Project Scientist
Research Emphasis
My postdoctoral work has focused on algorithmic methods for reconstructing transcriptional regulatory networks, the systems properties of integrated transcriptional regulatory and metabolic networks, and trying to discern what the topology of metabolic networks implies about their regulation. I am also interested in the engineering applications of in silico reconstructed organisms and their use for multicellular modeling.
Education
2001 Ph.D. Computer Science University of California, Santa Cruz Advisor: Kevin Karplus
1998 M.Sc. Computer Engineering University of California, Santa Cruz
1992 B.A. Physics University of Colorado, Boulder
Research Experience
Postdoctoral researcher, 2003-present Systems Biology Lab Bioengineering Department University of California, San Diego.
Research Scientist, 2002-2003 Bioinformatics Department deCODE Genetics, Iceland
Ph.D. student, 1995-2001 Bioinformatics Lab Department of Computer Science University of California, Santa Cruz
Undergraduate researcher, 1990-1992 Plasma Physics Lab Physics Department University of Colorado, Boulder
Teaching Experience
University of California, Santa Cruz 1996 Teaching assistant for Discrete Mathematics
Honors and Awards
University of California President's MICRO Fellowship, 1996.
University of Colorado, Undergraduate Research Opportunities Program Grant, 1990, 1991, 1992.
Computer Skills
Programming languages: C/C++, Python/Jython, Matlab, R, Java, MPI, Fortran, Perl
Operating systems: Linux, Windows
Other: MySQL, Apache
Publications
Articles
Conrad, T.M., Joyce, A.R., Applebee, M.K., Barrett, C.L., Xie, B., Gao, Y., and Palsson, B.O., Whole-genome Resequencing of Escherichia coli K-12 MG1655 Undergoing Short-term Laboratory Evolution in Lactate Minimal Media Reveals Flexible Selection of Adaptive Mutations, "Genome Biology", to appear.
Barrett, C.L., Herrgard, M.J., and Palsson, B.Ø., Decomposing complex reaction networks using random sampling, principal component analysis, and basis rotation,BMC Systems Biology, 3:30 (2009).
Cho, B.K., Zengler, K., Knight, E.M., Park, Y.S., Qiu, Y., Barrett, C.L., Lovley, D., and Palsson, B.O. (2008). Genome-wide analysis of protein-DNA interactions in bacteria, Microbial Systems Biology, in press.
Cho, B.K., Barrett, C.L., Knight, E.M., Park, Y.S., and Palsson, B.O., Genome-wide Analysis of the global transcriptional regulatory protein Lrp in Escherichia coli, Proceedings of the National Academy of Sciences, 105:19462-19467 (2008).
Katzman, S., Barrett, C., Thiltgen, R., Karchin, R., and Karplus, K., PREDICT-2ND: a tool for generalized protein local structure prediction, Bioinformatics, 24(21):2453-2459 (2008).
Cho, B.K., Knight, E.M., Barrett, C.L., and Palsson, B.O., Genome-wide Analysis of Fis Binding in Escherichia coli Indicates a Causative Role for A-/AT-tracts, Genome Research, 18:900-910 (2008).
Barrett, C.L., Kim, T.Y., Kim, H.U., Palsson, B.O., and Lee, S.Y., "Systems biology as a foundation for genome-scale synthetic biology", Current Opinion in Biotechnology, 17:'5 (2006).
Barrett, C.L. and Palsson, B.O., "Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach", PLoS Computational Biology, 2:5 (2006)
Barrett, C.L., Price, N.D., and Palsson, B.O., Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition, BMC Bioinformatics, 7:132 (2006).
Barrett, C.L., Herring, C.D., Reed, J.L., and Palsson, B.O., The Global Transcriptional Regulatory Network for Metabolism in Escherichia coli Exhibits Few Dominant Functional States, Proceedings of the National Academy of Sciences, 102(52):19103-8 (2005).
K. Karplus, R. Karchin, C. Barrett, S. Tu, M. Cline, M. Diekhans, L. Grate, J. Casper, R. Hughey., What is the value added by human intervention in protein structure prediction?, Proteins: Structure, Function and Genetics, 45(S5):86-91 (2002)
Gough, J., Chothia, C., Karplus, K., Barrett, C., and Hughey, R., "Optimal hidden Markov models for all sequences of known structure", "Currents in Computational Molecular Biology", S. Miyano, R. Shamir, and T. Takagi, editors. Universal Academy Press Inc., December 2000.
K. Karplus, C. Barrett, M. Cline, M. Diekhans, L. Grate, R. Hughey., Predicting protein structure using only sequence information1097-0134(1999)37:3+%3C121::AID-PROT16%3E3.0.CO;2-Q/abstract), Proteins: Structure, Function and Genetics, 37(Supp. 3):121-125 (1999).
Fischer, D., Barrett, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D., Karplus, K., Kelley, L, MacCallum, R., Pawowski, B., Rost, B., Rychlewski, L., and Sternberg, M., "CAFASP-1: Critical assessment of fully automated structure prediction methods", "Proteins: Structure, Function and Genetics", "37(S3)":209-217 (1999).
J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia., Citation Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homologues as Pairwise Methods, J. Mol. Biol. 284(4):1201-1210 (1998).
K. Karplus, C. Barrett, and R. Hughey, Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 14(10):846-856 (1998).
K. Karplus, K. Sjolander, C. Barrett, M. Cline, R. Hughey, D. Haussler, L. Holm, and C. Sander, Predicting protein structure using hidden Markov models1097-0134(1997)1+%3C134::AID-PROT18%3E3.0.CO;2-P/abstract), Proteins: Structure, Function and Genetics, 29(S1):134-139 (1997).
Barrett, C. and Hughey, R. and Karplus, K., Scoring Hidden Markov Models, CABIOS 13(2):191-199 (1997).
Barrett, C. and Robertson, S., Guiding of a Gun Plasma by a Permanent Magnet Octopole Field, Review of Scientific Instruments, 62(10), October 1991
Invited Talks
Barrett, C. "An introduction to the constraints-based approach to systems biology". Colorado State University at Fort Collins, April, 2006.
Barrett, C. "Investigation of non-pairwise protein score functions using sets of decoy protein structures". deCODE Genetics, Reykjavik, Iceland, 2002.
Cline, C. Barrett, C., and Karplus, K. "Making the most of your hidden Markov models". Intelligent Systems in Molecular Biology, Heidelberg, Germany, 1999. Tutorial.
K. Karplus, C. Barrett, M. Cline, M. Diekhans, L. Grate, andR. Hughey. "Predicting protein structure using only sequence information". Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP3). Asilomar, California, 1998.
Contact Information
Email Address: cbarrett@bioeng.ucsd.edu
Phone: (858)822-1168
Mailing Address: 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412