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.
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]
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.
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.