Jennifer Reed

Faculty Fellow Researcher

I am a Faculty Fellow in the Bioengineering Department at UCSD. I teach classes part time as a lecturer while continuing my research. My research interests involve (1) expanding and developing regulatory and metabolic models of microorganisms and (2) analyzing these models to better understand an organism’s phenotype and capabilities.




Reed, J.L., Patel, T.R., Chen, K.H., Joyce, A.R., Applebee, M.K., Herring, C.D., Bui, O.T., Knight, E.K., Fong, S.S. and Palsson, B.Ø., "Systems Approach to Refining Genome Annotation," PNAS, accepted (2006). Joyce, A.R., Reed, J.L., White, A., Edwards, R., Osterman, A., Baba, T., Mori, H., Lesely, S.A., Palsson B.Ø, and Agarwalla, S., "Experimental and computational assessment of conditionally essential genes in E. coli," Journal of Bacteriology, accepted (2006).

Reed, J.L., Famili, I., Thiele, I. and Palsson, B.Ø., "Towards multidimensional genome annotation," Nature Reviews Genetics, 7:130-141 (2006).

Barrett, J.A., Herring, C.D., Reed, J.L. and Palsson, B.Ø., "The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states," PNAS, 102:19103-19108 (2005).

Papin, J.A., Reed, J.L. and Palsson, B.Ø., "Hierarchical thinking in network biology: the unbiased modularization of biochemical networks," Trends in Biochemical Sciences, 29:641-647 (2004).

Price, N.D., Reed, J.L. and Palsson, B.Ø., "Genome-scale Models of Microbial Cells:Evaluating the consequences of constraints," Nature Reviews Microbiology, 2:886-897 (2004).

Reed, J.L. and Palsson, B.Ø., "Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states" Genome Research, 14:1797-1805 (2004).

Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J., and Palsson, B.Ø., "Integrating high-throughput and computational data elucidates bacterial networks", Nature, 429: 92-96 (2004).

Reed, J.L., Vo, T.D., Schilling, C.H., and Palsson, B.Ø., "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)", Genome Biology, 4(9): R54.1-R54.12 (2003).

Reed, J.L. and Palsson, B.Ø., "Thirteen Years of Building Constraints-Based in silico Models of Escherichia coli," Journal of Bacteriology, 185(9): pp. 2692-2699 (2003).

Price, N.D., Reed, J.L., Papin, J.A., Wiback, S.J., and Palsson, B.Ø., "Network-based Analysis of Regulation in the Human Red Blood Cell", Journal of Theoretical Biology, 225(2): 1985-194 (2003).

Price, N.D., Reed, J.L., Papin, J.A., Famili, I. and Palsson, B.Ø., "Analysis of Metabolic Capabilities using Singular Value Decomposition of Extreme Pathway Matrices", Biophysical Journal 84:794-804 (2003).

Antzutkin, O.N., Balbach, J.J., Leapman, R.D., Rizzo, N.W., Reed, J., and Tycko, R., "Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils", PNAS 97:13045-13050 (2000).

Balbach, J.J., Ishii, Y., Antzutkin, O.N., Leapman, R.D., Rizzo, N.W., Dyda, F., Reed, J., and Tycko, R.,"Amyloid fibril formation by A beta 16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR", Biochemistry 39:13748-13759 (2000).

Book Chapters

Reed, J.L., Fong, S.S. and Palsson, B. Ø. "Phenomics." In Microbial Diversity and Bioprospecting. Washington, D.C.: ASM Press, 2003.

Reed, J.L. and Palsson, B. Ø. "Systems Biology: A Four Step Process." In Introduction to Bioengineering. Under Review, 2006.


Constraint-Based Modelling of Large-Scale Metabolic Systems Talk at Consortium for Post-Genome Science Manchester, England September 2004 Jennifer L. Reed and Bernhard O. Palsson

Constraint-Based Metabolic and Regulatory Models of Escherichia coli Talk at SIGSIM (satellite meeting at ISMB/ECCB 2004) Glasgow, Scotland July 2004 Jennifer L. Reed and Bernhard O. Palsson

E. coli i2K: A Genome-Scale Model of Metabolism, Regulation, and Transcription and Translation in Escherichia coli Talk at 2nd International E. coli Alliance Conference on Systems Biology Banff, Canada June 2004 Jennifer L. Reed and Bernhard O. Palsson

Constraint-Based Modelling of Large-Scale Metabolic Systems Talk at Southern California Biomedical Engineering Student Symposium Los Angeles, CA January 2004 Jennifer L. Reed, T.D. Vo, C.H. Schilling, M. W. Covert, E. M. Knight, M.J. Herrgard and Bernhard O. Palsson

Constraint-Based Models of Escherichia coli Metabolism: An Expanded Genome-Scale Metabolic Model of E. coli K-12 Poster at 4th International Conference on Systems Biology St. Louis, MO November 2003 Jennifer L. Reed, Thuy D. Vo, Christophe H. Schilling and Bernhard O. Palsson

Contact Information

Email Address:

Phone: (858)534-4783

Mailing Address: 9500 Gilman Drive Mail Code 0412 La Jolla, CA 92093-0412



417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

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