Stanford University, Stanford, CA
Ph.D. in Biomedical Informatics

The Johns Hopkins University
M.S. in Bioinformatics

University of Southern California
B.S. in Computer Science
Honors: Cum Laude

In progress




William R. Hewlett Fellowship (a Stanford Graduate Fellowship)
Next-Gen Tomorrow's PI, Genome Technology Magazine
Student Travel Award, Pacific Symposium on Biocomputing
National Institute of Biomedical Imaging and Bioengineering Fellowship
National Library of Medicine Training Grant, Stanford University
National Institutes of Health Post baccalaureate IRTA
Presidential Scholar, University of Southern California
Thematic Options Program, University of Southern California
Resident Honors Program, University of Southern California

June 2008 (3 years)
Jan. 2008
Jan. 2008
Oct. 2007 (1 year)
Sept. 2006 (3 years)
Aug. 2005 - Aug. 2006
Aug. 1999 - May 2003
Aug. 1999 - May 2001
Aug. 1999 - May 2000

Journal Publications

Chen DP, Dudley JT, Butte AJ. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. BMC Bioinformatics 2010, 11(Suppl 9):S4 (28 October 2010)

Zheng M, Ravindran P, Wang J, Epstein RH, Chen DP, Butte AJ, Peltz G. An Optimistic Prognosis for the Clinical Utility of Laboratory Test Data. Anesth Analg. 2010 Sep 1 

Chen DP, Morgan AA, Butte AJ. Validating pathophysiological models of aging using clinical electronic medical records. J Biomed Inform. 2010 Jun;43(3):358-64.

Yao J, Chen D. Live level set: A hybrid method of livewire and level set for medical image segentation. Med Phys. 2008 Sep;35(9):4112-20.

Peer Reviewed Conference Publications

Zimmerman NH, Patel C, Chen DP. CHMP: A collaborative medical history portal. AMIA Annu Symp Proc. 2008 Nov 6:859-63.

Dudley J, Chen DP, Butte AJ. Using SNOMED-CT for translational genomics data integration. KR-MED 2008.

Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Novel integration of hospital  electronic medical records and gene expression measurements to identify genetic markers of maturation. Pac Symp Biocomput. 2008;:243-54.

Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity. AMIA Annu Symp Proc. 2007 Oct 11:115-9.

Chen D, Yao J. Improved livewire methods for segmentation on low contrast and noisy images. Proceedings of SPIE 2007 Mar;6512.

Yao J, Chen D, Lu W, Premkumar A. Uterine fibroid segmentation and volume measurement on MRI. Proceedings of SPIE 2006 Mar; 6413.


Chen DP, Sikka D, Butte AJ. Elucidating the effects of disease on pediatric development using data from electronic medical records. Stanford Bioscience Admissions Poster Session. Stanford University, Stanford, CA. March 5, 2009

Chen DP, Butte AJ. Integration of clinical and gene expression data to create genome-clinome networks. National Library of Medicine Informatics Training Conference. National Library of Medicine. Bethesda, MD. July 7-9, 2008.

Chen DP, Butte AJ. Integration of hospital electronic medical records and gene expression measurements to find aging related biomarkers and associated genes. NSF Biomedical Informatics Workshop. Menucha, OR. December 3-5, 2007.

Chen DP, Butte AJ. Using clinical laboratory data and gene expression measurements to infer gene function.  National Library of Medicine Informatics Training Conference. Stanford University, Stanford, CA. June 26-27, 2007.

Chen DP, Yao J. The measurement and segmentation of uterine fibroid using magnetic resonance imaging. National Institutes of Health Summer Poster Session. National Institutes of Health, Bethesda, MD. August 2005.

Teaching Experience

Stanford Institutes of Medicine Summer Research Program Mentor. Student was named an Intel Science Talent Search semifinalist for 2009 and awarded the grand prize award for Best Biological Technical Paper at the Synopsys Silicon Valley Science and Technology Championship in 2009. June 2008 - August 2008

Teaching Assistant, Representations and Algorithms in Computational Molecular biology
(BIOMEDIN 214), Stanford University. April 2008 - June 2008

Teaching Assistant, Translational Biomedical Informatics (BIOMEDIN 217), Stanford University. January 2008 - March 2008

Related Experience

Stimulomics, Inc.
Founder, CFO
April 2009 - present

Menome, Inc.
Founder, CFO
August 2008 - December 2009

National Institutes of Health - Department of Diagnostic Radiology, Bethesda, MD
Post baccalaureate IRTA Fellow
August 2005 - August 2006
Developed a hybrid method of image segmentation by combining level sets and livewire to generate more accurate boundaries for noisy, inhomogeneous, and gapped boundaries.

National Institutes of Health - Department of Diagnostic Radiology, Bethesda, MD
Summer Intern
May 2005 - August 2005
Developed a semi-automatic segmentation method used by radiology technicians for the purpose of acquiring volumetric information of uterine leiomyomas. Developed software to concurrently register and visualize current anatomic pointer position in axial, coronal, and sagittal slices of MRI scans.

Rhodes Publications, Los Angeles, CA
Web Programmer
February 2003 - December 2004
Developed e-commerce based employment and retail sites. Managed internal computer systems: networking, database administration, and systems administration.

Relevant Knowledge and Skills

Clinical data analysis, electronic health records, parametric statistics, non-parametric statistics, randomization, bootstrap, machine learning, gene expression analysis (microarrays, functional analysis), temporal abstraction


C, C++, Java, Perl, Python, Ruby, JSP, PHP, Ruby on Rails, HTML, Flex, MySQL, Oracle 10i, R, LINUX, Windows


American Medical Informatics Association
American Association for the Advancement of Science

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