Jonathan Karr

Education

Stanford University, Stanford CA
Ph.D. in Biophysics, 2014
M.S. in Medicine, 2014
Massachusetts Institute of Technology, Cambridge MA
S.B. in Physics, 2006
S.B. in Brain & Cognitive Sciences, 2006

Honors & awards

NSF INSPIRE Award
NIH/NIGMS Maximizing Investigators' Research Award
Genomeweb Young Investigator
National Academy of Sciences / Kavli Foundation Frontiers of Science Fellow
Keystone Symposia NSF Scholarship
James S. McDonnell Foundation Postdoctoral Fellowship Awards in Studying Complex Systems
Sage Congress Young Investigator Award
Keystone Symposia Future of Science Fund Scholarship
Stanford School of Medicine Excellence in Teaching Award
National Defense Science and Engineering Graduate Fellowship
National Science Foundation Graduate Fellowship
Department of Homeland Security Graduate Fellowship
Stanford University Translational Medicine Scholarship
Stanford University Graduate Fellowship
MIT Phi Beta Kappa
MIT Sigma Pi Sigma
MIT Department of Brain & Cognitive Sciences Award for Outstanding Academics

Professional experience

Department of Genetics & Genomic Sciences, Mount Sinai School of Medicine, New York NY, 2014–present
Fellow
Developed comprehensive computational models of health and disease.
Department of Bioengineering, Stanford University, Stanford CA, 2007–2014
Research Assistant to Prof. Markus Covert
Developed the first comprehensive "whole-cell" computational model. Developed a novel hybrid mathematical framework. Assembled a new molecular biology database. Designed and integrated sub-models of 28 cellular processes. Developed novel algorithms for parameter estimation. Constructed new tools for exploratory data analysis. Conducted a forward genetic screen to validate the model. Investigated the molecular determinants of M. genitalium growth and division to discover new biology. Published work in Cell and Bioinformatics. Mentored several undergraduate and graduate students.
Department of Brain & Cognitive Sciences, MIT, Cambridge MA, Spring 2006
Research Assistant to Prof. Jim DiCarlo
Helped develop novel assistive surgical technology to support visual system research in non-human primates. Developed a device that detects the 3-D localization of implanted electrodes and fiducial markers in rhesus monkeys using two pairs of x-ray sources and detectors. Integrated x-ray hardware into an existing surgical systems. Implemented hardware control and image acquisition and processing software. Technology was published in J Neurophysiology.
Department of Brain & Cognitive Sciences, MIT, Cambridge MA, Summers 2004–05
Research Assistant to Prof. Michale Fee
Developed novel assistive surgical technology to support systems neuroscience research of learning and memory in song birds. Designed and constructed technology that guides the localization of electrode implantation in songbirds. Integrated technology into existing experimental protocols.
Biotechnology Division, NIST, Gaithersburg MD, Summer 2003
Research Assistant to Dr. Adolfas Gaigalas
Improved fluorescence measurement techniques by modulating excitation to reduce quenching. Integrated modulation hardware into an existing imaging system.
Neuroscience Division, Walter Reed Army Institute of Research, Forest Glen MD, Summers 2001–02
Research Assistant to Dr. Richard Bauman
Evaluated the neuroprotective efficacy of pharmaceuticals against trauma. Simulated brain injury in rats by blunt head trauma and hypoxia. Quantitated neuroprotective efficacy using cognitive (Morris water maze) and vestibulomotor (beam-balance and narrow beam-walk) tasks.

Peer-reviewed publications

Karr JR, Llorens V, Lluch-Senar M, Serrano L & Covert MW. A whole-cell model of Mycoplasma pneumoniae guides biological design. (In preparation).
Cokelaer T, Bansal M, Bare C, Bila E, Bot BM, Neto EC, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Nore R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G & Saez-Rodriguez J. DREAMTools: a Python package for scoring collaborative challenges. F1000Res 4, 1030 (2015).
Kazakiewicz D*, Karr JR*,†, Langner KM & Plewczynski D. Combined systems and structural modeling repositions antibiotics for Mycoplasma genitalium pii, S1476-9271(15)30089-X (2015).
Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA & Meyer P. Summary of the DREAM8 parameter estimation challenge: Toward parameter identification for whole-cell models. PLoS Comput Biol 11, e1004096 (2015).
Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N & Covert MW. NetworkPainter: Dynamic intracellular pathway animation in Cytobank. BMC Bioinformatics 16, 172 (2015).
Karr JR*, Phillips NC* & Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database (2014).
Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B & Covert MW. Accelerated discovery via a whole-cell model. Nat Methods 10, 1192–1195 (2013).
Lee R*, Karr JR* & Covert MW. WholeCellViz: data visualization for whole-cell models. BMC Bioinformatics 14 (2013).
Purcell O, Jain B, Karr JR, Covert MW & Lu T. Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112 (2013).
Karr JR, Sanghvi JC, Macklin DN, Arora A & Covert MW. WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res 41 D787–792(2013).
Karr JR*, Sanghvi JC*, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI & Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389–401 (2012).
Covert MW, Xiao N, Chen TJ & Karr JR. Integrated flux balance analysis model of Escherichia coli. Bioinformatics 24, 2044–2050 (2008).
*These authors contributed equally to this work
Corresponding author

Conference Proceedings

Goldberg AP, Chew YH & Karr JR. Toward scalable whole-cell modeling of human cells. ACM SIGSIM Conf Princip Adv Discrete Simul, 259–262 (2016).
Kovatch P, Costa A, Chen R, Klein R, Costa KD, Hajjar RJ, Fayad Z, Margolies L, Mendelson D, Yankelevitz D, Goldberg AP, Karr JR, Rice JJ & Gurev V. The potential for exascale to transform healthcare. Supercomput Front (2016).
Chang R, Karr JR & Schadt EE. Causal inference in biology networks with integrated belief propagation. Pac Symp Biocomput, 359–70 (2015).

Reviews & perspectives

Medley JK & Karr JR. Guidelines for reproducibly building and simulating systems biology models. IEEE Trans Biomed Eng 63, 2015–2020 (2016).
Waltemath D*, Karr JR* et al. Toward community standards and software for whole-cell modeling. IEEE Trans Biomed Eng 63, 2007–2014 (2016).
Karr JR, Takahasi K & Funahashi A. The principles of whole-cell modeling, 27, 18–24 (2015).

Lay articles

Karr JR, Chew YH & Goldberg AP. Whole-cell computational models can predict how genes influence behavior. Atlas of Science (2015).

Invited presentations

ISMB Conference. Orlando FL, July 2016.
Seattle Modeling Workshop. Seattle WA, May 2016.
Bioinformatics and Systems Biology Conference. Lunteren NL, Apr 2016.
Bioinformatics and Systems Biology Conference PhD Retreat. Lunteren NL, Apr 2016.
Whole-Cell Modeling Summer School. Barcelona SP, Apr 2016.
Advances in Systems and Synthetic Biology Workshop. Evry FR, Mar 2016.
COMBINE Forum. Salt Lake City UT, Oct 2015.
Whole-Cell Modeling School. Rostock GR, Mar 2015.
Integrative Cell Models Workshop, Lorentz Center. Leiden NL, Jan 2015.
Japan-American Frontiers of Science Symposium. Tokyo JP, Dec 2014.
Systems Biology and Systems Medicine School, Lake Como School of Advanced Studies. Como IT, Sep 2014.
International Conference on Systems Biology. Copenhagen DK, Aug 2013.

Contributed presentations

NY BIG Conference. New York NY, June 2016.
Keystone Symposium – Precision Genome Engineering and Synthetic Biology. Breckenridge CO, Mar 2013.
Biological Computation at Stanford Symposium. Stanford CA, Oct 2012.
Microbiology Student Symposium. UC Berkeley, Apr 2012.
Bay Area Microbial Pathogenesis Symposium. UCSF, Mar 2012.
Keystone Symposium – Complex Traits. Breckenridge CO, Feb 2012.
Biophysics Graduate Program Conference. Stanford CA, Jan 2012.
Biological Computation at Stanford Symposium. Stanford CA, Nov 2011.
Biophysical Society Annual Meeting. Baltimore MD, Mar 2011.
Biological Computation at Stanford Symposium. Stanford CA, Nov 2010.
KMZ Tri-Lab Retreat. Santa Cruz CA, Dec 2009.

Seminars

University of Connecticut Health Center. Farmington CT, April 2017
Brigham and Women's Hospital. Boston MA, Oct 2016
National Institute for Agricultural Research. Jouy-en-Josas FR, Mar 2016
National Centre for Scientific Research. Paris FR, Mar 2016
Children's Hospital of Pennsylvania/University of Pennsylvania, Department of Biomedical and Health Informatics. Philadelphia, Feb 2016
Mt Sinai School of Medicine, Dept of Genetics & Genomic Sciences. New York NY, Jun 2015
University of Bordeaux / National Institute for Agricultural Research (INRA). Bordeaux FR, Mar 2015.
National Research Council Institute of Systems Informatics Analysis (IASI-CNR). Rome IT, Sep 2014.
IBM Center for Computational Biology. Yorktown Heights, Feb 2014.
Center for Regulatory Genomics. Barcelona, Sep 2013.
Massachusetts Institute of Technology Synthetic Biology Center. Cambrige MA, Apr 2013.
Northeastern University Center for Complex Network Research. Boston MA, Apr 2013.
Stanford University Department of Pediatrics. Stanford CA, Apr 2013.
Massachusetts General Hospital Center of Systems Biology. Boston MA, Apr 2013.
Mt Sinai School of Medicine, Dept of Genetics & Genomic Sciences. New York NY, Apr 2013
Columbia University Computational Biology & Bioinformatics Center. New York NY, Apr 2013
University of California San Diego, Department of Medicine. La Jolla CA, Apr 2013
Seminar Series in BioMathematical Methodology. Stanford CA, Jul 2012.
Molecular Biophysics Seminar. Stanford CA, Nov 2011.
Bioengineering Department Colloquium. Stanford CA, Oct 2007.

Professional service

Co-organizer, SysMod ISCB Significant Interest Group, 2016–present
Co-organizer, Whole-Cell Modeling Summer School, 2016
Reviewer, National Science Foundation, 2016
Member, Scientific Committee, Pacific Symposium on Biocomputing, 2015–present
Ad hoc reviewer, National Institutes of Health BUILD Initiative, 2015
Ad hoc reviewer, National Science Foundation, 2014
Organizer, Graduate fellowships information session, Mount Sinai, 2014–2015
Reviewer, NSF Graduate Research Fellowship Program, 2013–present
Organizer, Whole-cell parameter estimation DREAM challenge, 2013
Member, International Scientific Committee, ICSB 2013
Member, Stanford Biophysics Graduate Program Student Committee, 2006–2013
Member, Stanford Biosciences Graduate Student Advisory Committee, 2012–2013
Co-organizer, "Writing for Success: Winning a Graduate Fellowship" Info Session, Soc Adv Chicanos & Native Americans in Science Conf, 2011
Co-organizer, Biological Computation at Stanford Symposium, 2009
Webmaster, International Conference on Systems Biology, 2009

Ad-hoc Reviewer

Bioinformatics
BMC Systems Biology
Cell
Computation
Computational Biology and Chemistry
Molecular Systems Biology
Nature
Nature Partner Journals Systems Biology and Applications
Pacific Symposium on Biocomputing
PLoS Computational Biology
PLoS One
Science
See review record at Publons.

Teaching

Organizer, Whole-Cell Modeling Summer School, Barcelona SP, Apr 2016
Organizer, Introduction to multi-algorithm whole-cell modeling, Paris FR, Mar 2016
Instructor, Whole-Cell Modeling Standards Workshop, Rostock GR, Mar 2015
Presented lecture on whole-cell modeling methods. Worked with students to develop and integrate sub-models of a new integrative whole-cell model.
Lecturer, Systems Biology and Systems Medicine School, Lake Como School of Advanced Studies, Como IT, Sep 2014
Presented lecture on integrative computational models.
Program assistant, Stanford Summer Research Program/Amgen Scholars Program, Stanford CA, Summer 2012
Led professional development workshops for undergraduate students focused on oral and poster presentations, CVs/resumes, and graduate school and fellowship applications.
Teaching Assistant, MCP 256: How cells work, Stanford University, Stanford CA, Spring 2008
Led in-class discussions. Tutored students. Created assignment solutions and evaluated assignments. Awarded the Stanford School of Medicine Excellence in Teaching Award to Biosciences Graduate Students.
Tutor, 8.01X: Electricity & Magnetism, MIT, Cambridge MA, Spring 2003
Reviewed course content and assignments with students.
Developer, MasteringPhysics CyberTutor Project, MIT, Cambridge MA, Spring 2003
Developed interactive online tutorials and problems for introductory physics courses.

Outreach

Mentor, Stanford Bioscience Student Association Mentoring Program, 2012–2013
Volunteer, Humanimal Connection, San Mateo CA, 2010–2013
Volunteer, MIT Educational Council, Cambridge MA, 2008–2012
Mentor, Stanford Medical Youth Science Program, Stanford CA, 2007–2011
Mentor, Stanford University Pre-Grad/Pre-Med Mentoring Program, Stanford CA, 2007–2008
Mentor, Stanford University Minority Medical Alliance Mentorship Program, Stanford CA, 2007
Volunteer, Recording for the Blind & Dyslexic, Cambridge MA, 2005