Liao, James C.
Systems Biology and Biological Regulation
Bioenergy and the Environment
Boelter Hall 5531
Dr. James C. Liao is a pioneer in Metabolic Engineering, Synthetic Biology, and Systems Biology. He received his B.S. degree from the National Taiwan University and Ph.D. from the University of Wisconsin-Madison. After working as a research scientist at Eastman Kodak Company in Rochester, N.Y., he started his academic career at Texas A&M University in 1990 and moved to UCLA in 1997. He was elected Fellow of the American Institute for Medical and Biological Engineering in 2002 and has received numerous awards including the NSF Young Investigator Award (1992), Merck Award for Metabolic Engineering (2006), FPBE Division award of American Institute of Chemical Engineers (AIChE) (2006), Charles Thom Award of the Society for Industrial Microbiology (2007), Marvin J. Johnson Award of the American Chemical Society (2009), Alpha Chi Sigma Award of AIChE (2009), James E. Bailey Award of the Society for Biological Engineering (2009), and Presidential Green Chemistry Challenge Award (2010).
Biomolecular & Metabolic Engineering
Our research has focused on metabolism, including its biochemistry, extension, and regulation. We use metabolic engineering,synthetic biology, and systems biology to construct microorganisms to produce next generation biofuels and to study the obesity problem in human. We also develop mathematical tools for investigating metabolism and guiding engineering design. Currently, our main projects include engineering proteins and biochemical pathways for CO2 fixation and produciton of fuels and chemicals. Our ultimate goal is to use biochemical methods to replace petroleum processing and to treat metabolic diseases.
Above: Next Generation Biofuels, CO2 fixation,Electricity to fuels, Cellulosic fuels,Protein biorefining
Honors & Awards
Presidential Green Chemistry Challenge Award from EPA
- Zhang, K.; Li, H.; Cho, K.M. and Liao, J.C. (2010) Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine. Proc Natl Acad Sci U S A. 107(14):6234-9. PMID: 20332210.
- Atsumi,S.; Higashide, W.; and Liao, J.C. (2009) Direct recycling of carbon dioxide to isobutyraldehyde using photosynthesis, Nat Biotechnol, 27, 1177-1180. PMID: 19915552
- Zhang, K., Sawaya, M.R., Eisenberg, D.S. and J.C. Liao (2008) Expanding Metabolism for Biosynthesis of Nonnatural Alcohols, Proc. Natl. Acad. Sci. USA 105: 20653–20658
- Dean, J.T.; Tran, L.; Beaven, S.; Tontonoz, P; Reue, K.; Dipple, K.D.; and Liao, J.C. (2009) Resistance to Diet-Induced Obesity in Mice with Synthetic Glyoxylate Shunt, Cell Metabolism, 9, 525–536. PMID: 19490907. (Selected for Faculty of 1000 Biology)
- Brynildsen, M.P.; and Liao, J.C. (2009) An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol. Sys. Biol. 5:277. PMID: 19536200
- Atsumi, S.; Li, Z. and Liao, J.C. (2009) Acetolactate Synthase from Bacillus subtilis Serves as a 2-Ketoisovalerate Decarboxylase for Isobutanol Biosynthesis in Escherichia coli, Appl. Env.Microbiol. 75: 6306–6311 PMID: 19684168
- Atsumi, S.; T. Hanai and J.C. Liao (2008) Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels, Nature, 451:86-89.
- Hanai, T., S. Atsumi, J. C. Liao (2007) Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl. Env. Microbiol. 73:7814–7818
- Atsumi, S., A. F. Cann, M. Connor, C.R. Shen, K. M. Smith, M.P. Brynildsen, K.J.Y. Chou, T. Hanai, and J. C. Liao (2008) Metabolic engineering of Escherichia coli for 1-butanol Production. Metabolic Eng. 10 (2008) 305–311
- Farmer, W.R. and J.C. Liao, (2000) Improving Lycopene Production in Escherichia coli by Engineering Metabolic Control. Nature Biotechnol., 18, 533-537.
Gene-Metabolic Circuits (Selected)
- Wong, W.W., T.Y. Tsai, J.C. Liao (2007) Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator. Mol. Systems. Biol., 3:130.
- Wong ,WW and Liao, JC. (2006) The design of intracellular oscillators that interact with metabolism. Cell. Mol. Life Sci., 1215-1220
- Fung, E., Wong, W.W., Suen, J.K., Bulter, T., Lee, S.G., and Liao, J.C. (2005) A synthetic gene-metabolic oscillator. Nature, 435, 118-122.
- Bulter, T, . Lee, S.-G., Wong, W.W., Fung, E., Connor, M.R. and Liao, J.C. (2004) Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl. Acad. Sci. USA, 101:2299-2304 [Commentary by Gerchman and Weiss, PNAS, 2004 101:2221-2222]
Systems Biology (Selected)
- Dean, J.T.; Rizk, M.L.; Tan, Y.; Dipple, K.M.; and Liao, J.C. (2010) Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt. Biophys J. 98:1385-95. PMID: 20409457.
- Rizk, M.L.; Liao, J.C. (2009) Ensemble modeling for aromatic production in Escherichia coli. PLoS One. 4(9):e6903.PMID: 19730732
- Contador, C.A.; Rizk, M.L.; Asenjo, J.A.; and Liao, J.C. (2009) Ensemble modeling for strain development of L-lysine-producing Escherichia coli. Metab. Eng. 11:221–233. PMID: 19379820
- Tran, L.M.; Rizk, M.L.; and J.C. Liao (2008) Ensemble Modeling of Metabolic Networks. Biophys J. 95:5606-17.
- Hyduke, D.R., Jarboe, L.R., Tran, L.M., Chou, K.J.Y., Liao, J.C. (2007) Integrated Network Analysis Identifies Nitric Oxide Response Networks and dihydroxyacid dehydratase as a Crucial Target in Escherichia coli. Proc. Natl. Acad. Sci. USA, 104, 8484-8489. [Highlighted in Chemical &, Engineering News, Aug. 20, 2007, Page 57].
- Brynildsen, M.P., Wu, T.Y., Jang, S.S. and Liao, J.C. (2007) Biological Network Mapping and Source Signal Deduction. Bioinformatics, 23:1775-1782.
- Brynildsen, M.P., Tran, L. M. and Liao, J.C. (2006) A Gibbs Sampler for the Identification of Gene Expression and Network Connectivity Consistency. Bioinformatics, 22, 3040-3046.
- Kao, K.C, Tran, L.M., Liao, J.C.(2005) A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysisi. J. Biol. Chem., 280, 36079-36087.
- Galbraith, S.J., Tran, L.M. and Liao, J.C. (2006) Transcriptome Network Component Analysis with Limited Microarray Data. Bioinformatics, 22, 1886-1894.
- Sabatti, C, Rohlin, L, Lange, K, and Liao, J.C. (2005) Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites. Bioinformatics, 21(7):922-31.
- Tran, L.M., M.P. Brynildsen, K. C. Kao, J. K. Suen and J. C. Liao (2005) gNCA: A framework for determining transcription factor activity based on transcriptome: Identifiability and numerical implementation. Metabolic Engineering., 7, 128-141
- Kao, K.C., Yang, Y., Boscolo, R., Sabatti, C., Roychowdhury, V. and Liao, J.C. (2004) Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli using network component analysis. Proc. Natl. Acad. Sci. USA, 101:641-646.
- Liao, J.C., Boscolo, R, Yang, Y.L., Tran,L.M., Sabatti, C., and Roychowdhury, V. (2003) Network component analysis: Reconstruction of regulatory signals in biological systems. Proc. Natl. Acad. Sci. USA, 100: 15522-15527.
- Sabatti, C. Rohlin, L, Oh, M.K., and Liao, J.C. (2002) Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucl. Acids. Res., 30: 2886-2893
- Tseng, G.C., M.-K.Oh, L Rohlin, J, C. Liao, and W.H. Wong (2001) Issues In cDNA Microarray Analysis: Quality Filtering Channel Normalization, Models of Variations and Assessment of Gene Effects Nucleic Acid Research, 29, 2549-2557.
Nitric Oxide Metabolism and Regulation (Selected)
- Jarboe, L.R.; D. R. Hyduke, L. M. Tran, K. J.Y. Chou and J. C. Liao (2008) Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis, J. Biol. Chem. 283:5148-57.
- Hyduke, D.R.; Jarboe, L.R.; Tran, L.M.; Chou, K.J.Y.; Liao, J.C. (2007) Integrated Network Analysis Identifies Nitric Oxide Response Networks and dihydroxyacid dehydratase as a Crucial Target in Escherichia coli, Proc. Natl. Acad. Sci. USA, 104, 8484-8489. [Highlighted in Chemical & Engineering News, Aug. 20, 2007, Page 57]
- Han, T.H., Hyduke, D.R., Vaughn, M.W.,. Fukuto, J.M., and Liao, J.C. (2002) Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions. Proc. Natl. Acad. Sci. USA, 99: 7763-7768.
- Joshi, M.S., Ferguson, T.B., Han,T.H., Hyduke, D.R., Liao,J.C., Rassaf, T., Bryan, N., Feelisch, M., and Lancaster, J.R. (2002) Nitric Oxide is Consumed, Rather than Conserved, by Reaction with Oxyhemoglobin under Physiological Conditions. Proc. Natl. Acad. Sci. USA, 99:10341-6.
- Huang, K.T., Han, T. H., Hyduke, D. R., Vaughn, M. W., Van Herle, H., Hein, T. W., Zhang, C., Kuo, L., and Liao, J.C. (2001) Modulation of Nitric Oxide Bioavailability by Erythrocytes. Proc. Natl. Acad. Sci. USA, 98, 11771-11776
- Vaughn, M.W., Kuang-Tse Huang, Lih Kuo, and J. C. Liao (2001) , “Erythrocyte Consumption of Nitric Oxide: Competition Experiment and Model Analysis. Nitric Oxide Biology and Chemistry, 5, 18-31.
- J. C. Liao, T.W. Hein, M. W. Vaughn, K.T. Huang, and L. Kuo (1999) Intravascular Flow Decreases Erythrocyte Consumption of Nitric Oxide. Proc. Natl. Acad. Sci. USA, 96:8757-8761.
- Vaughn, M.W., K.T Huang, L. Kuo, and J. C. Liao (1999) Erythrocytes Possess an Intrinsic Barrier to Nitric Oxide Consumption. J. Biol. Chem., 275, 2342-2348.