Selected Publications in Categories 

Metabolic Engineering and Biofuels

Hanai, T.; S. Atsumi; J. C. Liao (2007) Engineered synthetic pathway for isopropanol production in Escherichia coli, Appl. Env. Microbiol. In print.

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 (2007) Metabolic engineering of Escherichia coli for 1-butanol Production, Metabolic Eng. In print.

Bernstein, J.R.; Bulter, T.; Shen, C.R. and Liao_, J.C. (2007) Directed Evolution of Ribosomal Protein S1 for Enhanced Translational Efficiency of High GC Rhodopseudomonas palustris DNA in Escherichia coli, J. Biol. Chem. 282(26):18929-36.

Braatsch, S.;Bernstein, J.R.; Lessner, F.; Morgan, J.; Liao, J.C.; Harwood, C.S.; and Beatty J.T. (2006)  Rhodopseudomonas palustris CGA009 has two ppsR genes that each encode repressors of photosynthesis gene expression, Biochemistry, 45(48):14441-51.

Farmer, W.R. and J.C. Liao, (2000) “Improving Lycopene Production in Escherichia coli by Engineering Metabolic Control” Nature Biotechnol. 18, 533-537.

Wang, C.W. and J.C. Liao (2001) “Alteration of Product Specificity of Rhodobacter sphaeroides Phytoene Desaturase by Directed Evolution” J. Biol. Chem.,  276, 41161-41164.

Farmer, W.R. and J.C. Liao, (2001) “Precursor Balancing for Metabolic Engineering of Lycopene Production in Escherichia coli” Biotechnol. Prog. 17, 57-61.

Barkovich, R. and J.C. Liao (2001) “Metabolic Engineering of Isoprenoids” Metabolic Engineering, 3:27-39. 

Gene-Metabolic Circuits

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 

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 analysis. 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.

Zhou, B.; D. Beckwith; L. R. Jarboe, and J.C. Liao (2005) Markov Chain Modeling of Pyelonephritis-Associated Pili Expression in Uropathogenic Escherichia coli, Biophysical J.  88, 2541–2553

Yang, Y.L.; Suen, J.; Brynildsen,M.P.; Galbraith, S.J.; Liao, J.C. (2005) Inferring yeast cell cycle regulators and interactions using transcription factor activities, BMC Genomics, 6(1):90.

Brynildsen, M.P.; Tran, L. M. and Liao, J.C.  (2006) Versatility and Connectivity Efficiency of Bipartite Transcription Networks, Biophysical Journal, 91 (8): 2749-2759.

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. 2005 Apr 1;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 (2005) 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. 2002 30: 2886-2893

Liao, JC and Sabatti, C. (2002) Microanalysis of DNA microarrays, ASM News, 68:432-437.

Oh, M.-K., L. Rohlin, and J.C. Liao (2002) “Global Expression Profiling of Acetate-grown Escherichia coli” J. Biol.Chem. 277,13175–13183.

Rohlin, L., M.K. Oh, and J.C. Liao (2002) DNA microarray for microbial biotechnology: gene expression profiles in Escherichia coli during protein overexpression, J. Chin. Inst. Chem. Eng, 33, 103-112.

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.

Oh, M.K., and J.C. Liao (2000) “Gene Expression Profiling by DNA microarrays and Metabolic Fluxes in Escherichia coli” Biotechnol. Prog.  16, 278-286. 

Oh, M.K., and J.C. Liao (2000) “DNA Microarray Detection of Metabolic Responses to Protein Overproduction in Escherichia coli” Metabolic Engineering, 2, 201-209.

Nitric Oxide Metabolism and Regulation

Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, and Liao JC (2003) “Regulation of Nitric Oxide Consumption by Hypoxic Red Blood Cells” Proc. Natl. Acad. Sci. USA, 100. 12504–12509

Liao, JC (2002) “Blood feud: Keeping hemoglobin from nixing NO”, Nature Medicine, 8: 1350-1351.

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

Chang, C.-I., J.C. Liao, and L. Kuo (2001) “Macrophage Arginase Promotes Tumor Cell Growth and Suppresses Nitric Oxide-Mediated Tumor Cytotoxicity, Cancer Research, 61, 1100-1106.

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. 

Hein, T.W., J. C. Liao,  and L.Kuo (2000) “Oxidized LDL specifically impairs endothelium-dependent, nitric oxide-mediated dilation of coronary microvessels” Am. J. Physiol. Heart Circ. Physiol. 278:H175-H183.

Chang, C.I.;  B. Zoghi; J. C. Liao; and L. Kuo (2000) “Interleukin-13 inhibits nitric oxide production through arginase induction in activated macrophages: Involvement of cAMP/PKA, tyrosine kinase, and p38 mitogen-activated protein kinase” J. Immunology. 165:2134-2141 

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.