California NanoSystems Institute
CNSI
Text Size: A A A A

James Liao, Ph.D.

   
Chair and Professor, Chemical and Biomolecular Engineering
Professor, Chemistry and Biochemistry
Member, California NanoSystems Institute
Faculty, Biomedical Engineering IDP, Molecular Biology IDP

Education:
Degrees:
Ph.D., University of Wisconsin, Madison, 1987

Contact Information:
Work Email Address: liaoj@seas.ucla.edu
Work Address: 5531 Boelter Hall
420 Westwood Plaza
Los Angeles, CA 90095
Home Page: http://www.seas.ucla.edu/~liaoj/
Work Phone Number: 1 (310) 825-1656
Fax Number: 1 (310) 206-4107
Research Interests:

We develop novel technologies for metabolic genomics research in microbial and human systems. Our research integrates molecular biology and chip-based technologies to investigate molecular recognition, signal amplification, and biological regulation.

Understanding how genes and proteins work at the genomic scale is essential for biomedical research and applications. Most commonly, the function and regulation of genes are studied one at a time, with tedious and time-consuming methods. Genomic technologies, such as DNA microarrays (or gene chips), have accelerated this process significantly. With the proper DNA probes, this technology allows the detection of mRNA levels at the genomic scale. This technology is coupled with large scale molecular cloning, directed evolution, and mass spectrometry to probe the biochemical activities in the cell. Specifically, we use these techniques to identify genes in new pathways, to determine roles of unknown genes, to uncover new roles of known genes, and to define the genetic control loops in the cell. In addition, the principles of biomolecular recognition and signal amplification in biological systems are used to design chip-based technologies for the high-throughput processing of biological samples. Meanwhile, mathematical and statistical tools are being developed for analyzing the large amount of data generated.


Technical Research Interest:

Professor Liao and his research group are focusing on elucidating and reconstructing biological regulatory networks at the systems level. Experimental and computational methods are being developed to understand, predict, and redesign cellular behavior. An integrative technique called Network Component Analysis (NCA) have been developed which utilizes mRNA expression and transcriptional network connectivity to determine network component dynamics, functions, and interactions. This approach has been applied to elucidate transcription factor dynamics in Saccharomyces cerevisiae cell-cycle regulation, detect cross-talks in Escherichia coli two component signaling pathways, and characterize E. coli carbon source transition. In addition, novel synthetic gene-metabolic circuits have been designed and constructed to demonstrate system-wide understanding of cellular regulation. To this end, artificial feedback regulation, cell-cell communication, and oscillatory circuits have been constructed, which demonstrate the design principles of gene-metabolic regulation in the cell.


Additional Information:

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).

Selected Publications:

Machado Hidevaldo B, Dekishima Yasumasa, Luo Hao, Lan Ethan I, Liao James C, A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols, Metabolic engineering, 2012, 14 (5), 504-11.
Felnagle Elizabeth A, Chaubey Asha, Noey Elizabeth L, Houk Kendall N, Liao James C, Engineering synthetic recursive pathways to generate non-natural small molecules, Nature chemical biology, 2012, 8 (6), 518-26.
Huo Yi-Xin, Wernick David G, Liao James C, Toward nitrogen neutral biofuel production, Current opinion in biotechnology, 2012, 23 (3), 406-13.
Marcheschi Ryan J, Li Han, Zhang Kechun, Noey Elizabeth L, Kim Seonah, Chaubey Asha, Houk K N, Liao James C, A synthetic recursive "+1" pathway for carbon chain elongation, ACS chemical biology, 2012, 7 (4), 689-97.
Lan Ethan I, Liao James C, ATP drives direct photosynthetic production of 1-butanol in cyanobacteria, Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (16), 6018-23.
Li Yongchao, Tschaplinski Timothy J, Engle Nancy L, Hamilton Choo Y, Rodriguez Miguel, Liao James C, Schadt Christopher W, Guss Adam M, Yang Yunfeng, Graham David E, Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations, Biotechnology for biofuels, 2012, 5 (1), 2.
Tran Linh M, Chang Chun-Ju, Plaisier Seema, Wu Shumin, Dang Julie, Mischel Paul S, Liao James C, Graeber Thomas G, Wu Hong, Determining PTEN functional status by network component deduced transcription factor activities, PloS one, 2012, 7 (2), e31053.
Li Han, Opgenorth Paul H, Wernick David G, Rogers Steve, Wu Tung-Yun, Higashide Wendy, Malati Peter, Huo Yi-Xin, Cho Kwang Myung, Liao James C, Integrated electromicrobial conversion of CO2 to higher alcohols, Science (New York, N.Y.), 2012, 335 (6076), 1596.
Tan Yikun, Liao James C, Metabolic ensemble modeling for strain engineers, Biotechnology journal, 2012, 7 (3), 343-53.
Smith Kevin M, Liao James C, An evolutionary strategy for isobutanol production strain development in Escherichia coli, Metabolic engineering, 2011, 13 (6), 674-81.
Dekishima Yasumasa, Lan Ethan I, Shen Claire R, Cho Kwang Myung, Liao James C, Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli, Journal of the American Chemical Society, 2011, 133 (30), 11399-401.
Lan Ethan I, Liao James C, Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide, Metabolic engineering, 2011, 13 (4), 353-63.
Yi-Xin Huo, Kwang Myung Cho, Jimmy G Lafontaine Rivera, Emma Monte, Claire R Shen, Yajun Yan & James C Liao, Conversion of proteins into biofuels by engineering nitrogen flux, Nature Biotechnology, 2011, 29, 346?351.
Wendy Higashide, Yongchao Li, Yunfeng Yang, and James C. Liao, Metabolic Engineering of Clostridium Cellulolyticum for Isobutanol Production from Cellulose, Appl. Environ. Microbiol, 2011, 77 (8), 2727-33.
Baez Antonino, Cho Kwang-Myung, Liao James C, High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal, Applied microbiology and biotechnology, 2011, 90 (5), 1681-90.
Shen Claire R, Lan Ethan I, Dekishima Yasumasa, Baez Antonino, Cho Kwang Myung, Liao James C, Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli, Applied and environmental microbiology, 2011, 77 (9), 2905-15.
Huo Yi-Xin, Cho Kwang Myung, Rivera Jimmy G Lafontaine, Monte Emma, Shen Claire R, Yan Yajun, Liao James C, Conversion of proteins into biofuels by engineering nitrogen flux, Nature biotechnology, 2011, 29 (4), 346-51.
Higashide Wendy, Li Yongchao, Yang Yunfeng, Liao James C, Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose, Applied and environmental microbiology, 2011, 77 (8), 2727-33.
Contador Carolina A, Andrews Barbara A, Liao James C, Asenjo Juan A, Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae, Biotechnology progress, 2011, 29 (4).
Harper Marc A, Chen Zugen, Toy Traci, Machado Iara M P, Nelson Stanley F, Liao James C, Lee Christopher J, Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants, PloS one, 2011, 6 (2), e16517.
Rizk Matthew L, Laguna Rick, Smith Kevin M, Tabita F Robert, Liao James C, Redox homeostasis phenotypes in RubisCO-deficient Rhodobacter sphaeroides via ensemble modeling, Biotechnology progress, 2011, 27 (1), 15-22.
Wang Wei, Hein Travis W, Zhang Cuihua, Zawieja David C, Liao James C, Kuo Lih, Oxidized low-density lipoprotein inhibits nitric oxide-mediated coronary arteriolar dilation by up-regulating endothelial arginase I, Microcirculation (New York, N.Y. : 1994), 2011, 18 (1), 36-45.
Tan Yikun, Rivera Jimmy G Lafontaine, Contador Carolina A, Asenjo Juan A, Liao James C, Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux, Metabolic engineering, 2011, 13 (1), 60-75.
Mainguet Samuel E, Liao James C, Bioengineering of microorganisms for C₃ to C₅ alcohols production, Biotechnology journal, 2010, 5 (12), 1297-308.
Atsumi Shota, Wu Tung-Yun, Machado Iara M P, Huang Wei-Chih, Chen Pao-Yang, Pellegrini Matteo, Liao James C, Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, Molecular systems biology, 2010, 6 (12), 449.
Inokuma Kentaro, Liao James C, Okamoto Masahiro, Hanai Taizo, Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping, Journal of bioscience and bioengineering, 2010, 110 (6), 696-701.
Wong Ieong, Atsumi Shota, Huang Wei-Chih, Wu Tung-Yun, Hanai Taizo, Lam Miu-Ling, Tang Ping, Yang Jian, Liao James C, Ho Chih-Ming, An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study, Lab on a chip, 2010, 10 (20), 2710-9.
Tran Linh M, Hyduke Daniel R, Liao James C, Trimming of mammalian transcriptional networks using network component analysis, BMC bioinformatics, 2010, 11 (20), 511.
Smith Kevin Michael, Cho Kwang-Myung, Liao James C, Engineering Corynebacterium glutamicum for isobutanol production, Applied microbiology and biotechnology, 2010, 87 (3), 1045-55.
Connor MR, Cann AF, Liao JC., 3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation, Appl Microbiol Biotechnol. , 2010, 86 (4), 1155-64.
Wong I, Atsumi S, Huang WC, Wu TY, Hanai T, Lam ML, Tang P, Yang J, Liao JC, Ho CM, An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study, Lab Chip, 2010, 10 (20), 2710-9.
Smith KM, Cho KM, Liao JC, Engineering Corynebacterium glutamicum for isobutanol production, Appl Microbiol Biotechnol, 2010, 87 (3), 1045-55.
Dean JT, Rizk ML, Tan Y, Dipple KM, Liao JC, Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt, Biophys J, 2010, 98 (8), 1385-95.
Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC, Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, Mol Syst Biol, 2010, 6, 449.
Zhang K, Li H, Cho KM, Liao JC., Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine, Proc Natl Acad Sci U S A, 2010, 107 (14), 6234-9.
Sriram G, Parr LS, Rahib L, Liao JC, Dipple KM, Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells, Metab Eng, 2010, 12 (4), 332-40.
Rizk ML, Laguna R, Smith KM, Tabita FR, Liao JC, Redox homeostasis phenotypes in RubisCO-deficient Rhodobacter sphaeroides via ensemble modeling, Biotechnol Prog. , 2010, 27 (1), 15-22.
Tran LM, Hyduke DR, Liao JC, Trimming of mammalian transcriptional networks using network component analysis, BMC Bioinformatics, 2010, 11 (511).
Connor Michael R, Cann Anthony F, Liao James C, 3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation, Applied microbiology and biotechnology, 2010, 86 (4), 1155-64.
Li Han, Cann Anthony F, Liao James C, Biofuels: biomolecular engineering fundamentals and advances, Annual review of chemical and biomolecular engineering, 2010, 1 (4), 19-36.
Dean Jason T, Rizk Matthew L, Tan Yikun, Dipple Katrina M, Liao James C, Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt, Biophysical journal, 2010, 98 (8), 1385-95.
Zhang Kechun, Li Han, Cho Kwang Myung, Liao James C, Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine, Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (14), 6234-9.
Atsumi Shota, Wu Tung-Yun, Eckl Eva-Maria, Hawkins Sarah D, Buelter Thomas, Liao James C, Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes, Applied microbiology and biotechnology, 2010, 85 (3), 651-7.
Cann Anthony F, Liao James C, Pentanol isomer synthesis in engineered microorganisms, Applied microbiology and biotechnology, 2010, 85 (4), 893-9.
Atsumi Shota, Higashide Wendy, Liao James C, Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde, Nature biotechnology, 2009, 27 (12), 1177-80.
Wong Wilson W, Liao James C, Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters, Metabolic engineering, 2009, 11 (6), 409-14.
Atsumi Shota, Li Zhen, Liao James C, Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli, Applied and environmental microbiology, 2009, 75 (19), 6306-11.
Yan Yajun, Lee Chia-Chi, Liao James C, Enantioselective synthesis of pure (R,R)-2,3-butanediol in Escherichia coli with stereospecific secondary alcohol dehydrogenases, Organic & biomolecular chemistry, 2009, 7 (19), 3914-7.
Rizk Matthew L, Liao James C, Ensemble modeling for aromatic production in Escherichia coli, PloS one, 2009, 4 (9), e6903.
Contador Carolina A, Rizk Matthew L, Asenjo Juan A, Liao James C, Ensemble modeling for strain development of L-lysine-producing Escherichia coli, Metabolic engineering, 2009, 11 (4-5), 221-33.
Brynildsen, M. P. Liao, J. C., An integrated network approach identifies the isobutanol response network of Escherichia coli, Mol Syst Biol, 2009, 5, 277.
Atsumi S, Higashide W, Liao JC., Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde, Nat Biotechnol. , 2009, 27 (2), 1177-80.
Yan Y, Lee CC, Liao JC., Enantioselective synthesis of pure (R,R)-2,3-butanediol in Escherichia coli with stereospecific secondary alcohol dehydrogenases, Org Biomol Chem. , 2009, 7 (19), 3914-7..
Rizk ML, Liao JC., Ensemble modeling for aromatic production in Escherichia coli, PLoS One, 2009, 4 (9), 6903.
Cann AF, Liao JC., Pentanol isomer synthesis in engineered microorganisms, Appl Microbiol Biotechnol, 2009, 85 (4), 893-9.
Connor Michael R, Liao James C, Microbial production of advanced transportation fuels in non-natural hosts, Current opinion in biotechnology, 2009, 20 (3), 307-15.
Dean Jason T, Tran Linh, Beaven Simon, Tontonoz Peter, Reue Karen, Dipple Katrina M, Liao James C, Resistance to diet-induced obesity in mice with synthetic glyoxylate shunt, Cell metabolism, 2009, 9 (6), 525-36.
Connor, M. R. Liao, J. C., Microbial production of advanced transportation fuels in non-natural hosts, Curr Opin Biotechnol, 2009.
Lai Denton, Lluncor Ben, Schröder Imke, Gunsalus Robert P, Liao James C, Monbouquette Harold G, Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate, Metabolic engineering, 2009, 11 (3), 184-91.
Contador, C. A. Rizk, M. L. Asenjo, J. A. Liao, J. C., Ensemble modeling for strain development of l-lysine-producing Escherichia coli, Metab Eng, 2009.
Yan Yajun, Liao James C, Engineering metabolic systems for production of advanced fuels, Journal of industrial microbiology & biotechnology, 2009, 36 (4), 471-9.
Rahib Lola, Sriram Ganesh, Harada Melissa K, Liao James C, Dipple Katrina M, Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency, Molecular genetics and metabolism, 2009, 96 (3), 106-12.
Ye Chun, Galbraith Simon J, Liao James C, Eskin Eleazar, Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast, PLoS computational biology, 2009, 5 (3), e1000311.
Jason T. Dean, Linh Tran, Simon Beaven, Peter Tontonoz, Karen Reue, Katrina M. Dipple, James C. Liao, Resistance to Diet-Induced Obesity in Mice with Synthetic Glyoxylate Shunt, Cell Metabolism , 2009, 9 (6), 525-536.
Wong Wilson W, Tran Linh M, Liao James C, A hidden square-root boundary between growth rate and biomass yield, Biotechnology and bioengineering, 2009, 102 (1), 73-80.
Brynildsen Mark P, Liao James C, An integrated network approach identifies the isobutanol response network of Escherichia coli, Molecular systems biology, 2009, 5 (1), 277.
Atsumi Shota, Liao James C, Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli, Applied and environmental microbiology, 2008, 74 (24), 7802-8.
Tran Linh M, Rizk Matthew L, Liao James C, Ensemble modeling of metabolic networks, Biophysical journal, 2008, 95 (12), 5606-17.
Zhang Kechun, Sawaya Michael R, Eisenberg David S, Liao James C, Expanding metabolism for biosynthesis of nonnatural alcohols, Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (52), 20653-8.
Atsumi Shota, Cann Anthony F, Connor Michael R, Shen Claire R, Smith Kevin M, Brynildsen Mark P, Chou Katherine J Y, Hanai Taizo, Liao James C, Metabolic engineering of Escherichia coli for 1-butanol production, Metabolic engineering, 2008, 10 (6), 305-11.
Cann Anthony F, Liao James C, Production of 2-methyl-1-butanol in engineered Escherichia coli, Applied microbiology and biotechnology, 2008, 81 (1), 89-98.
Liao James C, Fetcho Joseph R, Shared versus specialized glycinergic spinal interneurons in axial motor circuits of larval zebrafish, The Journal of neuroscience : the official journal of the Society for Neuroscience, 2008, 28 (48), 12982-92.
Atsumi Shota, Liao James C, Metabolic engineering for advanced biofuels production from Escherichia coli, Current opinion in biotechnology, 2008, 19 (5), 414-9.
Connor Michael R, Liao James C, Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol, Applied and environmental microbiology, 2008, 74 (18), 5769-75.
Bernstein Jeffrey R, Bulter Thomas, Liao James C, Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin, Metabolic engineering, 2008, 10 (3-4), 131-40.
Shota Atsumi, Taizo Hanai & James C. Liao, Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels, Nature, 2008, 451, 86-89.
Chou Katherine J, Dodd Joanna, Liao James C, Interactions of nitrosylhemoglobin and carboxyhemoglobin with erythrocyte, Nitric oxide : biology and chemistry / official journal of the Nitric Oxide Society, 2008, 18 (2), 122-35.
Lee Sun-Gu, Liao James C, Control of acetate production rate in Escherichia coli by regulating expression of single-copy pta using lacI(Q) in multicopy plasmid, Journal of microbiology and biotechnology, 2008, 18 (2), 334-7.
Jarboe Laura R, Hyduke Daniel R, Tran Linh M, Chou Katherine J Y, Liao James C, Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis, The Journal of biological chemistry, 2008, 283 (8), 5148-57.
Sriram Ganesh, Rahib Lola, He Jian-Sen, Campos Allison E, Parr Lilly S, Liao James C, Dipple Katrina M, Global metabolic effects of glycerol kinase overexpression in rat hepatoma cells, Molecular genetics and metabolism, 2008, 93 (2), 145-59.
Boscolo Riccardo, Liao James C, Roychowdhury Vwani P, An information theoretic exploratory method for learning patterns of conditional gene coexpression from microarray data, IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 2008, 5 (1), 15-24.
Atsumi Shota, Hanai Taizo, Liao James C, Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels, Nature, 2008, 451 (7174), 86-9.
Watanabe Junji, Chou Katherine J, Liao James C, Miao Yunan, Meng Hsiang-Hui, Ge Helen, Grijalva Victor, Hama Susan, Kozak Kathy, Buga Georgette, Whitelegge Julian P, Lee Terry D, Farias-Eisner Robin, Navab Mohamad, Fogelman Alan M, Reddy Srinivasa T, Differential association of hemoglobin with proinflammatory high density lipoproteins in atherogenic/hyperlipidemic mice. A novel biomarker of atherosclerosis, The Journal of biological chemistry, 2007, 282 (32), 23698-707.
Brynildsen Mark P, Wu Tung-Yun, Jang Shi-Shang, Liao James C, Biological network mapping and source signal deduction, Bioinformatics (Oxford, England), 2007, 23 (14), 1783-91.
Brynildsen, M.P.; Wu, T.Y.; Jang, S.S. and Liao, J.C., Biological Network Mapping and Source Signal Deduction, Bioinformatics, 2007, 23, 1775-1782.
Watanabe, J.; K.J. Chou, J. C. Liao, Y. Miao, H. Meng, H. Ge, V. Grijalva, K. Kozak, J. P. Whitelegge, T. D. Lee, R. Farias-Eisner, M. Navab, A. M. Fogelman, S.T. Reddy , Differential association of hemoglobin with proinflammatory high density lipoproteins in atherogenic/hyperlipidemic mice. A novel biomarker of atherosclerosis, J. Biol. Chem, 2007, 282 (32), 23698-707.
Bernstein, J.R.; Bulter, T.; Shen, C.R. and Liao, J.C. , Directed Evolution of Ribosomal Protein S1 for Enhanced Translational Efficiency of High GC Rhodopseudomonas palustris DNA in Escherichia coli,, J. Biol. Chem. , 2007, 282 (26), 18929-36.
Ohta, A.T., P.Y. Chiou, T.H. Han, J.C. Liao, U. Bhardwaj, E.R.B. McCabe, F.Yu, R. Sun, and M.C. Wu , Dynamic cell and microparticle control via optoelectronic tweezers, J. Microelectromechanical Systems, 2007, 16, 491-499.
Hanai, T.; S. Atsumi; J. C. Liao , Engineered synthetic pathway for isopropanol production in Escherichia coli, Appl. Env. Microbiol, 2007, 73 (24), 7814-8.
Sriram, G.; L. Rahib; J.S. He; A.E.Campos; L. S Parr; J.C. Liao; K.M. Dipple, Global Metabolic Effects of Glycerol Kinase Overexpression in Rat Hepatoma Cells, Molecular Genetics and Metabolism, 2007, 93 (2), 145-159.
Rahib, L., MacLennan, N.K., Horvath, S., Liao, J.C., and Dipple, K.M, Glycerol Kinase Deficiency Alters Expression of Genes Involved in Lipid Metabolism, Carbohydrate Metabolism, and Insulin Signaling, G. Eur. J. Hum. Genet. , 2007, 15 (6), 646-657.
Hyduke, D.R.; Jarboe, L.R.; Tran, L.M.; Chou, K.J.Y.; Liao, J.C., Integrated Network Analysis Identifies Nitric Oxide Response Networks and dihydroxyacid dehydratase as a Crucial Target in Escherichia coli, Proc. Natl. Acad. Sci. USA, 2007, 104, 8484-8489.
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, Metabolic engineering of Escherichia coli for 1-butanol Production, Metabolic Eng, 2007, 10 (6), 305-11.
Han, T. H.; Perloff, J.K.; and Liao, J.C., Nitric Oxide Metabolism in Adults with Cyanotic Congenital Heart Disease, Am. J. Cardiology, 2007, 99 (5), 691-5.
Wong, W.W., T.Y. Tsai, J.C. Liao , Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator, Mol. Systems. Biol, 2007, 3, 130.
Bernstein Jeffrey R, Bulter Thomas, Shen Claire R, Liao James C, Directed evolution of ribosomal protein S1 for enhanced translational efficiency of high GC Rhodopseudomonas palustris DNA in Escherichia coli, The Journal of biological chemistry, 2007, 282 (26), 18929-36.
Rahib Lola, MacLennan Nicole K, Horvath Steve, Liao James C, Dipple Katrina M, Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling, European journal of human genetics : EJHG, 2007, 15 (6), 646-57.
Hyduke Daniel R, Jarboe Laura R, Tran Linh M, Chou Katherine J Y, Liao James C, Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli, Proceedings of the National Academy of Sciences of the United States of America, 2007, 104 (20), 8484-9.
Han Tae H, Perloff Joseph K, Liao James C, Nitric oxide metabolism in adults with cyanotic congenital heart disease, The American journal of cardiology, 2007, 99 (5), 691-5.
Wong Wilson W, Tsai Tony Y, Liao James C, Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator, Molecular systems biology, 2007, 3 (5), 130.
Brynildsen, M. P. Tran, L. M. Liao, J. C., A Gibbs sampler for the identification of gene expression and network connectivity consistency, Bioinformatics, 2006, 22 (24), 3040-6.
Brynildsen Mark P, Tran Linh M, Liao James C, A Gibbs sampler for the identification of gene expression and network connectivity consistency, Bioinformatics (Oxford, England), 2006, 22 (24), 3040-6.
Braatsch Stephan, Bernstein Jeffrey R, Lessner Faith, Morgan Jennifer, Liao James C, Harwood Caroline S, Beatty J Thomas, Rhodopseudomonas palustris CGA009 has two functional ppsR genes, each of which encodes a repressor of photosynthesis gene expression, Biochemistry, 2006, 45 (48), 14441-51.
Brynildsen Mark P, Tran Linh M, Liao James C, Versatility and connectivity efficiency of bipartite transcription networks, Biophysical journal, 2006, 91 (8), 2749-59.
Oh, MK; Cha, MJ; Lee, SG; Rohlin, L and Liao, JC., Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate, J. Microbiol. Biotechnol, 2006, 16 (4), 543-549.
Liao, J.C. , Systems Biology: Where does chemical engineering stand? , J. Chin. Inst. Chem. Eng. in print. (invited paper) , 2006, 103-106.
MacLennan, N.K., Rahib, L., Shin, C., Fang, Z., Horvath, S., Dean J., Liao, J.C., McCabe, E.R.B. and Dipple, K.M., Targeted Disruption of Glycerol Kinase Gene In Mice: Expression Analysis in Liver Shows Alterations in Network Partners Related to Glycerol Kinase Activity, Human Molec. Genet. , 2006, 15 (3), 405-415.
Wong, WW and Liao, JC., The design of intracellular oscillators that interact with metabolism, Cell. Mol. Life Sci, 2006, 63 (11), 1215-1220.
Galbraith, S.J.; Tran, L.M. and Liao, J.C., Transcriptome Network Component Analysis with Limited Microarray Data, Bioinformatics, Accepted , 2006, 22 (15), 1886-1894.
Brynildsen, M.P., Tran, L. M. and Liao, J.C., Versatility and Connectivity Efficiency of Bipartite Transcription Networks, Biophysical Journal, Accepted, 2006, 91 (8), 2749-59.
Boscolo Riccardo, Sabatti Chiara, Liao James C, Roychowdhury Vwani P, A generalized framework for network component analysis, IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 2005, 2 (4), 289-301.
Kao Katy C, Tran Linh M, Liao James C, A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis, The Journal of biological chemistry, 2005, 280 (43), 36079-87.
Boscolo, R.; Sabatti, C.; Liao, J.C. and Roychowdhury, V.P., A Generalized Framework for Network Component Analysis, IEEE Trans. Comp. Biol. Bioinfomatics , 2005, 2 (4), 289-301.
Kao, K.C; Tran, L.M.; Liao, J.C., A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis, J. Biol. Chem. , 2005, 280 (43), 36079-36087.
Fung, E.; Wong, W.W.; Suen, J.K.; Bulter, T.; Lee, S.G.; and Liao, J.C., A synthetic gene-metabolic oscillator, Nature, 2005, 435 (7038), 118-122.
Hyduke, D. R. Liao, J. C., Analysis of nitric oxide donor effectiveness in resistance vessels, Am J Physiol Heart Circ Physiol, 2005, 288 (5), H2390-9.
Yang, Y.L. and Liao, J.C., Determination of functional interactions among signalling pathways in Escherichia coli K-12, Metabolic Engineering, 2005, 7 (4), 280-290.
Han, T.H.; Pelling, A; Jeon, T.J.; Gimzewski, J.K. and Liao, J.C, Erythrocyte nitric oxide transport reduced by a submembrane cytoskeletal barrier, Biochimica et Biophysica Acta, 2005, 1723 (1-3), 135-42.
Rohlin, L. Trent, J. D. Salmon, K. Kim, U. Gunsalus, R. P. Liao, J. C., Heat shock response of Archaeoglobus fulgidus, J Bacteriol, 2005, 187 (17), 6046-57.
Yang, Y.L.; Suen, J.; Brynildsen,M.P.; Galbraith, S.J.; Liao, J.C., Inferring yeast cell cycle regulators and interactions using transcription factor activities, BMC Genomics, 2005, 6 (1), 90.
Zhou, B. Beckwith, D. Jarboe, L. R. Liao, J. C., Markov Chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli, Biophys J, 2005, 88 (4), 2541-53.
Sriram, G; Martinez, J.A.; McCabe, E.R.B.; Liao, J.C.; and Dipple, K.M., Single-gene disorders: what role could moonlighting enzymes play?, Am. J. Hum. Genet, 2005, 76 (6), 911-924.
Rohlin, L.;Trent, J.D.; Salmon, K; Kim, U.; Gunsalus, R.P.; and Liao, J.C., The heat-shock response of Archaeoglobus fulgidus, J. Bacteriol, 2005, 187 (17), 6046-6057.
Brynildsen, M. P. Wong, W. W. Liao, J. C., Transcriptional regulation and metabolism, Biochem Soc Trans, 2005, 33 (Pt 6), 1423-6.
Brynildsen, M.P.;Wong, W.W.; and Liao, J.C. , Transcriptional regulation and metabolism, Biochem. Soc. Trans. , 2005, 33 (6), 1423-1426.
Sabatti, C; Rohlin, L; Lange, K; and Liao, J.C., Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites, Bioinformatics. 2005 Apr 1, 2005, 21 (7), 922-31.
Tran, L. M. Brynildsen, M. P. Kao, K. C. Suen, J. K. Liao, J. C., gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation, Metab Eng, 2005, 7 (2), 128-41.
Jarboe, L. R. Beckwith, D. Liao, J. C., Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli, Biotechnol Bioeng, 2004, 88 (2), 189-203.
Jarboe Laura R, Beckwith David, Liao James C, Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli, Biotechnology and bioengineering, 2004, 88 (2), 189-203.
Liao James C, Neuromuscular control of trout swimming in a vortex street: implications for energy economy during the Karman gait, The Journal of experimental biology, 2004, 207 (Pt 20), 3495-506.
Liao James C, Custom design of metabolism, Nature biotechnology, 2004, 22 (7), 823-4.
Liao, J.C., Custom Design of Metabolism, Nature Biotechnol, 2004, 22 (7), 823-824.
Bulter, T;. Lee, S.-G.; Wong, W.W.; Fung, E.; Connor, M.R. and Liao, J.C., Design of artificial cell-cell communication using gene and metabolic networks, Proc. Natl. Acad. Sci. USA, 2004, 101 (8), 2299-2304 [Commentary by Gerchman and Weiss, PNAS, 2004 101:2221-2222].
Han, T.H.; Fukuto,J.M., and Liao, J.C., Reductive nitrosylation and S-nitrosation of hemoglobin in inhomogeneous nitric oxide solutions, Nitric Oxide Biology and Chemistry, 2004, 10 (2), 74-82.
Jarboe, L.R; Beckwith, D; Liao, J.C., Stochastic modeling of pap operon regulation in uropathogenic Escherichia coli, Biotechnol. Bioeng, 2004, 88 (2), 189-203.
Kao, K. C. Yang, Y. L. Boscolo, R. Sabatti, C. Roychowdhury, V. Liao, J. C., Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis, Proc Natl Acad Sci U S A, 2004, 101 (2), 641-6.
Bulter, T. Bernstein, J. R. Liao, J. C., A perspective of metabolic engineering strategies: moving up the systems hierarchy, Biotechnol Bioeng, 2003, 84 (7), 815-21.
Liao, J. C. Boscolo, R. Yang, Y. L. Tran, L. M. Sabatti, C. Roychowdhury, V. P., Network component analysis: reconstruction of regulatory signals in biological systems, Proc Natl Acad Sci U S A, 2003, 100 (26), 15522-7.
Bulter, T.; J.R. Bernstein; and J.C. Liao, A perspective of metabolic engineering strategies: moving up the systems hierarchy, Biotechnol. Bioeng, 2003, 84 (7), 815-821.
Hyduke, D. R. Rohlin, L. Kao, K. C. Liao, J. C., A software package for cDNA microarray data normalization and assessing confidence intervals, OMICS, 2003, 7 (3), 227-34.
El-Farra, N.H.;P. D. Christofides and J. C. Liao, Analysis of Nitric Oxide Transport Barriers in Blood Vessels Using a Distributed Multi-cellular Model, Annals of Biomedical Engineering, 2003, 31, 294-309.
El-Farra, N. H. Christofides, P. D. Liao, J. C., Analysis of nitric oxide consumption by erythrocytes in blood vessels using a distributed multicellular model, Ann Biomed Eng, 2003, 31 (3), 294-309.
Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, and Liao JC, Regulation of Nitric Oxide Consumption by Hypoxic Red Blood Cells, Proc. Natl. Acad. Sci. USA, 2003, 100 (21), 12504-12509.
Wang, C.W.;T.H. Han, and J. C. Liao, Sequence Analysis for Metabolic Evolution of Archaeoglobus fulgidus Geranylgeranyl Diphosphate Synthase in Escherichia coli for Carotenoid Biosynthesis, J. Chin. Inst. Chem. Eng , 2003, 34, 47-56.
Hatzimanikatis, V. Liao, J. C., A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering, Biotechnol Bioeng, 2002, 79 (5), 504-8.
Liao, JC, Blood feud: Keeping hemoglobin from nixing NO, Nature Medicine, 2002, 8 (12), 1350-1351.
Sabatti, C. Rohlin, L, Oh, M.K., and Liao, J.C., Co-expression pattern from DNA microarray experiments as a tool for operon prediction, Nucl. Acids. Res. , 2002, 30 (13), 2886-2893.
Rohlin, L., M.-K. Oh, and J. C. Liao, DNA Microarray For Microbial Biotechnology: Gene Expression Profiles in Escherichia coli During Protein Overexpression (invited paper), J. Chin. Inst. Chem. Eng, 2002, 33, 103-112 .
Liao, JC and Sabatti, C., Microanalysis of DNA microarrays, ASM News, 2002, 68, 432-437.
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., Nitric Oxide is Consumed, Rather than Conserved, by Reaction with Oxyhemoglobin under Physiological Conditions, Proc. Natl. Acad. Sci. USA, 2002, 99 (16), 10341-10346.
Han, T. H. Hyduke, D. R. Vaughn, M. W. Fukuto, J. M. Liao, J. C., Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions, Proc Natl Acad Sci U S A, 2002, 99 (11), 7763-8.
Oh, M. K. Rohlin, L. Kao, K. C. Liao, J. C., Global expression profiling of acetate-grown Escherichia coli, J Biol Chem, 2002, 277 (15), 13175-83.
Farmer, W. R. Liao, J. C., Acetate-inducible protein overexpression from the glnAp2 promoter of Escherichia coli, Biotechnol Bioeng, 2001, 75 (5), 504-9.
Wang, C. W. Liao, J. C., Alteration of product specificity of Rhodobacter sphaeroides phytoene desaturase by directed evolution, J Biol Chem, 2001, 276 (44), 41161-4.
Huang, K. T. Han, T. H. Hyduke, D. R. Vaughn, M. W. Van Herle, H. Hein, T. W. Zhang, C. Kuo, L. Liao, J. C., Modulation of nitric oxide bioavailability by erythrocytes, Proc Natl Acad Sci U S A, 2001, 98 (20), 11771-6.
Vaughn, M. W. Huang, K. T. Kuo, L. Liao, J. C., Erythrocyte consumption of nitric oxide: competition experiment and model analysis, Nitric Oxide, 2001, 5 (1), 18-31.
Barkovich, R. Liao, J. C., Metabolic engineering of isoprenoids, Metab Eng, 2001, 3 (1), 27-39.
Rohlin, L. Oh, M. K. Liao, J. C., Microbial pathway engineering for industrial processes: evolution, combinatorial biosynthesis and rational design, Curr Opin Microbiol, 2001, 4 (3), 330-5.
Farmer, W. R. Liao, J. C., Precursor balancing for metabolic engineering of lycopene production in Escherichia coli, Biotechnol Prog, 2001, 17 (1), 57-61.
Oh, M. K. Liao, J. C., DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli, Metab Eng, 2000, 2 (3), 201-9.
Wang, C. Oh, M. K. Liao, J. C., Directed evolution of metabolically engineered Escherichia coli for carotenoid production, Biotechnol Prog, 2000, 16 (6), 922-6.
Oh, M. K. Liao, J. C., Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli, Biotechnol Prog, 2000, 16 (2), 278-86.
Farmer, W. R. Liao, J. C., Improving lycopene production in Escherichia coli by engineering metabolic control, Nat Biotechnol, 2000, 18 (5), 533-7.
Vaughn, M. W. Huang, K. T. Kuo, L. Liao, J. C., Erythrocytes possess an intrinsic barrier to nitric oxide consumption, J Biol Chem, 2000, 275 (4), 2342-8.