研究領域與專長

廖俊智教授的研究領域為代謝及合成生物學, 特別在以微生物合成燃料的領域，及基礎代謝路徑的改造。此外，他更發展出網路構成要素分析法(Network Component Analysis) 及Ensemble Modeling，用以分析複雜的轉錄組調控，及設計人工基因轉錄調控迴路。

學經歷
經歷
  • 2016 – 迄今   院長, 中央研究院
  • 2016   特聘研究員, 中央研究院生物化學研究所
  • 2016   院士, 美國發明家學院
  • 2015   院士, 美國國家科學院
  • 2014   院士, 中央研究院
  • 2014   工業應用科學獎, 美國國家科學院
  • 2013   ENI再生能源獎, 義大利總統頒授
  • 2013   院士, 美國國家工程學院
  • 2012   再生能源創新獎, 美國白宮
  • 2012 – 2016   系主任, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 2011 – 2016   合聘教授, 美國加卅大學洛杉磯校區 化學暨生物化學系
  • 2011 – 2016   Ralph M. Parsons 基金會講座教授, 美國加卅大學洛杉磯校區 化學暨生物分子工程系Ralph M. Parsons
  • 2010 – 2016   合聘教授, 美國加卅大學洛杉磯校區 分子生物研究所
  • 2010   綠色化學學術組總統獎, 美國環保署
  • 2009 – 2012   副系主任, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 2008 – 2011   校長講座教授, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 2007 – 2016   能源研究副主任, 美國加卅大學洛杉磯校區 基因體暨蛋白質體研究所
  • 2003 – 2007   副主任, 美國加卅大學洛杉磯校區 仿細胞太空探索研究所
  • 2002 – 2007   副系主任, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 1997 – 2016   教授, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 1993 – 1997   合聘副教授, 美國德卅農工大學 生物化學暨生物物理系
  • 1993 – 1997   副教授, 美國德卅農工大學 化學工程系
  • 1990 – 1993   助理教授, 美國德卅農工大學(Texas A&M University ) 化學工程系
  • 1987 – 1989   研究科學家, 美國紐約卅羅徹斯特柯達公司 (Eastman Kodak Company)
學歷
  • 1982 – 1987   博士, 化學工程, 美國威斯康辛大學麥迪生校區
  • 1976 – 1980   學士, 化學工程系, 國立臺灣大學
主要著作
Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway.
Yu H, Li X, Duchoud F, Chuang DS, Liao JC
Nature communications (2018)
Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism.
Lin PP, Jaeger AJ, Wu TY, Xu SC, Lee AS, Gao F, Chen PW, Liao JC
Proc Natl Acad Sci USA (2018)
Metabolic repair through emergence of new pathways in Escherichia coli.
Pontrelli S, Fricke RCB, Teoh ST, Lavina WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC
Nature chemical biology (2018)
Synthetic non-oxidative glycolysis enables complete carbon conservation.
Bogorad IW, Lin TS, Liao JC
Nature (2013)
Integrated electromicrobial conversion of CO2 to higher alcohols.
Li, H.; P.H. Opgenorth; D.G. Wernick; S. Rogers; T.-Y.Wu; W. Higashide; P. Malati; Y. Huo, K.-M. Cho, and J.C. Liao
Science (2012)
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde.
Atsumi, S.; Higashide, W.; and J.C. Liao
Nature Biotechnol (2009)
Resistance to Diet-Induced Obesity in Mice with Synthetic Glyoxylate Shunt.
Dean, J.T.; Tran, L.; Beaven, S.; Tontonoz, P; Reue, K.; Dipple, K.D.; and J.C. Liao
Cell Metabolism (2009)
Expanding Metabolism for Biosynthesis of Nonnatural Alcohols.
Zhang, K., Sawaya, M.R., Eisenberg, D.S. and J.C. Liao
Proc. Natl. Acad. Sci. USA (2008)
Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels.
Atsumi, S.; T. Hanai and J.C. Liao
Nature (2008)
A synthetic gene-metabolic oscillator.
Fung, E.; Wong, W.W.; Suen, J.K.; Bulter, T.; Lee, S.G.; and J.C. Liao
Nature (2005)
著作列表
  1. Ohtake T, Kawase N, Pontrelli S, Nitta K, Lavina WA, Shen CR, Putri SP, (Liao JC), Fukusaki E  (2022-04)  Frontiers in microbiology  13, 871624  "Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production."
  2. Luo S, Lin PP, Nieh LY, Liao GB, Tang PW, Chen C, (Liao JC)*  (2022-02)  Nature Catalysis  5(2), 154-162  "A cell-free self-replenishing CO2-fixing system"
  3. Guo JY, Liu IJ, Lin HT, Wang MJ, Chang YL, Lin SC, Liao MY, Hsu WC, Lin YL, (Liao JC), Wu HC  (2021-06)  Journal of biomedical science  28(1), 43  "Identification of COVID-19 B-cell epitopes with phage-displayed peptide library."
  4. Chuang DS, (Liao JC)*  (2021-05)  Metabolic Engineering  65, 255-262  "Role of cyanobacterial phosphoketolase in energy regulation and glucose secretion under dark anaerobic and osmotic stress conditions."
  5. Yang HC, Chen CH, Wang JH, Liao HC, Yang CT, Chen CW, Lin YC, Kao CH, Lu MJ, (Liao JC)*  (2020-12)  Proceedings of the National Academy of Sciences of the United States of America  117(48), 30679-30686  "Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations."
  6. Chen FY, Jung HW, Tsuei CY, (Liao JC)  (2020-08)  Cell  182(4), 933-946  "Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol."
  7. Pontrelli S, Chiu TY, Lan EI, Chen FY, Chang P, (Liao JC)  (2018-11)  Metabolic engineering  50, 16-46  "Escherichia coli as a host for metabolic engineering."
  8. Pontrelli S, Fricke RCB, Teoh ST, Lavina WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, (Liao JC)  (2018-11)  Nature chemical biology  14(11), 1005-1009  "Metabolic repair through emergence of new pathways in Escherichia coli."
  9. Yu H, (Liao JC)  (2018-09)  Nature communications  9(1), 3992  "A modified serine cycle in Escherichia coli coverts methanol and CO2 to two-carbon compounds."
  10. Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, (Liao JC)  (2018-09)  Metabolic engineering  49, 153-163  "Directed strain evolution restructures metabolism for 1-butanol production in minimal media."
  11. Chen CT, Chen FY, Bogorad IW, Wu TY, Zhang R, Lee AS, (Liao JC)  (2018-09)  Metabolic engineering  49, 257-266  "Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production."
  12. Yu H, Li X, Duchoud F, Chuang DS, (Liao JC)  (2018-05)  Nature communications  9(1), 2008  "Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway."
  13. Lin PP, Jaeger AJ, Wu TY, Xu SC, Lee AS, Gao F, Chen PW, (Liao JC)  (2018-04)  Proceedings of the National Academy of Sciences of the United States of America  115(14), 3538-3546  "Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism."
  14. Nitta K, Lavina WA, Pontrelli S, (Liao JC), Putri SP, Fukusaki E  (2017-11)  Journal of bioscience and bioengineering  124(5), 498-505  "Orthogonal partial least squares/projections to latent structures regression-based metabolomics approach for identification of gene targets for improvement of 1-butanol production in Escherichia coli."
  15. Chen PW, Theisen MK, (Liao JC)  (2017-08)  Current opinion in biotechnology  46, 114-119  "Metabolic systems modeling for cell factories improvement."
  16. Lafontaine Rivera JG, Theisen MK, Chen PW, (Liao JC)  (2017-05)  Metabolic engineering  41, 144-151  "Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites."
  17. Ohtake T, Pontrelli S, Lavina WA, (Liao JC), Putri SP, Fukusaki E  (2017-05)  Metabolic engineering  41, 135-143  "Metabolomics-driven approach to solving a CoA imbalance for improved 1-butanol production in Escherichia coli."
  18. Soh LMJ, Mak WS, Lin PP, Mi L, Chen FY, Damoiseaux R, Siegel JB, (Liao JC)  (2017-04)  ACS synthetic biology  6(4), 610-618  "Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design."
  19. Wang J, Jain R, Shen X, Sun X, Cheng M, (Liao JC), Yuan Q, Yan Y  (2017-03)  Metabolic engineering  40, 148-156  "Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose."
  20. Xiong W, Lin PP, Magnusson L, Warner L, (Liao JC), Maness PC, Chou KJ  (2016-11)  Proceedings of the National Academy of Sciences of the United States of America  113(46), 13180-13185  "CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum."
  21. Wu TY, Chen CT, Liu JT, Bogorad IW, Damoiseaux R, (Liao JC)  (2016-06)  Applied microbiology and biotechnology  100(11), 4969-4983  "Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1."
  22. (Liao JC), Mi L, Pontrelli S, Luo S  (2016-04)  Nature Reviews Microbiology  14(5), 288-304  "Fuelling the future: microbial engineering for the production of sustainable biofuels."
  23. Chen CT, (Liao JC)  (2016-03)  FEMS microbiology letters  363(5), fnw020  "Frontiers in microbial 1-butanol and isobutanol production."
  24. Theisen MK, Lafontaine Rivera JG, (Liao JC)  (2016-03)  PLoS computational biology  12(3), e1004800  "Stability of Ensemble Models Predicts Productivity of Enzymatic Systems."
  25. Wernick DG, Pontrelli SP, Pollock AW, (Liao JC)  (2016-02)  Scientific reports  6, 20224  "Sustainable biorefining in wastewater by engineered extreme alkaliphile Bacillus marmarensis."
  26. Noguchi S, Putri SP, Lan EI, Lavina WA, Dempo Y, Bamba T, (Liao JC), Fukusaki E  (2016)  Metabolomics : Official journal of the Metabolomic Society  12, 26  "Quantitative target analysis and kinetic profiling of acyl-CoAs reveal the rate-limiting step in cyanobacterial 1-butanol production."
  27. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, (Liao JC), Siegel JB  (2015-11)  Nature communications  6, 10005  "Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway."
  28. Lin PP, Mi L, Morioka AH, Yoshino KM, Konishi S, Xu SC, Papanek BA, Riley LA, Guss AM, (Liao JC)  (2015-09)  Metabolic engineering  31, 44-52  "Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum."
  29. Lan EI, Chuang DS, Shen CR, Lee AM, Ro SY, (Liao JC)  (2015-09)  Metabolic engineering  31, 163-170  "Metabolic engineering of cyanobacteria for photosynthetic 3-hydroxypropionic acid production from CO2 using Synechococcus elongatus PCC 7942."
  30. Lafontaine Rivera JG, Lee Y, (Liao JC)  (2015-08)  Integrative biology : quantitative biosciences from nano to macro  7(8), 895-903  "An entropy-like index of bifurcational robustness for metabolic systems."
  31. Chung NC, Huang YH, Chang CH, (Liao JC), Yang CH, Chen CC, Liu IY  (2015-03)  PloS one  10(3), e0118832  "Behavior training reverses asymmetry in hippocampal transcriptome of the cav3.2 knockout mice."
  32. Li H, (Liao JC)  (2015-02)  ACS synthetic biology  4(2), 101-106  "A synthetic anhydrotetracycline-controllable gene expression system in Ralstonia eutropha H16."
  33. Sumner LW, Styczynski M, McLean J, Fiehn O, Jander G, (Liao J), Sumner S, Britz-McKibbin P, Welti R, Jones AD, Dorrestein PC, Bearden D, Kaddurah-Daouk R  (2015-02)  Metabolomics  11(1), 3-5  "Introducing the USA Plant, Algae and Microbial Metabolomics Research Coordination Network (PAMM-NET)."
  34. Ho CK, Rahib L, (Liao JC), Sriram G, Dipple KM  (2015-01)  Molecular genetics and metabolism  114(1), 66-72  "Mathematical modeling of the insulin signal transduction pathway for prediction of insulin sensitivity from expression data."
  35. Bogorad IW, Chen CT, Theisen MK, Wu TY, Schlenz AR, Lam AT, (Liao JC)  (2014-11)  Proceedings of the National Academy of Sciences of the United States of America  111(45), 15928-15933  "Building carbon-carbon bonds using a biocatalytic methanol condensation cycle."
  36. Khodayari A, Zomorrodi AR, (Liao JC), Maranas CD  (2014-09)  Metabolic engineering  25, 50-62  "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data."
  37. Lee Y, Lafontaine Rivera JG, (Liao JC)  (2014-09)  Metabolic engineering  25, 63-71  "Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways."
  38. Lin PP, Rabe KS, Takasumi JL, Kadisch M, Arnold FH, (Liao JC)  (2014-07)  Metabolic engineering  24, 1-8  "Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius."
  39. Li X, Shen CR, (Liao JC)  (2014-06)  Photosynthesis research  120(3), 301-310  "Isobutanol production as an alternative metabolic sink to rescue the growth deficiency of the glycogen mutant of Synechococcus elongatus PCC 7942."
  40. Choi KY, Wernick DG, Tat CA, (Liao JC)  (2014-05)  Metabolic engineering  23, 53-61  "Consolidated conversion of protein waste into biofuels and ammonia using Bacillus subtilis."
  41. Nielsen J, Fussenegger M, Keasling J, Lee SY, (Liao JC), Prather K, Palsson B  (2014-05)  Nature chemical biology  10(5), 319-322  "Engineering synergy in biotechnology."
  42. Harper M, Gronenberg L, (Liao J), Lee C  (2014-02)  PloS one  9(2), e88072  "Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis."
  43. Li H, (Liao JC)  (2014-01)  ACS synthetic biology  3(1), 13-20  "Development of an NADPH-dependent homophenylalanine dehydrogenase by protein engineering."
  44. Hu WS, (Liao JC)  (2013-11)  Current Opinion in Chemical Engineering  2(4), 363-364  "Biotechnology and bioprocess engineering."
  45. Kusakabe T, Tatsuke T, Tsuruno K, Hirokawa Y, Atsumi S, (Liao JC), Hanai T  (2013-11)  Metabolic engineering  20, 101-108  "Engineering a synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light."
  46. Wernick DG, Choi KY, Tat CA, Lafontaine Rivera JG, (Liao JC)  (2013-11)  Genome announcements  1(6), e00967-13  "Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297."
  47. Bogorad IW, Lin TS, (Liao JC)  (2013-10)  Nature  502(7473), 693-697  "Synthetic non-oxidative glycolysis enables complete carbon conservation."
  48. Mainguet SE, Gronenberg LS, Wong SS, (Liao JC)  (2013-09)  Metabolic engineering  19, 116-127  "A reverse glyoxylate shunt to build a non-native route from C4 to C2 in Escherichia coli."
  49. Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, Foster CE, (Liao JC), Lin XN  (2013-09)  Proceedings of the National Academy of Sciences of the United States of America  110(36), 14592-14597  "Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass."
  50. Lan EI, Dekishima Y, Chuang DS, (Liao JC)  (2013-09)  AIChE Journal  59(9), 3167-3175  "Metabolic engineering of 2-pentanone synthesis in Escherichia coli."
  51. Zomorrodi AR, Lafontaine Rivera JG, (Liao JC), Maranas CD  (2013-09)  Biotechnology journal  8(9), 1090-1104  "Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks."
  52. Li H, (Liao JC)  (2013-08)  Energy & Environmental Science  6(10), 2892-2899  "Biological conversion of carbon dioxide to photosynthetic fuels and electrofuels."
  53. Gronenberg LS, Marcheschi RJ, (Liao JC)  (2013-06)  Current opinion in chemical biology  17(3), 462-471  "Next generation biofuel engineering in prokaryotes."
  54. Lan EI, (Liao JC)  (2013-05)  Bioresource technology  135, 339-349  "Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources."
  55. Marcheschi RJ, Gronenberg LS, (Liao JC)  (2013-05)  Biotechnology journal  8(5), 545-555  "Protein engineering for metabolic engineering: current and next-generation tools."
  56. Shen CR, (Liao JC)  (2013-05)  Metabolic engineering  17, 12-22  "Synergy as design principle for metabolic engineering of 1-propanol production in Escherichia coli."
  57. Lan EI, Ro S, (Liao JC)  (2013-04)  Energy & Environmental Science  6(9), 2672-2681  "Oxygen-tolerant coenzyme A-acylating aldehyde dehydrogenase facilitates efficient photosynthetic n-butanol biosynthesis in cyanobacteria."
  58. Wernick DG, (Liao JC)  (2013-02)  Applied microbiology and biotechnology  97(4), 1397-1406  "Protein-based biorefining: metabolic engineering for production of chemicals and fuel with regeneration of nitrogen fertilizers."
  59. Li H, (Liao JC)  (2013-01)  Microbial cell factories  12, 4  "Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol."
  60. (Liao JC), Hu WS  (2012-11)  Current Opinion in Chemical Engineering  1(4), 353-354  "Bio-based chemical engineering."
  61. Machado HB, Dekishima Y, Luo H, Lan EI, (Liao JC)  (2012-09)  Metabolic engineering  14(5), 504-511  "A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols."
  62. Shen CR, (Liao JC)  (2012-09)  Energy & Environmental Science  5(11), 9574-9583  "Photosynthetic production of 2-methyl-1-butanol from CO2 in cyanobacterium Synechococcus elongatus PCC7942 and characterization of the native acetohydroxyacid synthase."
  63. (Liao JC), Messing J  (2012-06)  Current Opinion in Biotechnology  23(3), 287-289  "Energy biotechnology."
  64. Huo YX, Wernick DG, (Liao JC)  (2012-06)  Current opinion in biotechnology  23(3), 406-413  "Toward nitrogen neutral biofuel production."
  65. Felnagle EA, Chaubey A, Noey EL, Houk KN, (Liao JC)  (2012-05)  Nature chemical biology  8(6), 518-526  "Engineering synthetic recursive pathways to generate non-natural small molecules."
  66. Tan Y, (Liao JC)  (2012-05)  Biotechnology journal  7(3), 343-353  "Metabolic ensemble modeling for strain engineers."
  67. Marcheschi RJ, Li H, Zhang K, Noey EL, Kim S, Chaubey A, Houk KN, (Liao JC)  (2012-04)  ACS chemical biology  7(4), 689-697  "A synthetic recursive "+1" pathway for carbon chain elongation."
  68. Lan EI, (Liao JC)  (2012-04)  Proceedings of the National Academy of Sciences of the United States of America  109(16), 6018-6023  "ATP drives direct photosynthetic production of 1-butanol in cyanobacteria."
  69. Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, (Liao JC)  (2012-03)  Science  335(6076), 1596  "Integrated electromicrobial conversion of CO2 to higher alcohols."
  70. Tran LM, Chang CJ, Plaisier S, Wu S, Dang J, Mischel PS, (Liao JC), Graeber TG, Wu H  (2012-02)  PloS one  7(2), e31053  "Determining PTEN functional status by network component deduced transcription factor activities."
  71. Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M Jr, (Liao JC), Schadt CW, Guss AM, Yang Y, Graham DE  (2012-01)  Biotechnology for biofuels  5(1), 2  "Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations."
  72. Hu CW, Chang YL, Chen SJ, Kuo-Huang LL, (Liao JC), Huang HC, Juan HF  (2011-12)  PloS one  6(12), e28329  "Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach."
  73. Smith KM, (Liao JC)  (2011-11)  Metabolic engineering  13(6), 674-681  "An evolutionary strategy for isobutanol production strain development in Escherichia coli."
  74. Dekishima Y, Lan EI, Shen CR, Cho KM, (Liao JC)  (2011-08)  Journal of the American Chemical Society  133(30), 11399-11401  "Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli."
  75. Contador CA, Andrews BA, (Liao JC), Asenjo JA  (2011-07)  Biotechnology progress  27(4), 925-936  "Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast Saccharomyces cerevisiae."
  76. Lan EI, (Liao JC)  (2011-07)  Metabolic engineering  13(4), 353-363  "Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide."
  77. Baez A, Cho KM, (Liao JC)  (2011-06)  Applied microbiology and biotechnology  90(5), 1681-1690  "High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal."
  78. Shen CR, Lan EI, Dekishima Y, Baez A, Cho KM, (Liao JC)  (2011-05)  Applied and environmental microbiology  77(9), 2905-2915  "Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli."
  79. Huo YX, Cho KM, Rivera JG, Monte E, Shen CR, Yan Y, (Liao JC)  (2011-04)  Nature biotechnology  29(4), 346-351  "Conversion of proteins into biofuels by engineering nitrogen flux."
  80. Higashide W, Li Y, Yang Y, (Liao JC)  (2011-04)  Applied and environmental microbiology  77(8), 2727-2733  "Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose."
  81. Harper MA, Chen Z, Toy T, Machado IM, Nelson SF, (Liao JC), Lee CJ  (2011-02)  PloS one  6(2), e16517  "Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants."
  82. Rizk ML, Laguna R, Smith KM, Tabita FR, (Liao JC)  (2011-02)  Biotechnology progress  27(1), 15-22  "Redox homeostasis phenotypes in RubisCO-deficient Rhodobacter sphaeroides via ensemble modeling."
  83. Wang W, Hein TW, Zhang C, Zawieja DC, (Liao JC), Kuo L  (2011-01)  Microcirculation  18(1), 36-45  "Oxidized low-density lipoprotein inhibits nitric oxide-mediated coronary arteriolar dilation by up-regulating endothelial arginase I."
  84. Tan Y, Rivera JG, Contador CA, Asenjo JA, (Liao JC)  (2011-01)  Metabolic engineering  13(1), 60-75  "Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux."
  85. Shen CR, (Liao JC)  (2011)  Methods in enzymology  497, 469-481  "A synthetic iterative pathway for ketoacid elongation."
  86. Mainguet SE, (Liao JC)  (2010-12)  Biotechnol J.  5(12), 1297-1308  "Bioengineering of microorganisms for C3 to C5 alcohols production."
  87. Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, (Liao JC)  (2010-12)  Molecular systems biology  6, 449  "Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli."
  88. Inokuma K, (Liao JC), Okamoto M, Hanai T  (2010-12)  Journal of bioscience and bioengineering  110(6), 696-701  "Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping."
  89. Wong I, Atsumi S, Huang WC, Wu TY, Hanai T, Lam ML, Tang P, Yang J, (Liao JC), Ho CM  (2010-10)  Lab on a chip  10(20), 2710-2719  "An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study."
  90. Tran LM, Hyduke DR, (Liao JC)  (2010-10)  BMC bioinformatics  11, 511  "Trimming of mammalian transcriptional networks using network component analysis."
  91. Smith KM, Cho KM, (Liao JC)  (2010-07)  Applied microbiology and biotechnology  87(3), 1045-1055  "Engineering Corynebacterium glutamicum for isobutanol production."
  92. Sriram G, Parr LS, Rahib L, (Liao JC), Dipple KM  (2010-07)  Metabolic engineering  12(4), 332-340  "Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells."
  93. Connor MR, Cann AF, (Liao JC)  (2010-04)  Applied microbiology and biotechnology  86(4), 1155-1164  "3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation."
  94. Dean JT, Rizk ML, Tan Y, Dipple KM, (Liao JC)  (2010-04)  Biophysical journal  98(8), 1385-1395  "Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt."
  95. Zhang K, Li H, Cho KM, (Liao JC)  (2010-04)  Proceedings of the National Academy of Sciences of the United States of America  107(14), 6234-6239  "Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine."
  96. Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, (Liao JC)  (2010-01)  Applied microbiology and biotechnology  85(3), 651-657  "Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes."
  97. Cann AF, (Liao JC)  (2010-01)  Applied microbiology and biotechnology  85(4), 893-899  "Pentanol isomer synthesis in engineered microorganisms."
  98. Li H, Cann AF, (Liao JC)  (2010)  Annual review of chemical and biomolecular engineering  1, 19-36  "Biofuels: biomolecular engineering fundamentals and advances."
  99. Atsumi S, Higashide W, (Liao JC)  (2009-12)  Nature biotechnology  27(12), 1177-1180  "Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde."
  100. Rizk ML, (Liao JC)  (2009-11)  Journal of the Taiwan Institute of Chemical Engineers  40(6), 595–601  "Ensemble modeling and related mathematical modeling of metabolic networks."
  101. Wong WW, (Liao JC)  (2009-11)  Metabolic engineering  11(6), 409-414  "Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters."
  102. Atsumi S, Li Z, (Liao JC)  (2009-10)  Applied and environmental microbiology  75(19), 6306-6311  "Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli."
  103. Yan Y, Lee CC, (Liao JC)  (2009-10)  Organic & biomolecular chemistry  7(19), 3914-3917  "Enantioselective synthesis of pure (R,R)-2,3-butanediol in Escherichia coli with stereospecific secondary alcohol dehydrogenases."
  104. Rizk ML, (Liao JC)  (2009-09)  PloS one  4(9), e6903  "Ensemble modeling for aromatic production in Escherichia coli."
  105. Contador CA, Rizk ML, Asenjo JA, (Liao JC)  (2009-09)  Metabolic engineering  11(4-5), 221-233  "Ensemble modeling for strain development of L-lysine-producing Escherichia coli."
  106. Brynildsen MP, (Liao JC)  (2009-06)  Molecular systems biology  5, 277  "An integrated network approach identifies the isobutanol response network of Escherichia coli."
  107. Connor MR, (Liao JC)  (2009-06)  Current opinion in biotechnology  20(3), 307-315  "Microbial production of advanced transportation fuels in non-natural hosts."
  108. Dean JT, Tran L, Beaven S, Tontonoz P, Reue K, Dipple KM, (Liao JC)  (2009-06)  Cell metabolism  9(6), 525-536  "Resistance to diet-induced obesity in mice with synthetic glyoxylate shunt."
  109. Lai D, Lluncor B, Schroder I, Gunsalus RP, (Liao JC), Monbouquette HG  (2009-05)  Metabolic engineering  11(3), 184-191  "Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate."
  110. Yan Y, (Liao JC)  (2009-04)  Journal of industrial microbiology & biotechnology  36(4), 471-479  "Engineering metabolic systems for production of advanced fuels."
  111. Rahib L, Sriram G, Harada MK, (Liao JC), Dipple KM  (2009-03)  Molecular genetics and metabolism  96(3), 106-112  "Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency."
  112. Ye C, Galbraith SJ, (Liao JC), Eskin E  (2009-03)  PLoS computational biology  5(3), e1000311  "Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast."
  113. Wong WW, Tran LM, (Liao JC)  (2009-01)  Biotechnology and bioengineering  102(1), 73-80  "A hidden square-root boundary between growth rate and biomass yield."
  114. Atsumi S, (Liao JC)  (2008-12)  Applied and environmental microbiology  74(24), 7802-7808  "Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli."
  115. Tran LM, Rizk ML, (Liao JC)  (2008-12)  Biophysical journal  95(12), 5606-5617  "Ensemble modeling of metabolic networks."
  116. Zhang K, Sawaya MR, Eisenberg DS, (Liao JC)  (2008-12)  Proceedings of the National Academy of Sciences of the United States of America  105(52), 20653-20658  "Expanding metabolism for biosynthesis of nonnatural alcohols."
  117. Shen CR, (Liao JC)  (2008-11)  Metabolic engineering  10(6), 312-320  "Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways."
  118. Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, (Liao JC)  (2008-11)  Metabolic engineering  10(6), 305-311  "Metabolic engineering of Escherichia coli for 1-butanol production."
  119. Cann AF, (Liao JC)  (2008-11)  Applied microbiology and biotechnology  81(1), 89-98  "Production of 2-methyl-1-butanol in engineered Escherichia coli."
  120. Atsumi S, (Liao JC)  (2008-10)  Current opinion in biotechnology  19(5), 414-419  "Metabolic engineering for advanced biofuels production from Escherichia coli."
  121. Connor MR, (Liao JC)  (2008-09)  Applied and environmental microbiology  74(18), 5769-5775  "Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol."
  122. (Liao JC), Higashide W  (2008-08)  Chemical Engineering Progress  104(8), S19-S23  "Metabolic engineering of next-generation biofuels."
  123. Bernstein JR, Bulter T, (Liao JC)  (2008-06)  Metabolic engineering  10(3-4), 131-140  "Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin."
  124. Chou KJ, Dodd J, (Liao JC)  (2008-03)  Nitric oxide-biology and chemistry  18(2), 122-135  "Interactions of nitrosylhemoglobin and carboxyhemoglobin with erythrocyte."
  125. Boscolo R, (Liao JC), Roychowdhury VP  (2008-02)  IEEE-ACM Transactions on Computational Biology and Bioinformatics  5(1), 15-24  "An information theoretic exploratory method for learning patterns of conditional gene coexpression from microarray data."
  126. Lee SG, (Liao JC)  (2008-02)  Journal of microbiology and biotechnology  18(2), 334-337  "Control of acetate production rate in Escherichia coli by regulating expression of single-copy pta using lacI(Q) in multicopy plasmid."
  127. Jarboe LR, Hyduke DR, Tran LM, Chou KJ, (Liao JC)  (2008-02)  The Journal of biological chemistry  283(8), 5148-5157  "Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis."
  128. Sriram G, Rahib L, He JS, Campos AE, Parr LS, (Liao JC), Dipple KM  (2008-02)  Molecular genetics and metabolism  93(2), 145-159  "Global metabolic effects of glycerol kinase overexpression in rat hepatoma cells."
  129. Atsumi S, Hanai T, (Liao JC)  (2008-01)  Nature  451(7174), 86-89  "Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels."
  130. Hanai T, Atsumi S, (Liao JC)  (2007-12)  Applied and environmental microbiology  73(24), 7814-7818  "Engineered synthetic pathway for isopropanol production in Escherichia coli."
  131. Watanabe J, Chou KJ, (Liao JC), Miao Y, Meng HH, Ge H, Grijalva V, Hama S, Kozak K, Buga G, Whitelegge JP, Lee TD, Farias-Eisner R, Navab M, Fogelman AM, Reddy ST  (2007-08)  The Journal of biological chemistry  282(32), 23698-23707  "Differential association of hemoglobin with proinflammatory high density lipoproteins in atherogenic/hyperlipidemic mice. A novel biomarker of atherosclerosis."
  132. Brynildsen MP, Wu TY, Jang SS, (Liao JC)  (2007-07)  Bioinformatics  23(14), 1783-1791  "Biological network mapping and source signal deduction."
  133. Wong WW, Tsai TY, (Liao JC)  (2007-07)  Molecular systems biology  3, 130  "Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator."
  134. Bernstein JR, Bulter T, Shen CR, (Liao JC)  (2007-06)  The Journal of biological chemistry  282(26), 18929-18936  "Directed evolution of ribosomal protein S1 for enhanced translational efficiency of high GC Rhodopseudomonas palustris DNA in Escherichia coli."
  135. Ohta AT, Chiou PY, Han TH, (Liao JC), Bhardwaj U, McCabe ERB, Yu F, Sun R, Wu MC  (2007-06)  Journal of Microelectromechanical Systems  16(3), 491-499  "Dynamic cell and microparticle control via optoelectronic tweezers."
  136. Rahib L, MacLennan NK, Horvath S, (Liao JC), Dipple KM  (2007-06)  European journal of human genetics  15(6), 646-657  "Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling."
  137. Hyduke DR, Jarboe LR, Tran LM, Chou KJ, (Liao JC)  (2007-05)  Proceedings of the National Academy of Sciences of the United States of America  104(20), 8484-8489  "Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli."
  138. Han TH, Perloff JK, (Liao JC)  (2007-03)  The American journal of cardiology  99(5), 691-695  "Nitric oxide metabolism in adults with cyanotic congenital heart disease."
  139. Brynildsen MP, Tran LM, (Liao JC)  (2006-12)  Bioinformatics  22(24), 3040-3046  "A Gibbs sampler for the identification of gene expression and network connectivity consistency."
  140. Braatsch S, Bernstein JR, Lessner F, Morgan J, (Liao JC), Harwood CS, Beatty JT  (2006-12)  Biochemistry  45(48), 14441-14451  "Rhodopseudomonas palustris CGA009 has two functional ppsR genes, each of which encodes a repressor of photosynthesis gene expression."
  141. Brynildsen MP, Tran LM, (Liao JC)  (2006-10)  Biophysical journal  91(8), 2749-2759  "Versatility and connectivity efficiency of bipartite transcription networks."
  142. Galbraith SJ, Tran LM, (Liao JC)  (2006-08)  Bioinformatics  22(15), 1886-1894  "Transcriptome network component analysis with limited microarray data."
  143. Wong WW, (Liao JC)  (2006-06)  Cellular and molecular life sciences  63(11), 1215-1220  "The design of intracellular oscillators that interact with metabolism."
  144. Oh MK, Cha MJ, Lee SG, Rohlin L, (Liao, JC)  (2006-04)  Journal of Microbiology and Biotechnology  16(4), 543-549  "Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate."
  145. MacLennan NK, Rahib L, Shin C, Fang Z, Horvath S, Dean J, (Liao JC), McCabe ER, Dipple KM  (2006-02)  Human molecular genetics  15(3), 405-415  "Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity."
  146. (Liao JC)  (2006-01)  Journal of the Chinese Institute of Chemical Engineers  37(1), 103-106  "Systems Biology: Where does chemical engineering stand?"
  147. Boscolo R, Sabatti C, (Liao JC), Roychowdhury VP  (2005-12)  IEEE-ACM Transactions on Computational Biology and Bioinformatics  2(4), 289-301  "A generalized framework for network component analysis."
  148. Brynildsen MP, Wong WW, (Liao JC)  (2005-12)  Biochemical Society transactions  33(Pt6), 1423-1426  "Transcriptional regulation and metabolism."
  149. Kao KC, Tran LM, (Liao JC)  (2005-10)  The Journal of biological chemistry  280(43), 36079-36087  "A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis."
  150. Rohlin L, Trent JD, Salmon K, Kim U, Gunsalus RP, (Liao JC)  (2005-09)  Journal of bacteriology  187(17), 6046-6057  "Heat shock response of Archaeoglobus fulgidus."
  151. Yang YL, (Liao JC)  (2005-07)  Metabolic engineering  7(4), 280-290  "Determination of functional interactions among signalling pathways in Escherichia coli K-12."
  152. Yang YL, Suen J, Brynildsen MP, Galbraith SJ, (Liao JC)  (2005-06)  BMC genomics  6, 90  "Inferring yeast cell cycle regulators and interactions using transcription factor activities."
  153. Sriram G, Martinez JA, McCabe ER, (Liao JC), Dipple KM  (2005-06)  American journal of human genetics  76(6), 911-924  "Single-gene disorders: what role could moonlighting enzymes play?"
  154. Fung E, Wong WW, Suen JK, Bulter T, Lee SG, (Liao JC)  (2005-05)  Nature  435(7038), 118-122  "A synthetic gene-metabolic oscillator."
  155. Hyduke DR, (Liao JC)  (2005-05)  American journal of physiology-Heart and circulatory physiology  288(5), H2390-H2399  "Analysis of nitric oxide donor effectiveness in resistance vessels."
  156. Han TH, Pelling A, Jeon TJ, Gimzewski JK, (Liao JC)  (2005-05)  Biochimica et biophysica acta-General Subjects  1723(1-3), 135-142  "Erythrocyte nitric oxide transport reduced by a submembrane cytoskeletal barrier."
  157. Zhou B, Beckwith D, Jarboe LR, (Liao JC)  (2005-04)  Biophysical journal  88(4), 2541-2553  "Markov Chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli."
  158. Sabatti C, Rohlin L, Lange K, (Liao JC)  (2005-04)  Bioinformatics  21(7), 922-931  "Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites."
  159. Tran LM, Brynildsen MP, Kao KC, Suen JK, (Liao JC)  (2005-03)  Metabolic engineering  7(2), 128-141  "gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation."
  160. Jarboe LR, Beckwith D, (Liao JC)  (2004-10)  Biotechnology and bioengineering  88(2), 189-203  "Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli."
  161. (Liao JC)  (2004-07)  Nature biotechnology  22(7), 823-824  "Custom design of metabolism."
  162. Han TH, Fukuto JM, (Liao JC)  (2004-03)  Nitric oxide-biology and chemistry  10(2), 74-82  "Reductive nitrosylation and S-nitrosation of hemoglobin in inhomogeneous nitric oxide solutions."
  163. Bulter T, Lee SG, Wong WW, Fung E, Connor MR, (Liao JC)  (2004-02)  Proceedings of the National Academy of Sciences of the United States of America  101(8), 2299-2304  "Design of artificial cell-cell communication using gene and metabolic networks."
  164. Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, (Liao JC)  (2004-01)  Proceedings of the National Academy of Sciences of the United States of America  101(2), 641-646  "Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis."
  165. Yang YL, (Liao JC)  (2004)  IEEE Engineering in Medicine and Biology Society  4, 2937-2940  "Network component analysis of Saccharamyces cerevisiae stress response."
  166. Bulter T, Bernstein JR, (Liao JC)  (2003-12)  Biotechnology and bioengineering  84(7), 815-821  "A perspective of metabolic engineering strategies: moving up the systems hierarchy."
  167. (Liao JC), Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP  (2003-12)  Proceedings of the National Academy of Sciences of the United States of America  100(26), 15522-15527  "Network component analysis: reconstruction of regulatory signals in biological systems."
  168. Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, (Liao JC)  (2003-10)  Proceedings of the National Academy of Sciences of the United States of America  100(21), 12504-12509  "Regulation of nitric oxide consumption by hypoxic red blood cells."
  169. Hyduke DR, Rohlin L, Kao KC, (Liao JC)  (2003-09)  Omics : a journal of integrative biology  7(3), 227-234  "A software package for cDNA microarray data normalization and assessing confidence intervals."
  170. El-Farra NH, Christofides PD, (Liao JC)  (2003-03)  Annals of biomedical engineering  31(3), 294-309  "Analysis of nitric oxide consumption by erythrocytes in blood vessels using a distributed multicellular model."
  171. Wang CW, Han TH. (Liao JC)  (2003-01)  Journal of the Chinese Institute of Chemical Engineers  34(1), 47-56  "Sequence Analysis for Metabolic Evolution of Archaeoglobus fulgidus Geranylgeranyl Diphosphate Synthase in Escherichia coli for Carotenoid Biosynthesis."
  172. (Liao JC)  (2002-12)  Nature medicine  8(12), 1350-1351  "Blood feud: keeping hemoglobin from nixing NO."
  173. Hatzimanikatis V, (Liao JC)  (2002-09)  Biotechnology and bioengineering  79(5), 504-508  "A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering."
  174. (Liao JC), Sabatti C  (2002-09)  ASM NEWS  68(9), 432-437  "Microanalysis of DNA microarrays."
  175. Joshi MS, Ferguson TB Jr, Han TH, Hyduke DR, (Liao JC), Rassaf T, Bryan N, Feelisch M, Lancaster JR Jr  (2002-08)  Proceedings of the National Academy of Sciences of the United States of America  99(16), 10341-10346  "Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions."
  176. Sabatti C, Rohlin L, Oh MK, (Liao JC)  (2002-07)  Nucleic acids research  30(13), 2886-2893  "Co-expression pattern from DNA microarray experiments as a tool for operon prediction."
  177. Han TH, Hyduke DR, Vaughn MW, Fukuto JM, (Liao JC)  (2002-05)  Proceedings of the National Academy of Sciences of the United States of America  99(11), 7763-7768  "Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions."
  178. Oh MK, Rohlin L, Kao KC, (Liao JC)  (2002-04)  The Journal of biological chemistry  277(15), 13175-13183  "Global expression profiling of acetate-grown Escherichia coli."
  179. Oh MK, (Liao JC)  (2002-01)  Journal of the Chinese Institute of Chemical Engineers  3(1), 103-112  "DNA Microarray For Microbial Biotechnology: Gene Expression Profiles in Escherichia coli During Protein Overexpression."
  180. Farmer WR, (Liao JC)  (2001-12)  Biotechnology and bioengineering  75(5), 504-509  "Acetate-inducible protein overexpression from the glnAp2 promoter of Escherichia coli."
  181. Wang CW, (Liao JC)  (2001-11)  The Journal of biological chemistry  276(44), 41161-41164  "Alteration of product specificity of Rhodobacter sphaeroides phytoene desaturase by directed evolution."
  182. Huang KT, Han TH, Hyduke DR, Vaughn MW, Van Herle H, Hein TW, Zhang C, Kuo L, (Liao JC)  (2001-09)  Proceedings of the National Academy of Sciences of the United States of America  98(20), 11771-11776  "Modulation of nitric oxide bioavailability by erythrocytes."
  183. Tseng GC, Oh MK, Rohlin L, (Liao JC), Wong WH  (2001-06)  Nucleic acids research  29(12), 2549-2557  "Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects."
  184. Rohlin L, Oh MK, (Liao JC)  (2001-06)  Current opinion in microbiology  4(3), 330-335  "Microbial pathway engineering for industrial processes: evolution, combinatorial biosynthesis and rational design."
  185. Vaughn MW, Huang KT, Kuo L, (Liao JC)  (2001-02)  NITRIC OXIDE-BIOLOGY AND CHEMISTRY  5(1), 18-31  "Erythrocyte consumption of nitric oxide: competition experiment and model analysis."
  186. Chang CI, (Liao JC), Kuo L  (2001-02)  Cancer research  61(3), 1100-1106  "Macrophage arginase promotes tumor cell growth and suppresses nitric oxide-mediated tumor cytotoxicity."
  187. Farmer WR, (Liao JC)  (2001-02)  Biotechnology progress  17(1), 57-61  "Precursor balancing for metabolic engineering of lycopene production in Escherichia coli."
  188. Barkovich R, (Liao JC)  (2001-01)  Metabolic engineering  3(1), 27-39  "Metabolic engineering of isoprenoids."
  189. Wang C, Oh MK, (Liao JC)  (2000-12)  Biotechnology progress  16(6), 922-926  "Directed evolution of metabolically engineered Escherichia coli for carotenoid production."
  190. Chang CI, Zoghi B, (Liao JC), Kuo L  (2000-08)  Journal of immunology  165(4), 2134-2141  "The involvement of tyrosine kinases, cyclic AMP/protein kinase A, and p38 mitogen-activated protein kinase in IL-13-mediated arginase I induction in macrophages: its implications in IL-13-inhibited nitric oxide production."
  191. Oh MK, (Liao JC)  (2000-07)  Metabolic engineering  2(3), 201-209  "DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli."
  192. Farmer WR, (Liao JC)  (2000-05)  Nature biotechnology  18(5), 533-537  "Improving lycopene production in Escherichia coli by engineering metabolic control."
  193. Oh MK, (Liao JC)  (2000-04)  Biotechnology progress  16(2), 278-286  "Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli."
  194. Vaughn MW, Huang KT, Kuo L, (Liao JC)  (2000-01)  The Journal of biological chemistry  275(4), 2342-2348  "Erythrocytes possess an intrinsic barrier to nitric oxide consumption."
  195. Hein TW, (Liao JC), Kuo L  (2000-01)  American journal of physiology-Heart and circulatory physiology  278(1), H175-H183  "oxLDL specifically impairs endothelium-dependent, NO-mediated dilation of coronary arterioles."
  196. (Liao JC), Hein TW, Vaughn MW, Huang KT, Kuo L  (1999-07)  Proceedings of the National Academy of Sciences of the United States of America  96(15), 8757-8761  "Intravascular Flow Decreases Erythrocyte Consumption of Nitric Oxide."
  197. (Liao JC), Oh MK  (1999-07)  Metabolic Engineering  1(3), 214-233  "Toward predicting metabolic fluxes in metabolically engineered strains."
  198. (Liao JC)  (1999-05)  Journal of Biotechnology  7(1-3), 259-262  "Inverse Flux Analysis."
  199. Lee B, Yen J, Yang L, (Liao JC)  (1999-03)  Biotechnology and Bioengineering  62(6), 722-729  "Incorporating qualitative knowledge in enzyme kinetic models using Fuzzy Logic."
  200. Wang CW, Oh MK, Liao JC  (1999-01)  Biotechnology and Bioengineering  62(2), 235-241  "Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli."
  201. (Liao JC), Delgado J  (1998-07)  Biotechnology Progress  14(4), 554-560  "Flux calculation using metabolic control constraints."
  202. Vaughn MW, Kuo L, (Liao JC)  (1998-06)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  274(6 Pt ), H2163-H2176  "Estimation of nitric oxide production and reaction rates in tissue using a mathematical model."
  203. Vaughn MW, Kuo L, (Liao JC)  (1998-05)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  274(5 Pt2), H1705-H1714  "Effective diffusion distance of nitric oxide in microcirculation."
  204. Yen J, (Liao JC), Lee B, Randolph D  (1998-04)  IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS  28(2), 173-191  "A hybrid approach to modeling metabolic systems using a genetic algorithm and simplex method."
  205. Huang KT, Kuo L, (Liao JC)  (1998-04)  Biochemical and Biophysical Research Communications  245(1), 33-37  "Lipopolysaccharide activates endothelial nitric oxide synthase through protein tyrosine kinase."
  206. Chang CI, (Liao JC), Kuo L.  (1998-01)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  274(1 Pt2), H342-H348  "Arginase modulates nitric oxide production in activated macrophages."
  207. Delgado J, (Liao JC)  (1997-08)  Biotechnology Progress  13(4), 361-367  "Inverse flux analysis for reduction of acetate excretion in Escherichia coli."
  208. Farmer WR, (Liao JC)  (1997-08)  Appl Environ Microbiol  63(8), 3205-3210  "Reduction of aerobic acetate production in Escherichia coli."
  209. (Liao JC), Kuo L  (1997-04)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  272(4 Pt2), H1571-H1581  "Interaction between adenosine and flow-induced dilation in coronary microvascular network."
  210. Lu JL, (Liao JC)  (1997-01)  Biotechnology and bioengineering  53(2), 132-138  "Metabolic engineering and control analysis for production of aromatics: Role of transaldolase."
  211. (Liao JC), Hou SY, Chao YP  (1996-10)  Biotechnology and bioengineering  52(1), 129-140  "Pathway analysis, engineering, and physiological considerations for redirecting central metabolism."
  212. Lu JL, Schmiege LM 3rd, Kuo L, (Liao JC)  (1996-08)  Biochemical and Biophysical Research Communications  225(1), 1-5  "Downregulation of Endothelial Constitutive Nitric Oxide Synthase Expression by Lipopolysaccharide."
  213. Millard CS, Chao YP, (Liao JC), Donnelly MI  (1996-05)  Appl Environ Microbiol  62(5),1808-1810  "Enhanced production of succinic acid by overexpression of phoephoenolpyruvate carboxylase in Escherichia coli."
  214. Tan HL, Delgado J, (Liao JC)  (1996-05)  AIChE Journal  42(5), 1454-1464  "Extension of Metabolic Control Analysis to Chemostat Bioreactors."
  215. Farmer WR, (Liao JC)  (1996-04)  Current Opinion in Biotechnology  7(2), 198-204  "Progress in metabolic engineering."
  216. Hung SC, (Liao JC)  (1996-01)  Appl Biochem Biotechnol  56(1), 37-47  "Effects of Ultraviolet Light Irradiation on Biotreatment of Organophosphates."
  217. Patnaik R, Spitzer RG, (Liao JC)  (1995-05)  Biotechnology and bioengineering  46(4), 361-370  "Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities."
  218. Hou SY, Chao YP, (Liao JC)  (1995-03)  J Bacteriol  177(6), 1620-1623  "A Mutant Phosphoenolpyruvate Carboxykinase in Escherichia coli Conferring Oxaloacetate Decarboxylase Activity."
  219. Delgado J, (Liao JC)  (1995)  Biosystems  36(1), 55-70  "Control of Metabolic Pathways by Time-scale Separation."
  220. (Liao JC), Chao YP, Patnaik R.  (1994-11)  Ann NY Acad Sci  745(1), 21-34  "Alteration of Biochemical Valves in the Central Metabolism of Escherichia coli."
  221. Patnaik R, (Liao JC)  (1994-11)  Appl Environ Microbiol  60(11), 3903-3908  "Engineering of Escherichia coli central metabolism for aromatic metabolite production with near theoretical yield."
  222. Chao YP, (Liao JC)  (1994-02)  J Biol Chem  269(7), 5122-5126  "Metabolic Responses to Substrate Futile Cycles in Escherichia coli."
  223. Wu SC, Jarvis DL, Dale BE, (Liao JC)  (1994-01)  Biotechnology Progress  10 (1), 55-59  "Heterologous Protein Expression Affects Death Kinetics of Baculovirus-infected Insect Cell Cultures."
  224. Chao YP, (Liao JC)  (1993-12)  Appl Environ Microbiol  59(12), 4261-4265  "Alteration of Growth Yield by Overexpression of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase in Escherichia coli."
  225. Chao YP, Patnaik R, Roof WD, Young RF, (Liao JC)  (1993-11)  J Bacteriol.  175(21), 6939-6944  "Control of Gluconeogenic Growth by pps and pck in Escherichia coli."
  226. (Liao JC),Delgado J  (1993-05)  Biotechnology Progress  9(3), 221-233  "Advances in metabolic control analysis."
  227. Delgado J, Meruane J, (Liao JC)  (1993-05)  Biotechnology and bioengineering  41(11), 1121-1128  "Experimental determination of flux control distribution in biochemical systems: in vitro model to analyze transient metabolite concentrations."
  228. (Liao JC)  (1993-04)  Current Opinion in Biotechnology  4(2), 211-216  "Modelling and analysis of metabolic pathways."
  229. Wu SC, Dale BE, (Liao JC)  (1993-01)  Biotechnology and bioengineering  41(1), 104-110  "Kinetic characterization of baculovirus-induced cell death in insect cell cultures."
  230. Patnaik R, Roof WD, Young RF, (Liao JC)  (1992-12)  J Bacteriol.  174(23), 7527-7532  "Stimulation of glucose catabolism in Escherichia coli by a potential futile cycle."
  231. (Liao JC), Delgado J  (1992-10)  Annals of the New York Academy of Sciences  665, 27-38  "Dynamic metabolic control theory. A methodology for investigating metabolic regulation using transient metabolic data."
  232. Delgado J, (Liao JC)  (1992-08)  Biochem J.  285(Pt 3), 965-972  "Metabolic control analysis using transient metabolite concentrations. Determination of metabolite concentration control coefficients."
  233. Delgado J, (Liao JC)  (1992-04)  Chemical Engineering Science  47(5), 1277-1289  "Identifying Constraints of Bioreaction Systems."
  234. Delgado J, (Liao JC)  (1992-03)  The Biochemical journal  282(Pt 3), 919-927  "Determination of Flux Control Coefficients from transient metabolite concentrations."
  235. Delgado J, (Liao JC)  (1991-01)  Biotech Progress  7(1), 15-20  "Identifying Rate-Controlling Enzymes in Metabolic Pathways without Kinetic Parameters."
  236. (Liao JC), Ng KC   (1990-03)  Ind. Eng. Chem. Res.  29(3), 361-366  "Effect of ice nucleators on snow making and spray freezing."
  237. (Liao JC)  (1989-01)  Biotechnology and bioengineering  33(5), 613-622  "Fermentation data analysis and state estimation in the presence of incomplete mass balance."
  238. (Liao JC), Lightfoot EN Jr, Jolly SO, Jacobson GK  (1988-05)  Biotechnology and bioengineering  31(8), 855-868  "Application of characteristic reaction paths: Rate-limiting capability of phosphofructokinase in yeast fermentation."
  239. (Liao JC), Lightfoot EN Jr  (1988-05)  Biotechnology and bioengineering  31(8), 847-854  "Characteristic reaction paths of biochemical reaction systems with time scale separation."
  240. (Liao JC), Lightfoot EN Jr  (1988-05)  Biotechnology and bioengineering  31(8), 869-879  "Lumping analysis of biochemical reaction systems with time scale separation."
  241. (Liao JC), Lightfoot EN Jr  (1987-06)  Journal of theoretical biology  126(3), 253-273  "Extending the quasi-steady state concept to analysis of metabolic networks."

廖俊智教授的研究領域為代謝及合成生物學, 特別在以微生物合成燃料的領域，及基礎代謝路徑的改造。此外，他更發展出網路構成要素分析法(Network Component Analysis) 及Ensemble Modeling，用以分析複雜的轉錄組調控，及設計人工基因轉錄調控迴路。

經歷
  • 2016 – 迄今   院長, 中央研究院
  • 2016   特聘研究員, 中央研究院生物化學研究所
  • 2016   院士, 美國發明家學院
  • 2015   院士, 美國國家科學院
  • 2014   院士, 中央研究院
  • 2014   工業應用科學獎, 美國國家科學院
  • 2013   ENI再生能源獎, 義大利總統頒授
  • 2013   院士, 美國國家工程學院
  • 2012   再生能源創新獎, 美國白宮
  • 2012 – 2016   系主任, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 2011 – 2016   合聘教授, 美國加卅大學洛杉磯校區 化學暨生物化學系
  • 2011 – 2016   Ralph M. Parsons 基金會講座教授, 美國加卅大學洛杉磯校區 化學暨生物分子工程系Ralph M. Parsons
  • 2010 – 2016   合聘教授, 美國加卅大學洛杉磯校區 分子生物研究所
  • 2010   綠色化學學術組總統獎, 美國環保署
  • 2009 – 2012   副系主任, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 2008 – 2011   校長講座教授, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 2007 – 2016   能源研究副主任, 美國加卅大學洛杉磯校區 基因體暨蛋白質體研究所
  • 2003 – 2007   副主任, 美國加卅大學洛杉磯校區 仿細胞太空探索研究所
  • 2002 – 2007   副系主任, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 1997 – 2016   教授, 美國加卅大學洛杉磯校區 化學暨生物分子工程系
  • 1993 – 1997   合聘副教授, 美國德卅農工大學 生物化學暨生物物理系
  • 1993 – 1997   副教授, 美國德卅農工大學 化學工程系
  • 1990 – 1993   助理教授, 美國德卅農工大學(Texas A&M University ) 化學工程系
  • 1987 – 1989   研究科學家, 美國紐約卅羅徹斯特柯達公司 (Eastman Kodak Company)
學歷
  • 1982 – 1987   博士, 化學工程, 美國威斯康辛大學麥迪生校區
  • 1976 – 1980   學士, 化學工程系, 國立臺灣大學
Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway.
Yu H, Li X, Duchoud F, Chuang DS, Liao JC
Nature communications (2018)
Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism.
Lin PP, Jaeger AJ, Wu TY, Xu SC, Lee AS, Gao F, Chen PW, Liao JC
Proc Natl Acad Sci USA (2018)
Metabolic repair through emergence of new pathways in Escherichia coli.
Pontrelli S, Fricke RCB, Teoh ST, Lavina WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC
Nature chemical biology (2018)
Synthetic non-oxidative glycolysis enables complete carbon conservation.
Bogorad IW, Lin TS, Liao JC
Nature (2013)
Integrated electromicrobial conversion of CO2 to higher alcohols.
Li, H.; P.H. Opgenorth; D.G. Wernick; S. Rogers; T.-Y.Wu; W. Higashide; P. Malati; Y. Huo, K.-M. Cho, and J.C. Liao
Science (2012)
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde.
Atsumi, S.; Higashide, W.; and J.C. Liao
Nature Biotechnol (2009)
Resistance to Diet-Induced Obesity in Mice with Synthetic Glyoxylate Shunt.
Dean, J.T.; Tran, L.; Beaven, S.; Tontonoz, P; Reue, K.; Dipple, K.D.; and J.C. Liao
Cell Metabolism (2009)
Expanding Metabolism for Biosynthesis of Nonnatural Alcohols.
Zhang, K., Sawaya, M.R., Eisenberg, D.S. and J.C. Liao
Proc. Natl. Acad. Sci. USA (2008)
Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels.
Atsumi, S.; T. Hanai and J.C. Liao
Nature (2008)
A synthetic gene-metabolic oscillator.
Fung, E.; Wong, W.W.; Suen, J.K.; Bulter, T.; Lee, S.G.; and J.C. Liao
Nature (2005)
  1. Ohtake T, Kawase N, Pontrelli S, Nitta K, Lavina WA, Shen CR, Putri SP, (Liao JC), Fukusaki E  (2022-04)  Frontiers in microbiology  13, 871624  "Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production."
  2. Luo S, Lin PP, Nieh LY, Liao GB, Tang PW, Chen C, (Liao JC)*  (2022-02)  Nature Catalysis  5(2), 154-162  "A cell-free self-replenishing CO2-fixing system"
  3. Guo JY, Liu IJ, Lin HT, Wang MJ, Chang YL, Lin SC, Liao MY, Hsu WC, Lin YL, (Liao JC), Wu HC  (2021-06)  Journal of biomedical science  28(1), 43  "Identification of COVID-19 B-cell epitopes with phage-displayed peptide library."
  4. Chuang DS, (Liao JC)*  (2021-05)  Metabolic Engineering  65, 255-262  "Role of cyanobacterial phosphoketolase in energy regulation and glucose secretion under dark anaerobic and osmotic stress conditions."
  5. Yang HC, Chen CH, Wang JH, Liao HC, Yang CT, Chen CW, Lin YC, Kao CH, Lu MJ, (Liao JC)*  (2020-12)  Proceedings of the National Academy of Sciences of the United States of America  117(48), 30679-30686  "Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations."
  6. Chen FY, Jung HW, Tsuei CY, (Liao JC)  (2020-08)  Cell  182(4), 933-946  "Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol."
  7. Pontrelli S, Chiu TY, Lan EI, Chen FY, Chang P, (Liao JC)  (2018-11)  Metabolic engineering  50, 16-46  "Escherichia coli as a host for metabolic engineering."
  8. Pontrelli S, Fricke RCB, Teoh ST, Lavina WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, (Liao JC)  (2018-11)  Nature chemical biology  14(11), 1005-1009  "Metabolic repair through emergence of new pathways in Escherichia coli."
  9. Yu H, (Liao JC)  (2018-09)  Nature communications  9(1), 3992  "A modified serine cycle in Escherichia coli coverts methanol and CO2 to two-carbon compounds."
  10. Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, (Liao JC)  (2018-09)  Metabolic engineering  49, 153-163  "Directed strain evolution restructures metabolism for 1-butanol production in minimal media."
  11. Chen CT, Chen FY, Bogorad IW, Wu TY, Zhang R, Lee AS, (Liao JC)  (2018-09)  Metabolic engineering  49, 257-266  "Synthetic methanol auxotrophy of Escherichia coli for methanol-dependent growth and production."
  12. Yu H, Li X, Duchoud F, Chuang DS, (Liao JC)  (2018-05)  Nature communications  9(1), 2008  "Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway."
  13. Lin PP, Jaeger AJ, Wu TY, Xu SC, Lee AS, Gao F, Chen PW, (Liao JC)  (2018-04)  Proceedings of the National Academy of Sciences of the United States of America  115(14), 3538-3546  "Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism."
  14. Nitta K, Lavina WA, Pontrelli S, (Liao JC), Putri SP, Fukusaki E  (2017-11)  Journal of bioscience and bioengineering  124(5), 498-505  "Orthogonal partial least squares/projections to latent structures regression-based metabolomics approach for identification of gene targets for improvement of 1-butanol production in Escherichia coli."
  15. Chen PW, Theisen MK, (Liao JC)  (2017-08)  Current opinion in biotechnology  46, 114-119  "Metabolic systems modeling for cell factories improvement."
  16. Lafontaine Rivera JG, Theisen MK, Chen PW, (Liao JC)  (2017-05)  Metabolic engineering  41, 144-151  "Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites."
  17. Ohtake T, Pontrelli S, Lavina WA, (Liao JC), Putri SP, Fukusaki E  (2017-05)  Metabolic engineering  41, 135-143  "Metabolomics-driven approach to solving a CoA imbalance for improved 1-butanol production in Escherichia coli."
  18. Soh LMJ, Mak WS, Lin PP, Mi L, Chen FY, Damoiseaux R, Siegel JB, (Liao JC)  (2017-04)  ACS synthetic biology  6(4), 610-618  "Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design."
  19. Wang J, Jain R, Shen X, Sun X, Cheng M, (Liao JC), Yuan Q, Yan Y  (2017-03)  Metabolic engineering  40, 148-156  "Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose."
  20. Xiong W, Lin PP, Magnusson L, Warner L, (Liao JC), Maness PC, Chou KJ  (2016-11)  Proceedings of the National Academy of Sciences of the United States of America  113(46), 13180-13185  "CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum."
  21. Wu TY, Chen CT, Liu JT, Bogorad IW, Damoiseaux R, (Liao JC)  (2016-06)  Applied microbiology and biotechnology  100(11), 4969-4983  "Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1."
  22. (Liao JC), Mi L, Pontrelli S, Luo S  (2016-04)  Nature Reviews Microbiology  14(5), 288-304  "Fuelling the future: microbial engineering for the production of sustainable biofuels."
  23. Chen CT, (Liao JC)  (2016-03)  FEMS microbiology letters  363(5), fnw020  "Frontiers in microbial 1-butanol and isobutanol production."
  24. Theisen MK, Lafontaine Rivera JG, (Liao JC)  (2016-03)  PLoS computational biology  12(3), e1004800  "Stability of Ensemble Models Predicts Productivity of Enzymatic Systems."
  25. Wernick DG, Pontrelli SP, Pollock AW, (Liao JC)  (2016-02)  Scientific reports  6, 20224  "Sustainable biorefining in wastewater by engineered extreme alkaliphile Bacillus marmarensis."
  26. Noguchi S, Putri SP, Lan EI, Lavina WA, Dempo Y, Bamba T, (Liao JC), Fukusaki E  (2016)  Metabolomics : Official journal of the Metabolomic Society  12, 26  "Quantitative target analysis and kinetic profiling of acyl-CoAs reveal the rate-limiting step in cyanobacterial 1-butanol production."
  27. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, (Liao JC), Siegel JB  (2015-11)  Nature communications  6, 10005  "Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway."
  28. Lin PP, Mi L, Morioka AH, Yoshino KM, Konishi S, Xu SC, Papanek BA, Riley LA, Guss AM, (Liao JC)  (2015-09)  Metabolic engineering  31, 44-52  "Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum."
  29. Lan EI, Chuang DS, Shen CR, Lee AM, Ro SY, (Liao JC)  (2015-09)  Metabolic engineering  31, 163-170  "Metabolic engineering of cyanobacteria for photosynthetic 3-hydroxypropionic acid production from CO2 using Synechococcus elongatus PCC 7942."
  30. Lafontaine Rivera JG, Lee Y, (Liao JC)  (2015-08)  Integrative biology : quantitative biosciences from nano to macro  7(8), 895-903  "An entropy-like index of bifurcational robustness for metabolic systems."
  31. Chung NC, Huang YH, Chang CH, (Liao JC), Yang CH, Chen CC, Liu IY  (2015-03)  PloS one  10(3), e0118832  "Behavior training reverses asymmetry in hippocampal transcriptome of the cav3.2 knockout mice."
  32. Li H, (Liao JC)  (2015-02)  ACS synthetic biology  4(2), 101-106  "A synthetic anhydrotetracycline-controllable gene expression system in Ralstonia eutropha H16."
  33. Sumner LW, Styczynski M, McLean J, Fiehn O, Jander G, (Liao J), Sumner S, Britz-McKibbin P, Welti R, Jones AD, Dorrestein PC, Bearden D, Kaddurah-Daouk R  (2015-02)  Metabolomics  11(1), 3-5  "Introducing the USA Plant, Algae and Microbial Metabolomics Research Coordination Network (PAMM-NET)."
  34. Ho CK, Rahib L, (Liao JC), Sriram G, Dipple KM  (2015-01)  Molecular genetics and metabolism  114(1), 66-72  "Mathematical modeling of the insulin signal transduction pathway for prediction of insulin sensitivity from expression data."
  35. Bogorad IW, Chen CT, Theisen MK, Wu TY, Schlenz AR, Lam AT, (Liao JC)  (2014-11)  Proceedings of the National Academy of Sciences of the United States of America  111(45), 15928-15933  "Building carbon-carbon bonds using a biocatalytic methanol condensation cycle."
  36. Khodayari A, Zomorrodi AR, (Liao JC), Maranas CD  (2014-09)  Metabolic engineering  25, 50-62  "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data."
  37. Lee Y, Lafontaine Rivera JG, (Liao JC)  (2014-09)  Metabolic engineering  25, 63-71  "Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways."
  38. Lin PP, Rabe KS, Takasumi JL, Kadisch M, Arnold FH, (Liao JC)  (2014-07)  Metabolic engineering  24, 1-8  "Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius."
  39. Li X, Shen CR, (Liao JC)  (2014-06)  Photosynthesis research  120(3), 301-310  "Isobutanol production as an alternative metabolic sink to rescue the growth deficiency of the glycogen mutant of Synechococcus elongatus PCC 7942."
  40. Choi KY, Wernick DG, Tat CA, (Liao JC)  (2014-05)  Metabolic engineering  23, 53-61  "Consolidated conversion of protein waste into biofuels and ammonia using Bacillus subtilis."
  41. Nielsen J, Fussenegger M, Keasling J, Lee SY, (Liao JC), Prather K, Palsson B  (2014-05)  Nature chemical biology  10(5), 319-322  "Engineering synergy in biotechnology."
  42. Harper M, Gronenberg L, (Liao J), Lee C  (2014-02)  PloS one  9(2), e88072  "Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis."
  43. Li H, (Liao JC)  (2014-01)  ACS synthetic biology  3(1), 13-20  "Development of an NADPH-dependent homophenylalanine dehydrogenase by protein engineering."
  44. Hu WS, (Liao JC)  (2013-11)  Current Opinion in Chemical Engineering  2(4), 363-364  "Biotechnology and bioprocess engineering."
  45. Kusakabe T, Tatsuke T, Tsuruno K, Hirokawa Y, Atsumi S, (Liao JC), Hanai T  (2013-11)  Metabolic engineering  20, 101-108  "Engineering a synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light."
  46. Wernick DG, Choi KY, Tat CA, Lafontaine Rivera JG, (Liao JC)  (2013-11)  Genome announcements  1(6), e00967-13  "Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297."
  47. Bogorad IW, Lin TS, (Liao JC)  (2013-10)  Nature  502(7473), 693-697  "Synthetic non-oxidative glycolysis enables complete carbon conservation."
  48. Mainguet SE, Gronenberg LS, Wong SS, (Liao JC)  (2013-09)  Metabolic engineering  19, 116-127  "A reverse glyoxylate shunt to build a non-native route from C4 to C2 in Escherichia coli."
  49. Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, Foster CE, (Liao JC), Lin XN  (2013-09)  Proceedings of the National Academy of Sciences of the United States of America  110(36), 14592-14597  "Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass."
  50. Lan EI, Dekishima Y, Chuang DS, (Liao JC)  (2013-09)  AIChE Journal  59(9), 3167-3175  "Metabolic engineering of 2-pentanone synthesis in Escherichia coli."
  51. Zomorrodi AR, Lafontaine Rivera JG, (Liao JC), Maranas CD  (2013-09)  Biotechnology journal  8(9), 1090-1104  "Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks."
  52. Li H, (Liao JC)  (2013-08)  Energy & Environmental Science  6(10), 2892-2899  "Biological conversion of carbon dioxide to photosynthetic fuels and electrofuels."
  53. Gronenberg LS, Marcheschi RJ, (Liao JC)  (2013-06)  Current opinion in chemical biology  17(3), 462-471  "Next generation biofuel engineering in prokaryotes."
  54. Lan EI, (Liao JC)  (2013-05)  Bioresource technology  135, 339-349  "Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources."
  55. Marcheschi RJ, Gronenberg LS, (Liao JC)  (2013-05)  Biotechnology journal  8(5), 545-555  "Protein engineering for metabolic engineering: current and next-generation tools."
  56. Shen CR, (Liao JC)  (2013-05)  Metabolic engineering  17, 12-22  "Synergy as design principle for metabolic engineering of 1-propanol production in Escherichia coli."
  57. Lan EI, Ro S, (Liao JC)  (2013-04)  Energy & Environmental Science  6(9), 2672-2681  "Oxygen-tolerant coenzyme A-acylating aldehyde dehydrogenase facilitates efficient photosynthetic n-butanol biosynthesis in cyanobacteria."
  58. Wernick DG, (Liao JC)  (2013-02)  Applied microbiology and biotechnology  97(4), 1397-1406  "Protein-based biorefining: metabolic engineering for production of chemicals and fuel with regeneration of nitrogen fertilizers."
  59. Li H, (Liao JC)  (2013-01)  Microbial cell factories  12, 4  "Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol."
  60. (Liao JC), Hu WS  (2012-11)  Current Opinion in Chemical Engineering  1(4), 353-354  "Bio-based chemical engineering."
  61. Machado HB, Dekishima Y, Luo H, Lan EI, (Liao JC)  (2012-09)  Metabolic engineering  14(5), 504-511  "A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols."
  62. Shen CR, (Liao JC)  (2012-09)  Energy & Environmental Science  5(11), 9574-9583  "Photosynthetic production of 2-methyl-1-butanol from CO2 in cyanobacterium Synechococcus elongatus PCC7942 and characterization of the native acetohydroxyacid synthase."
  63. (Liao JC), Messing J  (2012-06)  Current Opinion in Biotechnology  23(3), 287-289  "Energy biotechnology."
  64. Huo YX, Wernick DG, (Liao JC)  (2012-06)  Current opinion in biotechnology  23(3), 406-413  "Toward nitrogen neutral biofuel production."
  65. Felnagle EA, Chaubey A, Noey EL, Houk KN, (Liao JC)  (2012-05)  Nature chemical biology  8(6), 518-526  "Engineering synthetic recursive pathways to generate non-natural small molecules."
  66. Tan Y, (Liao JC)  (2012-05)  Biotechnology journal  7(3), 343-353  "Metabolic ensemble modeling for strain engineers."
  67. Marcheschi RJ, Li H, Zhang K, Noey EL, Kim S, Chaubey A, Houk KN, (Liao JC)  (2012-04)  ACS chemical biology  7(4), 689-697  "A synthetic recursive "+1" pathway for carbon chain elongation."
  68. Lan EI, (Liao JC)  (2012-04)  Proceedings of the National Academy of Sciences of the United States of America  109(16), 6018-6023  "ATP drives direct photosynthetic production of 1-butanol in cyanobacteria."
  69. Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, (Liao JC)  (2012-03)  Science  335(6076), 1596  "Integrated electromicrobial conversion of CO2 to higher alcohols."
  70. Tran LM, Chang CJ, Plaisier S, Wu S, Dang J, Mischel PS, (Liao JC), Graeber TG, Wu H  (2012-02)  PloS one  7(2), e31053  "Determining PTEN functional status by network component deduced transcription factor activities."
  71. Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M Jr, (Liao JC), Schadt CW, Guss AM, Yang Y, Graham DE  (2012-01)  Biotechnology for biofuels  5(1), 2  "Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations."
  72. Hu CW, Chang YL, Chen SJ, Kuo-Huang LL, (Liao JC), Huang HC, Juan HF  (2011-12)  PloS one  6(12), e28329  "Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach."
  73. Smith KM, (Liao JC)  (2011-11)  Metabolic engineering  13(6), 674-681  "An evolutionary strategy for isobutanol production strain development in Escherichia coli."
  74. Dekishima Y, Lan EI, Shen CR, Cho KM, (Liao JC)  (2011-08)  Journal of the American Chemical Society  133(30), 11399-11401  "Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli."
  75. Contador CA, Andrews BA, (Liao JC), Asenjo JA  (2011-07)  Biotechnology progress  27(4), 925-936  "Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast Saccharomyces cerevisiae."
  76. Lan EI, (Liao JC)  (2011-07)  Metabolic engineering  13(4), 353-363  "Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide."
  77. Baez A, Cho KM, (Liao JC)  (2011-06)  Applied microbiology and biotechnology  90(5), 1681-1690  "High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal."
  78. Shen CR, Lan EI, Dekishima Y, Baez A, Cho KM, (Liao JC)  (2011-05)  Applied and environmental microbiology  77(9), 2905-2915  "Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli."
  79. Huo YX, Cho KM, Rivera JG, Monte E, Shen CR, Yan Y, (Liao JC)  (2011-04)  Nature biotechnology  29(4), 346-351  "Conversion of proteins into biofuels by engineering nitrogen flux."
  80. Higashide W, Li Y, Yang Y, (Liao JC)  (2011-04)  Applied and environmental microbiology  77(8), 2727-2733  "Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose."
  81. Harper MA, Chen Z, Toy T, Machado IM, Nelson SF, (Liao JC), Lee CJ  (2011-02)  PloS one  6(2), e16517  "Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants."
  82. Rizk ML, Laguna R, Smith KM, Tabita FR, (Liao JC)  (2011-02)  Biotechnology progress  27(1), 15-22  "Redox homeostasis phenotypes in RubisCO-deficient Rhodobacter sphaeroides via ensemble modeling."
  83. Wang W, Hein TW, Zhang C, Zawieja DC, (Liao JC), Kuo L  (2011-01)  Microcirculation  18(1), 36-45  "Oxidized low-density lipoprotein inhibits nitric oxide-mediated coronary arteriolar dilation by up-regulating endothelial arginase I."
  84. Tan Y, Rivera JG, Contador CA, Asenjo JA, (Liao JC)  (2011-01)  Metabolic engineering  13(1), 60-75  "Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux."
  85. Shen CR, (Liao JC)  (2011)  Methods in enzymology  497, 469-481  "A synthetic iterative pathway for ketoacid elongation."
  86. Mainguet SE, (Liao JC)  (2010-12)  Biotechnol J.  5(12), 1297-1308  "Bioengineering of microorganisms for C3 to C5 alcohols production."
  87. Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, (Liao JC)  (2010-12)  Molecular systems biology  6, 449  "Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli."
  88. Inokuma K, (Liao JC), Okamoto M, Hanai T  (2010-12)  Journal of bioscience and bioengineering  110(6), 696-701  "Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping."
  89. Wong I, Atsumi S, Huang WC, Wu TY, Hanai T, Lam ML, Tang P, Yang J, (Liao JC), Ho CM  (2010-10)  Lab on a chip  10(20), 2710-2719  "An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study."
  90. Tran LM, Hyduke DR, (Liao JC)  (2010-10)  BMC bioinformatics  11, 511  "Trimming of mammalian transcriptional networks using network component analysis."
  91. Smith KM, Cho KM, (Liao JC)  (2010-07)  Applied microbiology and biotechnology  87(3), 1045-1055  "Engineering Corynebacterium glutamicum for isobutanol production."
  92. Sriram G, Parr LS, Rahib L, (Liao JC), Dipple KM  (2010-07)  Metabolic engineering  12(4), 332-340  "Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells."
  93. Connor MR, Cann AF, (Liao JC)  (2010-04)  Applied microbiology and biotechnology  86(4), 1155-1164  "3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation."
  94. Dean JT, Rizk ML, Tan Y, Dipple KM, (Liao JC)  (2010-04)  Biophysical journal  98(8), 1385-1395  "Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt."
  95. Zhang K, Li H, Cho KM, (Liao JC)  (2010-04)  Proceedings of the National Academy of Sciences of the United States of America  107(14), 6234-6239  "Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine."
  96. Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, (Liao JC)  (2010-01)  Applied microbiology and biotechnology  85(3), 651-657  "Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes."
  97. Cann AF, (Liao JC)  (2010-01)  Applied microbiology and biotechnology  85(4), 893-899  "Pentanol isomer synthesis in engineered microorganisms."
  98. Li H, Cann AF, (Liao JC)  (2010)  Annual review of chemical and biomolecular engineering  1, 19-36  "Biofuels: biomolecular engineering fundamentals and advances."
  99. Atsumi S, Higashide W, (Liao JC)  (2009-12)  Nature biotechnology  27(12), 1177-1180  "Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde."
  100. Rizk ML, (Liao JC)  (2009-11)  Journal of the Taiwan Institute of Chemical Engineers  40(6), 595–601  "Ensemble modeling and related mathematical modeling of metabolic networks."
  101. Wong WW, (Liao JC)  (2009-11)  Metabolic engineering  11(6), 409-414  "Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters."
  102. Atsumi S, Li Z, (Liao JC)  (2009-10)  Applied and environmental microbiology  75(19), 6306-6311  "Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli."
  103. Yan Y, Lee CC, (Liao JC)  (2009-10)  Organic & biomolecular chemistry  7(19), 3914-3917  "Enantioselective synthesis of pure (R,R)-2,3-butanediol in Escherichia coli with stereospecific secondary alcohol dehydrogenases."
  104. Rizk ML, (Liao JC)  (2009-09)  PloS one  4(9), e6903  "Ensemble modeling for aromatic production in Escherichia coli."
  105. Contador CA, Rizk ML, Asenjo JA, (Liao JC)  (2009-09)  Metabolic engineering  11(4-5), 221-233  "Ensemble modeling for strain development of L-lysine-producing Escherichia coli."
  106. Brynildsen MP, (Liao JC)  (2009-06)  Molecular systems biology  5, 277  "An integrated network approach identifies the isobutanol response network of Escherichia coli."
  107. Connor MR, (Liao JC)  (2009-06)  Current opinion in biotechnology  20(3), 307-315  "Microbial production of advanced transportation fuels in non-natural hosts."
  108. Dean JT, Tran L, Beaven S, Tontonoz P, Reue K, Dipple KM, (Liao JC)  (2009-06)  Cell metabolism  9(6), 525-536  "Resistance to diet-induced obesity in mice with synthetic glyoxylate shunt."
  109. Lai D, Lluncor B, Schroder I, Gunsalus RP, (Liao JC), Monbouquette HG  (2009-05)  Metabolic engineering  11(3), 184-191  "Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate."
  110. Yan Y, (Liao JC)  (2009-04)  Journal of industrial microbiology & biotechnology  36(4), 471-479  "Engineering metabolic systems for production of advanced fuels."
  111. Rahib L, Sriram G, Harada MK, (Liao JC), Dipple KM  (2009-03)  Molecular genetics and metabolism  96(3), 106-112  "Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency."
  112. Ye C, Galbraith SJ, (Liao JC), Eskin E  (2009-03)  PLoS computational biology  5(3), e1000311  "Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast."
  113. Wong WW, Tran LM, (Liao JC)  (2009-01)  Biotechnology and bioengineering  102(1), 73-80  "A hidden square-root boundary between growth rate and biomass yield."
  114. Atsumi S, (Liao JC)  (2008-12)  Applied and environmental microbiology  74(24), 7802-7808  "Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli."
  115. Tran LM, Rizk ML, (Liao JC)  (2008-12)  Biophysical journal  95(12), 5606-5617  "Ensemble modeling of metabolic networks."
  116. Zhang K, Sawaya MR, Eisenberg DS, (Liao JC)  (2008-12)  Proceedings of the National Academy of Sciences of the United States of America  105(52), 20653-20658  "Expanding metabolism for biosynthesis of nonnatural alcohols."
  117. Shen CR, (Liao JC)  (2008-11)  Metabolic engineering  10(6), 312-320  "Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways."
  118. Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, (Liao JC)  (2008-11)  Metabolic engineering  10(6), 305-311  "Metabolic engineering of Escherichia coli for 1-butanol production."
  119. Cann AF, (Liao JC)  (2008-11)  Applied microbiology and biotechnology  81(1), 89-98  "Production of 2-methyl-1-butanol in engineered Escherichia coli."
  120. Atsumi S, (Liao JC)  (2008-10)  Current opinion in biotechnology  19(5), 414-419  "Metabolic engineering for advanced biofuels production from Escherichia coli."
  121. Connor MR, (Liao JC)  (2008-09)  Applied and environmental microbiology  74(18), 5769-5775  "Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol."
  122. (Liao JC), Higashide W  (2008-08)  Chemical Engineering Progress  104(8), S19-S23  "Metabolic engineering of next-generation biofuels."
  123. Bernstein JR, Bulter T, (Liao JC)  (2008-06)  Metabolic engineering  10(3-4), 131-140  "Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin."
  124. Chou KJ, Dodd J, (Liao JC)  (2008-03)  Nitric oxide-biology and chemistry  18(2), 122-135  "Interactions of nitrosylhemoglobin and carboxyhemoglobin with erythrocyte."
  125. Boscolo R, (Liao JC), Roychowdhury VP  (2008-02)  IEEE-ACM Transactions on Computational Biology and Bioinformatics  5(1), 15-24  "An information theoretic exploratory method for learning patterns of conditional gene coexpression from microarray data."
  126. Lee SG, (Liao JC)  (2008-02)  Journal of microbiology and biotechnology  18(2), 334-337  "Control of acetate production rate in Escherichia coli by regulating expression of single-copy pta using lacI(Q) in multicopy plasmid."
  127. Jarboe LR, Hyduke DR, Tran LM, Chou KJ, (Liao JC)  (2008-02)  The Journal of biological chemistry  283(8), 5148-5157  "Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis."
  128. Sriram G, Rahib L, He JS, Campos AE, Parr LS, (Liao JC), Dipple KM  (2008-02)  Molecular genetics and metabolism  93(2), 145-159  "Global metabolic effects of glycerol kinase overexpression in rat hepatoma cells."
  129. Atsumi S, Hanai T, (Liao JC)  (2008-01)  Nature  451(7174), 86-89  "Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels."
  130. Hanai T, Atsumi S, (Liao JC)  (2007-12)  Applied and environmental microbiology  73(24), 7814-7818  "Engineered synthetic pathway for isopropanol production in Escherichia coli."
  131. Watanabe J, Chou KJ, (Liao JC), Miao Y, Meng HH, Ge H, Grijalva V, Hama S, Kozak K, Buga G, Whitelegge JP, Lee TD, Farias-Eisner R, Navab M, Fogelman AM, Reddy ST  (2007-08)  The Journal of biological chemistry  282(32), 23698-23707  "Differential association of hemoglobin with proinflammatory high density lipoproteins in atherogenic/hyperlipidemic mice. A novel biomarker of atherosclerosis."
  132. Brynildsen MP, Wu TY, Jang SS, (Liao JC)  (2007-07)  Bioinformatics  23(14), 1783-1791  "Biological network mapping and source signal deduction."
  133. Wong WW, Tsai TY, (Liao JC)  (2007-07)  Molecular systems biology  3, 130  "Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator."
  134. Bernstein JR, Bulter T, Shen CR, (Liao JC)  (2007-06)  The Journal of biological chemistry  282(26), 18929-18936  "Directed evolution of ribosomal protein S1 for enhanced translational efficiency of high GC Rhodopseudomonas palustris DNA in Escherichia coli."
  135. Ohta AT, Chiou PY, Han TH, (Liao JC), Bhardwaj U, McCabe ERB, Yu F, Sun R, Wu MC  (2007-06)  Journal of Microelectromechanical Systems  16(3), 491-499  "Dynamic cell and microparticle control via optoelectronic tweezers."
  136. Rahib L, MacLennan NK, Horvath S, (Liao JC), Dipple KM  (2007-06)  European journal of human genetics  15(6), 646-657  "Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling."
  137. Hyduke DR, Jarboe LR, Tran LM, Chou KJ, (Liao JC)  (2007-05)  Proceedings of the National Academy of Sciences of the United States of America  104(20), 8484-8489  "Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli."
  138. Han TH, Perloff JK, (Liao JC)  (2007-03)  The American journal of cardiology  99(5), 691-695  "Nitric oxide metabolism in adults with cyanotic congenital heart disease."
  139. Brynildsen MP, Tran LM, (Liao JC)  (2006-12)  Bioinformatics  22(24), 3040-3046  "A Gibbs sampler for the identification of gene expression and network connectivity consistency."
  140. Braatsch S, Bernstein JR, Lessner F, Morgan J, (Liao JC), Harwood CS, Beatty JT  (2006-12)  Biochemistry  45(48), 14441-14451  "Rhodopseudomonas palustris CGA009 has two functional ppsR genes, each of which encodes a repressor of photosynthesis gene expression."
  141. Brynildsen MP, Tran LM, (Liao JC)  (2006-10)  Biophysical journal  91(8), 2749-2759  "Versatility and connectivity efficiency of bipartite transcription networks."
  142. Galbraith SJ, Tran LM, (Liao JC)  (2006-08)  Bioinformatics  22(15), 1886-1894  "Transcriptome network component analysis with limited microarray data."
  143. Wong WW, (Liao JC)  (2006-06)  Cellular and molecular life sciences  63(11), 1215-1220  "The design of intracellular oscillators that interact with metabolism."
  144. Oh MK, Cha MJ, Lee SG, Rohlin L, (Liao, JC)  (2006-04)  Journal of Microbiology and Biotechnology  16(4), 543-549  "Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate."
  145. MacLennan NK, Rahib L, Shin C, Fang Z, Horvath S, Dean J, (Liao JC), McCabe ER, Dipple KM  (2006-02)  Human molecular genetics  15(3), 405-415  "Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity."
  146. (Liao JC)  (2006-01)  Journal of the Chinese Institute of Chemical Engineers  37(1), 103-106  "Systems Biology: Where does chemical engineering stand?"
  147. Boscolo R, Sabatti C, (Liao JC), Roychowdhury VP  (2005-12)  IEEE-ACM Transactions on Computational Biology and Bioinformatics  2(4), 289-301  "A generalized framework for network component analysis."
  148. Brynildsen MP, Wong WW, (Liao JC)  (2005-12)  Biochemical Society transactions  33(Pt6), 1423-1426  "Transcriptional regulation and metabolism."
  149. Kao KC, Tran LM, (Liao JC)  (2005-10)  The Journal of biological chemistry  280(43), 36079-36087  "A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis."
  150. Rohlin L, Trent JD, Salmon K, Kim U, Gunsalus RP, (Liao JC)  (2005-09)  Journal of bacteriology  187(17), 6046-6057  "Heat shock response of Archaeoglobus fulgidus."
  151. Yang YL, (Liao JC)  (2005-07)  Metabolic engineering  7(4), 280-290  "Determination of functional interactions among signalling pathways in Escherichia coli K-12."
  152. Yang YL, Suen J, Brynildsen MP, Galbraith SJ, (Liao JC)  (2005-06)  BMC genomics  6, 90  "Inferring yeast cell cycle regulators and interactions using transcription factor activities."
  153. Sriram G, Martinez JA, McCabe ER, (Liao JC), Dipple KM  (2005-06)  American journal of human genetics  76(6), 911-924  "Single-gene disorders: what role could moonlighting enzymes play?"
  154. Fung E, Wong WW, Suen JK, Bulter T, Lee SG, (Liao JC)  (2005-05)  Nature  435(7038), 118-122  "A synthetic gene-metabolic oscillator."
  155. Hyduke DR, (Liao JC)  (2005-05)  American journal of physiology-Heart and circulatory physiology  288(5), H2390-H2399  "Analysis of nitric oxide donor effectiveness in resistance vessels."
  156. Han TH, Pelling A, Jeon TJ, Gimzewski JK, (Liao JC)  (2005-05)  Biochimica et biophysica acta-General Subjects  1723(1-3), 135-142  "Erythrocyte nitric oxide transport reduced by a submembrane cytoskeletal barrier."
  157. Zhou B, Beckwith D, Jarboe LR, (Liao JC)  (2005-04)  Biophysical journal  88(4), 2541-2553  "Markov Chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli."
  158. Sabatti C, Rohlin L, Lange K, (Liao JC)  (2005-04)  Bioinformatics  21(7), 922-931  "Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites."
  159. Tran LM, Brynildsen MP, Kao KC, Suen JK, (Liao JC)  (2005-03)  Metabolic engineering  7(2), 128-141  "gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation."
  160. Jarboe LR, Beckwith D, (Liao JC)  (2004-10)  Biotechnology and bioengineering  88(2), 189-203  "Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli."
  161. (Liao JC)  (2004-07)  Nature biotechnology  22(7), 823-824  "Custom design of metabolism."
  162. Han TH, Fukuto JM, (Liao JC)  (2004-03)  Nitric oxide-biology and chemistry  10(2), 74-82  "Reductive nitrosylation and S-nitrosation of hemoglobin in inhomogeneous nitric oxide solutions."
  163. Bulter T, Lee SG, Wong WW, Fung E, Connor MR, (Liao JC)  (2004-02)  Proceedings of the National Academy of Sciences of the United States of America  101(8), 2299-2304  "Design of artificial cell-cell communication using gene and metabolic networks."
  164. Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, (Liao JC)  (2004-01)  Proceedings of the National Academy of Sciences of the United States of America  101(2), 641-646  "Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis."
  165. Yang YL, (Liao JC)  (2004)  IEEE Engineering in Medicine and Biology Society  4, 2937-2940  "Network component analysis of Saccharamyces cerevisiae stress response."
  166. Bulter T, Bernstein JR, (Liao JC)  (2003-12)  Biotechnology and bioengineering  84(7), 815-821  "A perspective of metabolic engineering strategies: moving up the systems hierarchy."
  167. (Liao JC), Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP  (2003-12)  Proceedings of the National Academy of Sciences of the United States of America  100(26), 15522-15527  "Network component analysis: reconstruction of regulatory signals in biological systems."
  168. Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, (Liao JC)  (2003-10)  Proceedings of the National Academy of Sciences of the United States of America  100(21), 12504-12509  "Regulation of nitric oxide consumption by hypoxic red blood cells."
  169. Hyduke DR, Rohlin L, Kao KC, (Liao JC)  (2003-09)  Omics : a journal of integrative biology  7(3), 227-234  "A software package for cDNA microarray data normalization and assessing confidence intervals."
  170. El-Farra NH, Christofides PD, (Liao JC)  (2003-03)  Annals of biomedical engineering  31(3), 294-309  "Analysis of nitric oxide consumption by erythrocytes in blood vessels using a distributed multicellular model."
  171. Wang CW, Han TH. (Liao JC)  (2003-01)  Journal of the Chinese Institute of Chemical Engineers  34(1), 47-56  "Sequence Analysis for Metabolic Evolution of Archaeoglobus fulgidus Geranylgeranyl Diphosphate Synthase in Escherichia coli for Carotenoid Biosynthesis."
  172. (Liao JC)  (2002-12)  Nature medicine  8(12), 1350-1351  "Blood feud: keeping hemoglobin from nixing NO."
  173. Hatzimanikatis V, (Liao JC)  (2002-09)  Biotechnology and bioengineering  79(5), 504-508  "A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering."
  174. (Liao JC), Sabatti C  (2002-09)  ASM NEWS  68(9), 432-437  "Microanalysis of DNA microarrays."
  175. Joshi MS, Ferguson TB Jr, Han TH, Hyduke DR, (Liao JC), Rassaf T, Bryan N, Feelisch M, Lancaster JR Jr  (2002-08)  Proceedings of the National Academy of Sciences of the United States of America  99(16), 10341-10346  "Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions."
  176. Sabatti C, Rohlin L, Oh MK, (Liao JC)  (2002-07)  Nucleic acids research  30(13), 2886-2893  "Co-expression pattern from DNA microarray experiments as a tool for operon prediction."
  177. Han TH, Hyduke DR, Vaughn MW, Fukuto JM, (Liao JC)  (2002-05)  Proceedings of the National Academy of Sciences of the United States of America  99(11), 7763-7768  "Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions."
  178. Oh MK, Rohlin L, Kao KC, (Liao JC)  (2002-04)  The Journal of biological chemistry  277(15), 13175-13183  "Global expression profiling of acetate-grown Escherichia coli."
  179. Oh MK, (Liao JC)  (2002-01)  Journal of the Chinese Institute of Chemical Engineers  3(1), 103-112  "DNA Microarray For Microbial Biotechnology: Gene Expression Profiles in Escherichia coli During Protein Overexpression."
  180. Farmer WR, (Liao JC)  (2001-12)  Biotechnology and bioengineering  75(5), 504-509  "Acetate-inducible protein overexpression from the glnAp2 promoter of Escherichia coli."
  181. Wang CW, (Liao JC)  (2001-11)  The Journal of biological chemistry  276(44), 41161-41164  "Alteration of product specificity of Rhodobacter sphaeroides phytoene desaturase by directed evolution."
  182. Huang KT, Han TH, Hyduke DR, Vaughn MW, Van Herle H, Hein TW, Zhang C, Kuo L, (Liao JC)  (2001-09)  Proceedings of the National Academy of Sciences of the United States of America  98(20), 11771-11776  "Modulation of nitric oxide bioavailability by erythrocytes."
  183. Tseng GC, Oh MK, Rohlin L, (Liao JC), Wong WH  (2001-06)  Nucleic acids research  29(12), 2549-2557  "Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects."
  184. Rohlin L, Oh MK, (Liao JC)  (2001-06)  Current opinion in microbiology  4(3), 330-335  "Microbial pathway engineering for industrial processes: evolution, combinatorial biosynthesis and rational design."
  185. Vaughn MW, Huang KT, Kuo L, (Liao JC)  (2001-02)  NITRIC OXIDE-BIOLOGY AND CHEMISTRY  5(1), 18-31  "Erythrocyte consumption of nitric oxide: competition experiment and model analysis."
  186. Chang CI, (Liao JC), Kuo L  (2001-02)  Cancer research  61(3), 1100-1106  "Macrophage arginase promotes tumor cell growth and suppresses nitric oxide-mediated tumor cytotoxicity."
  187. Farmer WR, (Liao JC)  (2001-02)  Biotechnology progress  17(1), 57-61  "Precursor balancing for metabolic engineering of lycopene production in Escherichia coli."
  188. Barkovich R, (Liao JC)  (2001-01)  Metabolic engineering  3(1), 27-39  "Metabolic engineering of isoprenoids."
  189. Wang C, Oh MK, (Liao JC)  (2000-12)  Biotechnology progress  16(6), 922-926  "Directed evolution of metabolically engineered Escherichia coli for carotenoid production."
  190. Chang CI, Zoghi B, (Liao JC), Kuo L  (2000-08)  Journal of immunology  165(4), 2134-2141  "The involvement of tyrosine kinases, cyclic AMP/protein kinase A, and p38 mitogen-activated protein kinase in IL-13-mediated arginase I induction in macrophages: its implications in IL-13-inhibited nitric oxide production."
  191. Oh MK, (Liao JC)  (2000-07)  Metabolic engineering  2(3), 201-209  "DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli."
  192. Farmer WR, (Liao JC)  (2000-05)  Nature biotechnology  18(5), 533-537  "Improving lycopene production in Escherichia coli by engineering metabolic control."
  193. Oh MK, (Liao JC)  (2000-04)  Biotechnology progress  16(2), 278-286  "Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli."
  194. Vaughn MW, Huang KT, Kuo L, (Liao JC)  (2000-01)  The Journal of biological chemistry  275(4), 2342-2348  "Erythrocytes possess an intrinsic barrier to nitric oxide consumption."
  195. Hein TW, (Liao JC), Kuo L  (2000-01)  American journal of physiology-Heart and circulatory physiology  278(1), H175-H183  "oxLDL specifically impairs endothelium-dependent, NO-mediated dilation of coronary arterioles."
  196. (Liao JC), Hein TW, Vaughn MW, Huang KT, Kuo L  (1999-07)  Proceedings of the National Academy of Sciences of the United States of America  96(15), 8757-8761  "Intravascular Flow Decreases Erythrocyte Consumption of Nitric Oxide."
  197. (Liao JC), Oh MK  (1999-07)  Metabolic Engineering  1(3), 214-233  "Toward predicting metabolic fluxes in metabolically engineered strains."
  198. (Liao JC)  (1999-05)  Journal of Biotechnology  7(1-3), 259-262  "Inverse Flux Analysis."
  199. Lee B, Yen J, Yang L, (Liao JC)  (1999-03)  Biotechnology and Bioengineering  62(6), 722-729  "Incorporating qualitative knowledge in enzyme kinetic models using Fuzzy Logic."
  200. Wang CW, Oh MK, Liao JC  (1999-01)  Biotechnology and Bioengineering  62(2), 235-241  "Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli."
  201. (Liao JC), Delgado J  (1998-07)  Biotechnology Progress  14(4), 554-560  "Flux calculation using metabolic control constraints."
  202. Vaughn MW, Kuo L, (Liao JC)  (1998-06)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  274(6 Pt ), H2163-H2176  "Estimation of nitric oxide production and reaction rates in tissue using a mathematical model."
  203. Vaughn MW, Kuo L, (Liao JC)  (1998-05)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  274(5 Pt2), H1705-H1714  "Effective diffusion distance of nitric oxide in microcirculation."
  204. Yen J, (Liao JC), Lee B, Randolph D  (1998-04)  IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS  28(2), 173-191  "A hybrid approach to modeling metabolic systems using a genetic algorithm and simplex method."
  205. Huang KT, Kuo L, (Liao JC)  (1998-04)  Biochemical and Biophysical Research Communications  245(1), 33-37  "Lipopolysaccharide activates endothelial nitric oxide synthase through protein tyrosine kinase."
  206. Chang CI, (Liao JC), Kuo L.  (1998-01)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  274(1 Pt2), H342-H348  "Arginase modulates nitric oxide production in activated macrophages."
  207. Delgado J, (Liao JC)  (1997-08)  Biotechnology Progress  13(4), 361-367  "Inverse flux analysis for reduction of acetate excretion in Escherichia coli."
  208. Farmer WR, (Liao JC)  (1997-08)  Appl Environ Microbiol  63(8), 3205-3210  "Reduction of aerobic acetate production in Escherichia coli."
  209. (Liao JC), Kuo L  (1997-04)  AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY  272(4 Pt2), H1571-H1581  "Interaction between adenosine and flow-induced dilation in coronary microvascular network."
  210. Lu JL, (Liao JC)  (1997-01)  Biotechnology and bioengineering  53(2), 132-138  "Metabolic engineering and control analysis for production of aromatics: Role of transaldolase."
  211. (Liao JC), Hou SY, Chao YP  (1996-10)  Biotechnology and bioengineering  52(1), 129-140  "Pathway analysis, engineering, and physiological considerations for redirecting central metabolism."
  212. Lu JL, Schmiege LM 3rd, Kuo L, (Liao JC)  (1996-08)  Biochemical and Biophysical Research Communications  225(1), 1-5  "Downregulation of Endothelial Constitutive Nitric Oxide Synthase Expression by Lipopolysaccharide."
  213. Millard CS, Chao YP, (Liao JC), Donnelly MI  (1996-05)  Appl Environ Microbiol  62(5),1808-1810  "Enhanced production of succinic acid by overexpression of phoephoenolpyruvate carboxylase in Escherichia coli."
  214. Tan HL, Delgado J, (Liao JC)  (1996-05)  AIChE Journal  42(5), 1454-1464  "Extension of Metabolic Control Analysis to Chemostat Bioreactors."
  215. Farmer WR, (Liao JC)  (1996-04)  Current Opinion in Biotechnology  7(2), 198-204  "Progress in metabolic engineering."
  216. Hung SC, (Liao JC)  (1996-01)  Appl Biochem Biotechnol  56(1), 37-47  "Effects of Ultraviolet Light Irradiation on Biotreatment of Organophosphates."
  217. Patnaik R, Spitzer RG, (Liao JC)  (1995-05)  Biotechnology and bioengineering  46(4), 361-370  "Pathway engineering for production of aromatics in Escherichia coli: Confirmation of stoichiometric analysis by independent modulation of AroG, TktA, and Pps activities."
  218. Hou SY, Chao YP, (Liao JC)  (1995-03)  J Bacteriol  177(6), 1620-1623  "A Mutant Phosphoenolpyruvate Carboxykinase in Escherichia coli Conferring Oxaloacetate Decarboxylase Activity."
  219. Delgado J, (Liao JC)  (1995)  Biosystems  36(1), 55-70  "Control of Metabolic Pathways by Time-scale Separation."
  220. (Liao JC), Chao YP, Patnaik R.  (1994-11)  Ann NY Acad Sci  745(1), 21-34  "Alteration of Biochemical Valves in the Central Metabolism of Escherichia coli."
  221. Patnaik R, (Liao JC)  (1994-11)  Appl Environ Microbiol  60(11), 3903-3908  "Engineering of Escherichia coli central metabolism for aromatic metabolite production with near theoretical yield."
  222. Chao YP, (Liao JC)  (1994-02)  J Biol Chem  269(7), 5122-5126  "Metabolic Responses to Substrate Futile Cycles in Escherichia coli."
  223. Wu SC, Jarvis DL, Dale BE, (Liao JC)  (1994-01)  Biotechnology Progress  10 (1), 55-59  "Heterologous Protein Expression Affects Death Kinetics of Baculovirus-infected Insect Cell Cultures."
  224. Chao YP, (Liao JC)  (1993-12)  Appl Environ Microbiol  59(12), 4261-4265  "Alteration of Growth Yield by Overexpression of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase in Escherichia coli."
  225. Chao YP, Patnaik R, Roof WD, Young RF, (Liao JC)  (1993-11)  J Bacteriol.  175(21), 6939-6944  "Control of Gluconeogenic Growth by pps and pck in Escherichia coli."
  226. (Liao JC),Delgado J  (1993-05)  Biotechnology Progress  9(3), 221-233  "Advances in metabolic control analysis."
  227. Delgado J, Meruane J, (Liao JC)  (1993-05)  Biotechnology and bioengineering  41(11), 1121-1128  "Experimental determination of flux control distribution in biochemical systems: in vitro model to analyze transient metabolite concentrations."
  228. (Liao JC)  (1993-04)  Current Opinion in Biotechnology  4(2), 211-216  "Modelling and analysis of metabolic pathways."
  229. Wu SC, Dale BE, (Liao JC)  (1993-01)  Biotechnology and bioengineering  41(1), 104-110  "Kinetic characterization of baculovirus-induced cell death in insect cell cultures."
  230. Patnaik R, Roof WD, Young RF, (Liao JC)  (1992-12)  J Bacteriol.  174(23), 7527-7532  "Stimulation of glucose catabolism in Escherichia coli by a potential futile cycle."
  231. (Liao JC), Delgado J  (1992-10)  Annals of the New York Academy of Sciences  665, 27-38  "Dynamic metabolic control theory. A methodology for investigating metabolic regulation using transient metabolic data."
  232. Delgado J, (Liao JC)  (1992-08)  Biochem J.  285(Pt 3), 965-972  "Metabolic control analysis using transient metabolite concentrations. Determination of metabolite concentration control coefficients."
  233. Delgado J, (Liao JC)  (1992-04)  Chemical Engineering Science  47(5), 1277-1289  "Identifying Constraints of Bioreaction Systems."
  234. Delgado J, (Liao JC)  (1992-03)  The Biochemical journal  282(Pt 3), 919-927  "Determination of Flux Control Coefficients from transient metabolite concentrations."
  235. Delgado J, (Liao JC)  (1991-01)  Biotech Progress  7(1), 15-20  "Identifying Rate-Controlling Enzymes in Metabolic Pathways without Kinetic Parameters."
  236. (Liao JC), Ng KC   (1990-03)  Ind. Eng. Chem. Res.  29(3), 361-366  "Effect of ice nucleators on snow making and spray freezing."
  237. (Liao JC)  (1989-01)  Biotechnology and bioengineering  33(5), 613-622  "Fermentation data analysis and state estimation in the presence of incomplete mass balance."
  238. (Liao JC), Lightfoot EN Jr, Jolly SO, Jacobson GK  (1988-05)  Biotechnology and bioengineering  31(8), 855-868  "Application of characteristic reaction paths: Rate-limiting capability of phosphofructokinase in yeast fermentation."
  239. (Liao JC), Lightfoot EN Jr  (1988-05)  Biotechnology and bioengineering  31(8), 847-854  "Characteristic reaction paths of biochemical reaction systems with time scale separation."
  240. (Liao JC), Lightfoot EN Jr  (1988-05)  Biotechnology and bioengineering  31(8), 869-879  "Lumping analysis of biochemical reaction systems with time scale separation."
  241. (Liao JC), Lightfoot EN Jr  (1987-06)  Journal of theoretical biology  126(3), 253-273  "Extending the quasi-steady state concept to analysis of metabolic networks."