James M. Carothers, Ph.D.

Assistant Professor, Chemical Engineering 

Adjunct Assistant Professor, Bioengineering

Member, Molecular Engineering & Sciences Institute

Member, Center for Synthetic Biology

University of Washington



University of California Berkeley, Berkeley, CA

Postdoctoral Fellowship in Synthetic Biology

Harvard University, Cambridge, MA

Ph.D., Biological Chemistry and Molecular Pharmacology

Yale University, New Haven, CT

B.S., Molecular Biophysics and Biochemistry

Selected awards

2016 University of Washington College of Engineering Junior Faculty Award (1 of 2)

2016 Diverse: Issues in Higher Education Emerging Scholars (1 of 12 in U.S., all academic disciplines)

University of Washington Inaugural Presidential Innovation Award (1 of 2 $500K research awards)

Alfred P. Sloan Research Fellowship (1 of 12 in Computational Molecular Biology selected in North America)

Jane Coffin Childs Memorial Fund Postdoctoral Fellowship (awarded to 5% of International applicants) 

National Science Foundation Graduate Fellowship (awarded to 10% of US applicants)

Harvard University Graduate Prize Fellowship

Yale University Harry Gray Browne Scholarship

Yale University James B. Clow Scholarship

American Honda Scholarship for First Place at National Science Olympiad

Selected previous research experience

University of California Berkeley and DOE Joint BioEnergy Institute, Emeryville, CA

Jane Coffin Childs Postdoctoral Research Fellow and Research Specialist with Professor Jay D. Keasling

Design-driven engineering of RNA-based genetic control systems to program function for synthetic biology applications in chemical synthesis using mechanistic biochemical and biophysical modeling, in vitro selection, RNA biochemistry and molecular biology.

Howard Hughes Medical Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA

National Science Foundation Graduate Fellow with Professor Jack W. Szostak

Experimental investigations of informational complexity and functional activity of synthetic ligand- binding RNA structures (aptamers) using information theory and statistical analysis, in vitro selection and 3D solution NMR.

Howard Hughes Medical Institute and Yale School of Medicine
, New Haven, CT

Undergraduate researcher with Professor Sankar Ghosh

Identification and molecular characterization of novel factors involved in Toll and Interleukin-1 signaling of NF-kB activation using bioinformatics, yeast two-hybrid cloning and mammalian tissue culture.

Selected teaching experience

BIOEN 423/523: Introduction to Synthetic Biology (40 students); NME 220: Introduction to Molecular and Nanoscale Principles (55-70 students)BIOEN 424/524: Advanced Synthetic Biology for Applications (8-15 students)ChemE 437: Chemical Engineering Laboratory Unit Ops II (Bioethanol production and processing)(24-65 students)

Selected leadership experience

Research Mentor, University of Washington, Seattle, WA

Hosted research experiences for >25 students from UW high school and beginning outreach programs, including: UW Early Engineering Institute (emphasis on students of color), WiSE UP Summer Bridge Program (women), and the UW Math Academy (low resource high schools)

Member, Faculty Council on Multicultural Affairs, University of Washington, Seattle, WA

Co-Founder, iCLEM Program, U.C. Berkeley and Joint BioEnergy Institute, Emeryville, CA

Created intensive 8-week paid research internship for low income San Francisco Bay Area high school students and teachers. >40 students and 15 teachers to date with 90% of participants attending college and 80% majoring in STEM fields.

Fellow, Startup Leadership Program, Sunnyvale, CA

Chosen for highly-selective training program. Organized and participated in 9 months of business workshops with leading entrepreneurs and VCs.

Selected recent presentations

Molecular Programming Project Symposium, Seattle, WA (2016)Synthetic Biology Congress, London, U.K. (2015); Society for Laboratory Automation Systems, Webinar (2015); Engineering Life, Nanobiology and Applied Physics Symposium, TU Delft, Netherlands (2014); BIO Pacific Rim Summit on Industrial Biotechnology & Bioenergy, San Diego, CA. (2013); AIChE National Meeting, San Francisco, CA. (2013); Computational Biology Seminar Series, Pacific Northwest National Laboratory, Richland, WA. (2013); 9th Computational and Theoretical Biology Symposium, Rice University, Houston, TX. (2012); ISMB Biological Systems Design, Long Beach, CA.; Synthetic Biology for Global Health, Rathenau Institute, The Hague, Netherlands. 

Selected review service

Proposal Review Panels: National Science Foundation – MCB (2016); National Science Foundation – CBET (2015); DOE/Joint Genome Institute (2015); WA Joint Center for Aerospace Technology Innovation (2015); NSF Graduate Fellowships (2015); DOE Genome Science Program – Microbes for Biofuels (2014); DOE/Joint Genome Institute (2014);NSF Graduate Fellowships (2014); Stanford Global Climate & Energy Proposals (2013); DOD/ASEE SMART Scholarship Program (2013); European Research Council Advanced/Starting Grant (2009)

Journal Peer Review: ACS Synthetic Biology; Biotechnology & Bioengineering; Chemical ReviewsComputational Biology & Chemistry; Metabolic Engineering; Microbial Cell Factory; Nature Biotechnology; Nature Chemical Biology; Nature Methods; Nature Reviews Microbiology; Nucleic Acids Research; PloS Computational Biology; RNA; Scientific Reports