Jonathan Karr
Academic Appointments
-
Ph.D. Student in Dean's Office, admitted Autumn 2006
-
Masters of Medicine, admitted Autumn 2006
- Graduate Minicourse Committee Member, Dean's Office
Key Documents
Contact Information
- Contact Information
Personal Information Email Tel (650) 498-6272
Professional Overview
Stanford Advisors
| Markus Covert: | Doctoral Dissertation Advisor (AC) |
Lab Affiliations
- Markus Covert, Covert Systems Biology Lab (6/1/2007 )
Education History
| Bachelor of Science: | Massachusetts Institute of Technology, Physics, Brain & Cognitive Sci (2006) |
Honors and Awards
- Postdoctoral Fellowship Awards in Studying Complex Systems, James S. McDonnell Foundation (September 2012)
- Future of Science Fund Scholarship, Keystone Symposia (February 2012)
- Young Investigator Award, Sage Congress (April 2012)
- Stanford School of Medicine Excellence in Teaching Award to Biosciences Graduate Students, Stanford University (2008)
- NSDEG Graduate Fellowship, US Department of Defense (2008)
- NSF Graduate Research Fellowship, National Science Foundation (2008)
Service, Volunteer, and Community Work
- Mentor, Stanford Medical Youth Science Program (2007 - 2011)
- Educational Counselor, MIT (9/1/2008)
- Organizer, Biological Computation at Stanford Symposium (11/3/2009)
- Webmaster, International Conference on Systems Biology (9/1/2009)
- Mentor, Stanford University Pre-Grad/Pre-Med Mentoring Program (10/1/2007 - 5/31/2009)
- Mentor, Stanford University Minority Medical Alliance Mentorship Program (9/1/2007 - 5/31/2008)
- Member, Biosciences Graduate Student Advisory Committee , Stanford University (5/18/2012 - present)
- Co-organizer, "Writing for Success: Winning a Graduate Fellowship" Information Session, Society for Advancement of Chicanos and Native Americans in Science Conference (10/2011)
- Co-organizer, Biological Computation at Stanford Symposium , Stanford University (11/2009)
- Webmaster, International Conference on Systems Biology (9/2009)
- Volunteer, Recording for the Blind & Dyslexic (2005)
- Program assistant, Stanford Summer Research Program (6/1/2012 - 8/31/2012)
Scientific Focus
Current Research Interests
I am interested in how cellular physiology arises from the interactions of biomolecules. Currently I'm developing a gene-complete computational model of the life cycle of a single Mycoplasma genitalium bacterial cell. The model accounts for the specific function of every RNA and protein gene product and tracks the dynamics of every metabolite, DNA, RNA, and protein molecule across the entire cell cycle.
Research Projects
- A Whole Cell Model of Mycoplasma genitalium (Dissertation)
Presentations
Publications
- WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res. 2013; (Database issue): D787-92
- A whole-cell computational model predicts phenotype from genotype. Cell. 2012; (2): 389-401
- Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics. 2008; (18): 2044-50
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