994.
- Weber G. Pediatric Infectious Disease Society Website. 1997-1998.
- Weber G. Center for Pediatric Research Website. 1997-2002.
- Weber G, Buescher ES, Wallace S. MediSeek: A web-based archived medical laboratory data retrieval system for Children's Hospital of The King's Daughters. 1998.
- Weber G. Franklin Ophthalmic Instruments Website. 1999.
- Weber G, Zimonopoulos G, Proud V. InfoGenetics web page design. 1999.
- Buescher ES, Weber G, Luckstead EF. JointInjury.com: Internet Resource for Information on Sports Injuries. 1999.
- Weber G. Shamrock Sportsfest Leukemia Fundraising Marathon Race Website. 1999-2002.
- Mar P, Weber G, Ohno-Machado L. FACTS: Finding Appropriate Clinical Trials Website. 1999.
- Kogan S, Weber G, Greenes R. HealthAware: Health Information Website. 1999.
- Weber G, Ohno-Machado L. Myocardial Infarction Risk Assessment Calculator: An internet-based interface to a logistic regression model that predicts MI risk. 1999.
- Weber G, Ohno-Machado L. Heart Attack Information Website: An interactive, multimedia web site providing health information. 1999.
- Weber G. iStationery.com Website. 1999.
- Weber G. Flexmind.com Website. 1999-2000.
- Weber G, Fortin JM, Col NF. CollegeHealth.net: A Website for college-aged women featuring interactive expert systems, on-line surveys, and logical algorithms related to tobacco use and other health topics. 2000.
- Matson D, Weber G. Rotavirus.com: Internet Resource for Information of Rotavirus Disease. 2000-2001.
- Weber G, Resnic F. Interventional Cardiology Database System for Brigham and Women's Hospital. 2000.
- Weber G. Gimbrone Lab Website. 2000.
- Weber G. Harvard Medical School MyCourses Web Portal. 2000.
- Weber G. Harvard College Quincy House Pre-Med, Pre-Law, and Qube Websites. 2000-2006.
- Weber G. Medical Decision Support Multimedia Website for the Boston Informatics Training Program. 2001.
- Comander J, Weber G, Gimbrone MA Jr, Garcia-Cardena G. Argus: Web-based Microarray Analysis Software. 2001.
- Weber G. Online Course Websites for the International Training in Medical Informatics Program. 2001.
- Weber G, Col NF. MyBreastCancer.org: Living a Healthy Life After Breast Cancer Website. 2001.
- Weber G. Meyerson Lab Website. 2001-2002.
- Weber G. Harvard Medical School Center for Educational Policy Website. 2001-2003.
- Weber G. Academy at Harvard Medical School Website. 2001-2006.
- Weber G. Dana Farber Cancer Institute Belfer Center Website. 2002.
- Weber G, Bird V. Different Shades of Autism CD-ROM, Presented by the American Academy of Pediatrics and the Veronica Bird Charitable Foundation. 2002.
- Weber G, Ohno-Machado L. Classify-R: Web-based application to aid in the construction and evaluation of predictive models. 2002.
- Weber G. Harvard Medical School Virtual Patient Website. 2002.
- Weber G. Harvard Medical School Faculty Development and Fellowship Program in General Internal Medicine Website. 2002-2006.
- Weber G, Cyr M, Landau C, Moulton A, Goldberg R, Guise J, Rockhill B, O'Connor A, Orr R, Boxwala A, Ng B, Foreman J, Fortin J. WISDOM: Women's Interactive System for Decisions on Menopause. 2003.
- Weber G, Halamka J, Beckett P, Lucy K, Alvarez J, Fournier M, Rouse R, Buckley J. Harvard Medical School eCommons Web Portal. 2003.
- Weber G. Database Design and Software Development for StreamSage, Inc. 2003-2004.
- Weber G. Mouse Retina SAGE Library: Online Data Analysis Tools for the Cepko Lab. 2003-2006.
- Weber G. Harvard Medicine Website: The Home Page for Harvard Medical School. 2004.
- Weber G, Lai M. Toxicology Database and Website for the Poison Control Center. 2005.
- Weber G. Analysis of the Estonia Tuberculosis Database. Center for Disease Control. 2005.
- Weber G, Ohno-Machado L, Racowsky C. Brigham and Women's Hospital In Vitro Fertilization Web Application. 2006.
- Weber G, Jeanmenne P, Jeanmenne T, Ohno-Machado L, Corrino J. Vertebral Compression Fractures Online Decision Support Tool. 2006.
- Weber G, Alvarez J, Beckett P, Gooley MD, Laitinen K, Lucy K, Price C, Rakauskas G, Rosen J, Zapatka S. MADRIS: Harvard Medical School's Medical and Dental Registration Information System. 2006.
- Weber G, Feldman S. Brigham and Women's Hospital Pap Smear Evaluation Center Electronic Medical Record and Research Database. 2006.
