Weber Lab

Introduction

Griffin Weber, M.D., Ph.D., is an Associate Professor of Medicine in the Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center (BIDMC) and Harvard Medical School (HMS); the Director of the Biomedical Research Informatics Core (BRIC) at BIDMC; and a Research Associate in the Department of Biomedical Informatics at HMS.

One of Dr. Weber's research areas is in expertise mining and social network analysis. He invented an open source social networking website for scientists called Profiles RNS (http://profiles.catalyst.harvard.edu). It automatically mines large datasets such as PubMed, NIH ExPORTER, and the U.S. patent database to discover investigators' research areas and scientific networks. It presents these connections using temporal, geospatial, and network visualizations. The software has numerous applications, ranging from finding individual collaborators and mentors to understanding the dynamics of an entire research community. Profiles RNS is now used at dozens of universities across the country.

Dr. Weber is also an investigator on Informatics for Integrating Biology and the Bedside (i2b2), an NIH National Center for Biomedical Computing, for which he helped developed a web-based open source platform that enables a variety of functions including queries of large clinical repositories for hypothesis testing and identification of patients for clinical trials (http://i2b2.org). He also created the original prototype software for the Shared Health Research Information Network (SHRINE), which is a federated query tool that connects i2b2 databases across multiple institutions. More than 100 institutions worldwide use i2b2 and SHRINE to support clinical research.

Dr. Weber received his M.D. and Ph.D. in computer science from Harvard University in 2007. While still a student, he became the first Chief Technology Officer of Harvard Medical School and built an educational web portal that provides interactive online content to over 500 courses. His past research projects also include analyzing DNA microarrays, modeling the growth of breast cancer tumors, and creating algorithms for predicting life expectancy.

Contact Information

Email: weber@hms.harvard.edu

Phone: 617-432-6134

Address: 10 Shattuck St, Room 316a, Boston, MA 02115

Research Projects

Modeling scientific workforce dynamics using social network analysis

The scientific workforce is increasingly relying on teams to solve the most critical intellectual and social problems that confront us today. Team collaborations, a growing trend across all disciplines, yield publications with higher intellectual impact than single researchers; and, the careers of young scientists are influenced by relationships with others in the community. The project is developing a systems-based approach to studying scientific workforce dynamics that models the mechanisms of how new collaborations form and how these influence both the effectiveness of teams and the career trajectories of individual scientists.

Visualizing healthcare system dynamics in biomedical Big Data

Biomedical Big Data, such as electronic health records (EHR) and administrative claims, are records of patients' interactions with the healthcare system; for example, the date of a diagnosis is when a physician entered the code into the EHR, not when the patient developed the disease. Most researchers are either unaware of the distinction or naively treat it as noise. However, the proposed research will show, using a novel Data Visualization, that these subtle effects of the healthcare system on observational clinical data actually contain valuable information that could benefit biomedical research, clinical care, and health care policy.

Publications

  1. Hauser TH, Salastekar N, Schaefer EJ, Desai T, Goldfine HL, Fowler KM, Weber GM, Welty F, Clouse M, Shoelson SE, Goldfine AB. Effect of Targeting Inflammation With Salsalate: The TINSAL-CVD Randomized Clinical Trial on Progression of Coronary Plaque in Overweight and Obese Patients Using Statins. JAMA Cardiol. 2016 Jul 1; 1(4):413-23.
  2. Warner ET, Carapinha R, Weber GM, Hill EV, Reede JY. Faculty Promotion and Attrition: The Importance of Coauthor Network Reach at an Academic Medical Center. J Gen Intern Med. 2016 Jan; 31(1):60-7.
  3. Warner ET, Carapinha R, Weber GM, Hill EV, Reede JY. Considering Context in Academic Medicine: Differences in Demographic and Professional Characteristics and in Research Productivity and Advancement Metrics Across Seven Clinical Departments. Acad Med. 2015 Aug; 90(8):1077-83.
  4. Donato J, Campigotto F, Uhlmann EJ, Coletti E, Neuberg D, Weber GM, Zwicker JI. Intracranial hemorrhage in patients with brain metastases treated with therapeutic enoxaparin: a matched cohort study. Blood. 2015 Jul 23; 126(4):494-9.
  5. Weber GM. Federated queries of clinical data repositories: Scaling to a national network. J Biomed Inform. 2015 Jun; 55:231-6.
  6. Weber GM, Mandl KD, Kohane IS. Finding the missing link for big biomedical data. JAMA. 2014 Jun 25; 311(24):2479-80.
  7. Mandl KD, Kohane IS, McFadden D, Weber GM, Natter M, Mandel J, Schneeweiss S, Weiler S, Klann JG, Bickel J, Adams WG, Ge Y, Zhou X, Perkins J, Marsolo K, Bernstam E, Showalter J, Quarshie A, Ofili E, Hripcsak G, Murphy SN. Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): architecture. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):615-20.
  8. Klann JG, Buck MD, Brown J, Hadley M, Elmore R, Weber GM, Murphy SN. Query Health: standards-based, cross-platform population health surveillance. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):650-6.
  9. Kahlon M, Yuan L, Daigre J, Meeks E, Nelson K, Piontkowski C, Reuter K, Sak R, Turner B, Weber GM, Chatterjee A. The use and significance of a research networking system. J Med Internet Res. 2014; 16(2):e46.
  10. Weber GM, Kohane IS. Extracting physician group intelligence from electronic health records to support evidence based medicine. PLoS One. 2013; 8(5):e64933.
  11. Weber GM. Identifying translational science within the triangle of biomedicine. J Transl Med. 2013; 11:126.
  12. Weber GM. How many patients are "normal"? Only 1.55%. AMIA Jt Summits Transl Sci Proc. 2013; 2013:79.
  13. McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS. SHRINE: enabling nationally scalable multi-site disease studies. PLoS One. 2013; 8(3):e55811.
  14. Weber GM. Federated queries of clinical data repositories: the sum of the parts does not equal the whole. J Am Med Inform Assoc. 2013 Jun; 20(e1):e155-61.
  15. Natter MD, Quan J, Ortiz DM, Bousvaros A, Ilowite NT, Inman CJ, Marsolo K, McMurry AJ, Sandborg CI, Schanberg LE, Wallace CA, Warren RW, Weber GM, Mandl KD. An i2b2-based, generalizable, open source, self-scaling chronic disease registry. J Am Med Inform Assoc. 2013 Jan 1; 20(1):172-9.
  16. Kohane IS, McMurry A, Weber G, MacFadden D, Rappaport L, Kunkel L, Bickel J, Wattanasin N, Spence S, Murphy S, Churchill S. The co-morbidity burden of children and young adults with autism spectrum disorders. PLoS One. 2012; 7(4):e33224.
  17. Murphy SN, Dubey A, Embi PJ, Harris PA, Richter BG, Turisco F, Weber GM, Tcheng JE, Keogh D. Current state of information technologies for the clinical research enterprise across academic medical centers. Clin Transl Sci. 2012 Jun; 5(3):281-4.
  18. Weber GM, Barnett W, Conlon M, Eichmann D, Kibbe W, Falk-Krzesinski H, Halaas M, Johnson L, Meeks E, Mitchell D, Schleyer T, Stallings S, Warden M, Kahlon M. Direct2Experts: a pilot national network to demonstrate interoperability among research-networking platforms. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i157-60.
  19. Wang KC, Jeanmenne A, Weber GM, Thawait SK, Thawait S, Carrino JA. An online evidence-based decision support system for distinguishing benign from malignant vertebral compression fractures by magnetic resonance imaging feature analysis. J Digit Imaging. 2011 Jun; 24(3):507-15.
  20. Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, Kohane I. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc. 2010 Mar-Apr; 17(2):124-30.
  21. Milo R, Jorgensen P, Moran U, Weber G, Springer M. BioNumbers--the database of key numbers in molecular and cell biology. Nucleic Acids Res. 2010 Jan; 38(Database issue):D750-3.
  22. Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc. 2009 Sep-Oct; 16(5):624-30.
  23. Shen LQ, Child A, Weber GM, Folkman J, Aiello LP. Rosiglitazone and delayed onset of proliferative diabetic retinopathy. Arch Ophthalmol. 2008 Jun; 126(6):793-9.
  24. Weber G, Weber G. Pizza Combinatorics Revisited. The College Mathematics Journal. 2006; 37(1):43-4.
  25. Weber G, Ohno-Machado L, Shieber S. Representation in stochastic search for phylogenetic tree reconstruction. J Biomed Inform. 2006 Feb; 39(1):43-50.
  26. Col NF, Weber G, Stiggelbout A, Chuo J, D'Agostino R, Corso P. Short-term menopausal hormone therapy for symptom relief: an updated decision model. Arch Intern Med. 2004 Aug 9-23; 164(15):1634-40.
  27. 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 Biol. 2004 Sep; 2(9):E247.
  28. Weber G, Vinterbo S, Ohno-Machado L. Multivariate selection of genetic markers in diagnostic classification. Artif Intell Med. 2004 Jun; 31(2):155-67.
  29. 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.
  30. Michaelson JS, Satija S, Moore R, Weber G, Halpern E, Garland A, Kopans DB. Journal of Women's Imaging. Estimates of Breast Cancer Growth Rate and Sojourn Time from Screening Database Information. 2003; (1):11-19.
  31. Michaelson JS, Satija S, Moore R, Weber G, Halpern E, Garland A, Kopans DB. Journal of Women's Imaging. Estimates of the Sizes at Which Breast Cancers Become Detectable on Mammographic and Clinical Grounds. 2003; (1):3-10.
  32. 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.
  33. Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M. Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet. 2002 Feb; 30(2):141-2.
  34. Col NF, Fortin JM, Weber G. Clearinghouse Number JC020766. Using the Web to Promote Smoking Cessation and Health for College-Aged Women. Educational Resources Information Center. 2002.
  35. Weber G, Vinterbo S, Ohno-Machado L. Building an asynchronous web-based tool for machine learning classification. Proc AMIA Symp. 2002; 869-73.
  36. Ohno-Machado L, Vinterbo S, Weber G. Journal of Intelligent and Fuzzy Systems. Classification of Gene Expression Data Using Fuzzy Logic. 2002; 12(1):19-24.
  37. Michaelson J, Satija S, Moore R, Weber G, Halpern E, Garland A, Puri D, Kopans DB. The pattern of breast cancer screening utilization and its consequences. Cancer. 2002 Jan 1; 94(1):37-43.
  38. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A. 2001 Nov 20; 98(24):13790-5.
  39. Comander J, Weber GM, Gimbrone MA, Garcia-Cardena G. Argus--a new database system for Web-based analysis of multiple microarray data sets. Genome Res. 2001 Sep; 11(9):1603-10.
  40. Michaelson JS, Satija S, Moore R, Weber G, Halpern E, Garland A, Kopans DB. Journal of Women's Imaging. Observations on Invasive Breast Cancer Diagnosed in a Service Screening and Diagnostic Breast Imaging Program. 2001; 3:99-104.
  41. Weber G, Weber G. Pizza Combinatorics. The College Mathematics Journal. 1995; 26(2):141-3.