James Liao

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Inferring yeast cell cycle regulators and interactions using transcription factor activities
    Young Lyeol Yang
    Department of Chemical Engineering, University of California, Los Angeles 90095, USA
    BMC Genomics 6:90. 2005
  2. pmc Trimming of mammalian transcriptional networks using network component analysis
    Linh M Tran
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095 1592, USA
    BMC Bioinformatics 11:511. 2010
  3. pmc Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 85:651-7. 2010
  4. pmc Pentanol isomer synthesis in engineered microorganisms
    Anthony F Cann
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 85:893-9. 2010
  5. pmc Intravascular flow decreases erythrocyte consumption of nitric oxide
    J C Liao
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 96:8757-61. 1999
  6. ncbi request reprint Acetate-inducible protein overexpression from the glnAp2 promoter of Escherichia coli
    W R Farmer
    Department of Chemical Engineering, 5531 Boelter Hall, University of California Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095, USA
    Biotechnol Bioeng 75:504-9. 2001
  7. pmc Network component analysis: reconstruction of regulatory signals in biological systems
    James C Liao
    Departments of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 100:15522-7. 2003
  8. pmc An integrated network approach identifies the isobutanol response network of Escherichia coli
    Mark P Brynildsen
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Mol Syst Biol 5:277. 2009
  9. ncbi request reprint Transcriptome network component analysis with limited microarray data
    Simon J Galbraith
    Department of Computer Science, University of California Los Angeles, CA, USA
    Bioinformatics 22:1886-94. 2006
  10. ncbi request reprint A Gibbs sampler for the identification of gene expression and network connectivity consistency
    Mark P Brynildsen
    Department of Chemical and Biomolecular Engineering, University of California Los Angeles, CA 90095, USA
    Bioinformatics 22:3040-6. 2006

Collaborators

  • Sun Gu Lee
  • Taizo Hanai
  • Robert Gunsalus
  • S Horvath
  • Edward R McCabe
  • Chiara Sabatti
  • Riccardo Boscolo
  • Young Lyeol Yang
  • Kenneth L Lange
  • Zhen Li
  • J P Whitelegge
  • Han Li
  • Srinivasa Reddy
  • M Navab
  • Imke Schröder
  • Stephan Braatsch
  • Shota Atsumi
  • Linh M Tran
  • Mark P Brynildsen
  • Michael R Connor
  • Daniel R Hyduke
  • Wilson W Wong
  • Tae H Han
  • Anthony F Cann
  • Lola Rahib
  • Thomas Bulter
  • Katy C Kao
  • Laura R Jarboe
  • Ganesh Sriram
  • Katrina M Dipple
  • Jeffrey R Bernstein
  • Claire R Shen
  • Kechun Zhang
  • Yajun Yan
  • Kwang Myung Cho
  • Matthew L Rizk
  • Lars Rohlin
  • Katherine J Chou
  • Katherine J Y Chou
  • Nicole K Maclennan
  • Eileen Fung
  • Wendy Higashide
  • Kevin Michael Smith
  • Denton Lai
  • Carolina A Contador
  • Tung Yun Wu
  • Junji Watanabe
  • Simon J Galbraith
  • Jason K Suen
  • Baiyu Zhou
  • David Beckwith
  • Jon M Fukuto
  • Nael H El-Farra
  • Min Kyu Oh
  • Mahesh S Joshi
  • W R Farmer
  • Yasumasa Dekishima
  • Antonino Baez
  • Ethan I Lan
  • Yongchao Li
  • Eva Maria Eckl
  • Thomas Buelter
  • Sarah D Hawkins
  • Lilly S Parr
  • Melissa K Harada
  • Harold G Monbouquette
  • Juan A Asenjo
  • Ben Lluncor
  • Chia Chi Lee
  • Joanna Dodd
  • Kevin M Smith
  • David S Eisenberg
  • Michael R Sawaya
  • Victor Grijalva
  • Robin Farias-Eisner
  • Georgette Buga
  • Tony Y Tsai
  • Shi Shang Jang
  • Kathy Kozak
  • Joseph K Perloff
  • Alan M Fogelman
  • Terry D Lee
  • Susan Hama
  • Hsiang Hui Meng
  • Helen Ge
  • Yunan Miao
  • Zixing Fang
  • Jason Dean
  • Cynthia Shin
  • Jonathan D Trent

Detail Information

Publications71

  1. pmc Inferring yeast cell cycle regulators and interactions using transcription factor activities
    Young Lyeol Yang
    Department of Chemical Engineering, University of California, Los Angeles 90095, USA
    BMC Genomics 6:90. 2005
    ..The goal of this work is to demonstrate the utility of TFAs in inferring transcription factor functions and interactions in Saccharomyces cerevisiae cell cycle regulation...
  2. pmc Trimming of mammalian transcriptional networks using network component analysis
    Linh M Tran
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095 1592, USA
    BMC Bioinformatics 11:511. 2010
    ..Thus, it is beneficial to identify key TF-gene interactions under the experimental condition based on transcriptome data. Such information would be useful in identifying key regulatory pathways and gene markers of TFs in further studies...
  3. pmc Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 85:651-7. 2010
    ..coli harboring the isobutanol synthesis pathway. Overexpression of yqhD or adhA in E. coli showed better production than ADH2, a result confirmed by activity measurements with isobutyraldehyde...
  4. pmc Pentanol isomer synthesis in engineered microorganisms
    Anthony F Cann
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 85:893-9. 2010
    ..Although the current production levels are still too low for immediate industrial applications, the approach holds significant promise for major breakthroughs in production efficiency...
  5. pmc Intravascular flow decreases erythrocyte consumption of nitric oxide
    J C Liao
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 96:8757-61. 1999
    ..However, intravascular flow only partially contributes to the reduced consumption of NO by RBCs, because without the flow, the NO consumption by RBCs is already about 3 orders of magnitude slower than free Hb...
  6. ncbi request reprint Acetate-inducible protein overexpression from the glnAp2 promoter of Escherichia coli
    W R Farmer
    Department of Chemical Engineering, 5531 Boelter Hall, University of California Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095, USA
    Biotechnol Bioeng 75:504-9. 2001
    ..Furthermore, compared to the P(tac) promoter, overexpression of a model protein using the modified glnAp2 promoter system did not cause significant growth inhibition, although a higher level of protein expression was achieved...
  7. pmc Network component analysis: reconstruction of regulatory signals in biological systems
    James C Liao
    Departments of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 100:15522-7. 2003
    ....
  8. pmc An integrated network approach identifies the isobutanol response network of Escherichia coli
    Mark P Brynildsen
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Mol Syst Biol 5:277. 2009
    ..The network described here could aid design and comprehension of alcohol tolerance, whereas the approach provides a general framework to characterize complex phenomena at the systems level...
  9. ncbi request reprint Transcriptome network component analysis with limited microarray data
    Simon J Galbraith
    Department of Computer Science, University of California Los Angeles, CA, USA
    Bioinformatics 22:1886-94. 2006
    ..On the other hand, such methods would inherently increase numerical challenges leading to multiple solutions. Therefore, solutions to both the problems are needed...
  10. ncbi request reprint A Gibbs sampler for the identification of gene expression and network connectivity consistency
    Mark P Brynildsen
    Department of Chemical and Biomolecular Engineering, University of California Los Angeles, CA 90095, USA
    Bioinformatics 22:3040-6. 2006
    ..The goal of this work was to develop a method with a minimal amount of assumptions, and thus widely applicable, that can identify agreement between gene expression and ChIP-chip data at a higher confidence level than current methods...
  11. ncbi request reprint Biological network mapping and source signal deduction
    Mark P Brynildsen
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Bioinformatics 23:1783-91. 2007
    ..Such information is often implicitly imbedded in the data. Here we develop a technique, network component mapping (NCM), to deduce bipartite network connectivity and regulatory signals from data without any need for prior information...
  12. ncbi request reprint gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation
    Linh M Tran
    Department of Chemical Engineering, University of California, Los Angeles, 5531 Boelter Hall, Los Angeles, CA 90095 1592, USA
    Metab Eng 7:128-41. 2005
    ..In addition, numerical techniques for robust decomposition are discussed. gNCA is then demonstrated using an Escherichia coli wild-type strain and an isogenic arcA deletion mutant during a carbon source transition...
  13. pmc Markov Chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli
    Baiyu Zhou
    Department of Chemical Engineering, University of California at Los Angeles, California 90095, USA
    Biophys J 88:2541-53. 2005
    ..This work demonstrates that the Markov Chain model captures the essence of the complex molecular mechanism and greatly simplifies the computation...
  14. ncbi request reprint A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis
    Katy C Kao
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
    J Biol Chem 280:36079-87. 2005
    ..Reduction of this flux causes insufficient activation of CRP and a global metabolic deficiency, which exemplifies a significant feedback interaction from metabolism to the a global regulatory system...
  15. pmc Ensemble modeling for aromatic production in Escherichia coli
    Matthew L Rizk
    Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS ONE 4:e6903. 2009
    ..This work demonstrates that EM is able to capture the result of enzyme overexpression on aromatic producing bacteria by successfully utilizing routinely generated enzyme tuning data to guide model learning...
  16. pmc Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose
    Wendy Higashide
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    Appl Environ Microbiol 77:2727-33. 2011
    ..Specifically, we have demonstrated the first production of isobutanol to approximately 660 mg/liter from crystalline cellulose by using this microorganism...
  17. pmc Versatility and connectivity efficiency of bipartite transcription networks
    Mark P Brynildsen
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, USA
    Biophys J 91:2749-59. 2006
    ....
  18. ncbi request reprint Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
    Chiara Sabatti
    Department of Human Genetics, UCLA Los Angeles, CA 90095 7088, USA
    Bioinformatics 21:922-31. 2005
    ..We illustrate these properties with examples in E.coli. The results of gene expression arrays are used both to guide the search and corroborate it...
  19. doi request reprint An information theoretic exploratory method for learning patterns of conditional gene coexpression from microarray data
    Riccardo Boscolo
    Department of Electrical Engineering, University of California, Los Angeles 90095, USA
    IEEE/ACM Trans Comput Biol Bioinform 5:15-24. 2008
    ..A selection of such interactions that carry a meaningful biological interpretation are discussed...
  20. ncbi request reprint A generalized framework for network component analysis
    Riccardo Boscolo
    Electrical Engineering Department, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:289-301. 2005
    ....
  21. ncbi request reprint Metabolic engineering of Escherichia coli for 1-butanol production
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Metab Eng 10:305-11. 2008
    ..Alternative genes and competing pathway deletions were evaluated for 1-butanol production. Results show promise for using E. coli for 1-butanol production...
  22. doi request reprint Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters
    Wilson W Wong
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Metab Eng 11:409-14. 2009
    ..Thus, this square-root relationship provides insight into how growth rate is altered by different physiological parameters...
  23. doi request reprint Production of 2-methyl-1-butanol in engineered Escherichia coli
    Anthony F Cann
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 81:89-98. 2008
    ..This work led to a strain of E. coli that produces 1.25 g/L 2MB in 24 h, a total alcohol content of 3 g/L, and with yields of up to 0.17 g 2MB/g glucose...
  24. ncbi request reprint Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli
    Laura R Jarboe
    Department of Chemical Engineering, University of California, University of California, Los Angeles, California 90095, USA
    Biotechnol Bioeng 88:189-203. 2004
    ..Our results also predict that pap expression is maximized at low growth rates and minimized at high growth rates. These predictions provide a basis for further experimental investigation...
  25. pmc Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli
    Daniel R Hyduke
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 104:8484-9. 2007
    ..Because mammals do not synthesize branched-chain amino acids, inhibition of dihydroxyacid dehydratase may have served to foster the role of NO in the immune arsenal...
  26. ncbi request reprint Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis
    Laura R Jarboe
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
    J Biol Chem 283:5148-57. 2008
    ..Contrastingly, perturbation of NsrR appeared to be a result of the submicromolar levels of NO released from GSNO and did not require GSNO internalization...
  27. pmc Co-expression pattern from DNA microarray experiments as a tool for operon prediction
    Chiara Sabatti
    Department of Human Genetics and Statistics and Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Nucleic Acids Res 30:2886-93. 2002
    ..These results provide a rationale for conducting expression studies comparing conditions that cause global changes in gene expression...
  28. ncbi request reprint A synthetic gene-metabolic oscillator
    Eileen Fung
    Department of Chemical Engineering, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 435:118-22. 2005
    ..This work demonstrates the possibility of using metabolic flux as a control factor in system-wide oscillation, as well as the predictability of a de novo gene-metabolic circuit designed using nonlinear dynamic analysis...
  29. doi request reprint Engineering metabolic systems for production of advanced fuels
    Yajun Yan
    Department of Chemical and Biomolecular Engineering, University of California at Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    J Ind Microbiol Biotechnol 36:471-9. 2009
    ..In this article, we briefly review the four major metabolic systems, the coenzyme-A mediated pathways, the keto acid pathways, the fatty acid pathway, and the isoprenoid pathways, that allow production of these fuel-grade chemicals...
  30. doi request reprint Microbial production of advanced transportation fuels in non-natural hosts
    Michael R Connor
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Curr Opin Biotechnol 20:307-15. 2009
    ..The isobutanol production process, in particular, has already reached near-industrial level. Although many of these processes are still being scaled-up for commercial production, their potential for practical application is promising...
  31. pmc Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol
    Michael R Connor
    University of California, Department of Chemical and Biomolecular Engineering, 5531 Boelter Hall, Los Angeles, CA 90095, USAdu
    Appl Environ Microbiol 74:5769-75. 2008
    ..This work demonstrates the feasibility of production of 3-methyl-1-butanol as a biofuel and shows promise in using E. coli as a host for production...
  32. pmc Design of artificial cell-cell communication using gene and metabolic networks
    Thomas Bulter
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:2299-304. 2004
    ..The behavior of the circuit shows remarkable predictability based on a mathematical design model...
  33. ncbi request reprint Global expression profiling of acetate-grown Escherichia coli
    Min Kyu Oh
    Department of Chemical Engineering, UCLA, Los Angeles, California 90095, USA
    J Biol Chem 277:13175-83. 2002
    ..In general, the gene expression profiles qualitatively agree with the metabolic flux changes and may serve as a predictor for gene function and metabolic flux distribution...
  34. pmc Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
    Katy C Kao
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:641-6. 2004
    ..We used Escherichia coli carbon source transition from glucose to acetate as a model system. Key results from this analysis were either consistent with physiology or verified by using independent measurements...
  35. doi request reprint Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, California 90095, USA
    Nature 451:86-9. 2008
    ..In particular, we have achieved high-yield, high-specificity production of isobutanol from glucose. The strategy enables the exploration of biofuels beyond those naturally accumulated to high quantities in microbial fermentation...
  36. ncbi request reprint Determination of functional interactions among signalling pathways in Escherichia coli K-12
    Young Lyeol Yang
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Metab Eng 7:280-90. 2005
    ..As this approach cannot distinguish between cross-talks and unidentified direct regulation, the results should provide incentives for further experimental testing...
  37. pmc Heat shock response of Archaeoglobus fulgidus
    Lars Rohlin
    Department of Chemical Engineering, 5531 Boelter Hall, University of California, Los Angeles, Los Angeles, CA 90095, USA
    J Bacteriol 187:6046-57. 2005
    ....
  38. ncbi request reprint A software package for cDNA microarray data normalization and assessing confidence intervals
    Daniel R Hyduke
    Department of Chemical Engineering, University of California at Los Angeles, California, USA
    OMICS 7:227-34. 2003
    ..This program is designed to perform these primary analytical operations on data from two-channel spotted, or in situ synthesized, DNA microarrays...
  39. ncbi request reprint Analysis of nitric oxide consumption by erythrocytes in blood vessels using a distributed multicellular model
    Nael H El-Farra
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095 1592, USA
    Ann Biomed Eng 31:294-309. 2003
    ....
  40. pmc Metabolic engineering for advanced biofuels production from Escherichia coli
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    Curr Opin Biotechnol 19:414-9. 2008
    ..These hosts could be readily manipulated to improve the production efficiency. This review summarizes recent progress in the engineering of Escherichia coli to produce advanced biofuels...
  41. pmc Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    Appl Environ Microbiol 74:7802-8. 2008
    ....
  42. pmc Expanding metabolism for biosynthesis of nonnatural alcohols
    Kechun Zhang
    Department of Chemical and Biomolecular Engineering and Chemistry, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 105:20653-8. 2008
    ..This work demonstrates an approach to build artificial metabolism beyond the natural metabolic network. Nonnatural metabolites such as long chain alcohols are now included in the metabolite family of living systems...
  43. pmc Transcriptomic and network component analysis of glycerol kinase in skeletal muscle using a mouse model of glycerol kinase deficiency
    Lola Rahib
    Biomedical Engineering Interdepartmental Program, Henry Samueli School of Engineering and Applied Science, University of California, Los Angeles, CA, USA
    Mol Genet Metab 96:106-12. 2009
    ..These findings support our previous studies in brown adipose tissue and demonstrate that the role of Gyk in muscle is due in part to its non-metabolic (moonlighting) activities...
  44. ncbi request reprint Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity
    Nicole K Maclennan
    Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 7088, USA
    Hum Mol Genet 15:405-15. 2006
    ..These studies show that Gyk deletion causes alterations in expression of genes in several regulatory networks and is the first time NCA has been used to expand on microarray data from a mouse KO model of a human disease...
  45. pmc Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli
    Shota Atsumi
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
    Appl Environ Microbiol 75:6306-11. 2009
    ..Mutational studies revealed that the replacement of Q487 with amino acids with small side chains (Ala, Ser, and Gly) diminished only the decarboxylase activity but maintained the synthase activity...
  46. pmc Single-gene disorders: what role could moonlighting enzymes play?
    Ganesh Sriram
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 7088, USA
    Am J Hum Genet 76:911-24. 2005
    ....
  47. ncbi request reprint Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling
    Lola Rahib
    Biomedical Engineering, Interdepartmental Program, Henry Samueli School of Engineering and Applied Science at UCLA, Los Angeles, CA 90095, USA
    Eur J Hum Genet 15:646-57. 2007
    ....
  48. pmc Engineering Corynebacterium glutamicum for isobutanol production
    Kevin Michael Smith
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 87:1045-55. 2010
    ..9 g/L isobutanol in a pycldh background. These results show promise in engineering C. glutamicum for higher chain alcohol production using the 2-keto acid pathways...
  49. pmc Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator
    Wilson W Wong
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
    Mol Syst Biol 3:130. 2007
    ....
  50. doi request reprint Ensemble modeling for strain development of L-lysine-producing Escherichia coli
    Carolina A Contador
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095 1592, USA
    Metab Eng 11:221-33. 2009
    ..This work demonstrates the usefulness, applicability, and scope that the Ensemble Modeling framework offers to build production strains...
  51. pmc Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli
    Claire R Shen
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Appl Environ Microbiol 77:2905-15. 2011
    ..These results demonstrate the importance of driving forces in the efficient production of nonnative products...
  52. pmc Moonlighting function of glycerol kinase causes systems-level changes in rat hepatoma cells
    Ganesh Sriram
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 7088, USA
    Metab Eng 12:332-40. 2010
    ..This systems biology approach further emphasizes GK's essential role in central and lipid metabolism and experimentally verifies GK's alternative (moonlighting) function of affecting GR transcription factor activity...
  53. doi request reprint Enantioselective synthesis of pure (R,R)-2,3-butanediol in Escherichia coli with stereospecific secondary alcohol dehydrogenases
    Yajun Yan
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531, Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
    Org Biomol Chem 7:3914-7. 2009
    ..coli to produce enantiomerically pure (R,R)-2,3-butanediol (2,3-BDO) from glucose with a titer of 6.1 g/L (enantio purity >99%), and yield of 0.31 g product/g glucose (62% of theoretical maximum)...
  54. pmc Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate
    Denton Lai
    Chemical and Biomolecular Engineering Department, University of California, Box 951592, Los Angeles, CA 90095 1592, USA
    Metab Eng 11:184-91. 2009
    ....
  55. ncbi request reprint A perspective of metabolic engineering strategies: moving up the systems hierarchy
    Thomas Bulter
    Department of Chemical Engineering, University of California, 405 Hilgard Avenue, Los Angeles, California 90095 1592, USA
    Biotechnol Bioeng 84:815-21. 2003
    ..As our understanding of regulation continues to expand rapidly, engineering of intracellular regulation will become an integral aspect of metabolic engineering...
  56. ncbi request reprint Nitric oxide metabolism in adults with cyanotic congenital heart disease
    Tae H Han
    Department of Chemical Engineering, University of California, Los Angeles, California, USA
    Am J Cardiol 99:691-5. 2007
    ....
  57. ncbi request reprint Directed evolution of ribosomal protein S1 for enhanced translational efficiency of high GC Rhodopseudomonas palustris DNA in Escherichia coli
    Jeffrey R Bernstein
    Department of Chemical and Biomolecular Engineering, UCLA, Los Angeles, California 90095, USA
    J Biol Chem 282:18929-36. 2007
    ..coli was achieved using an S1 mutant selected against multiple genes from R. palustris. This method opens new opportunities for the expression of GC-rich genes in E. coli...
  58. ncbi request reprint Differential association of hemoglobin with proinflammatory high density lipoproteins in atherogenic/hyperlipidemic mice. A novel biomarker of atherosclerosis
    Junji Watanabe
    Atherosclerosis Research Unit, Department of Medicine Cardiology, University of California, Los Angeles, California 90095, USA
    J Biol Chem 282:23698-707. 2007
    ..Our data suggest that Hb contributes to the proinflammatory nature of HDL in mouse and human models of atherosclerosis and may serve as a novel biomarker for atherosclerosis...
  59. ncbi request reprint Reductive nitrosylation and S-nitrosation of hemoglobin in inhomogeneous nitric oxide solutions
    Tae H Han
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095, USA
    Nitric Oxide 10:74-82. 2004
    ..The remaining SNO-Hb is likely formed from NO oxidation products...
  60. pmc Interactions of nitrosylhemoglobin and carboxyhemoglobin with erythrocyte
    Katherine J Chou
    Department of Chemical and Biomolecular Engineering, University of California, UCLA, Los Angeles, CA 90095, USA
    Nitric Oxide 18:122-35. 2008
    ....
  61. pmc Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine
    Kechun Zhang
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:6234-9. 2010
    ..18 g/g glucose yield, 26% of the theoretical maximum). This work opens the possibility of total biosynthesis of other nonnatural chiral compounds that could be useful pharmaceutical intermediates...
  62. pmc Transfer of the high-GC cyclohexane carboxylate degradation pathway from Rhodopseudomonas palustris to Escherichia coli for production of biotin
    Jeffrey R Bernstein
    Biomedical Engineering Interdepartmental Program, University of California, Los Angeles, CA, USA
    Metab Eng 10:131-40. 2008
    ....
  63. doi request reprint A hidden square-root boundary between growth rate and biomass yield
    Wilson W Wong
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
    Biotechnol Bioeng 102:73-80. 2009
    ..The relationship also explains how growth rate is affected by the yield and sheds lights on strain design for product formation...
  64. pmc Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions
    Tae H Han
    Department of Chemical Engineering, University of California, Los Angeles, CA 90095 1592, USA
    Proc Natl Acad Sci U S A 99:7763-8. 2002
    ..These results were supported further by mathematically modeling NO-Hb reactions and diffusion...
  65. pmc 3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation
    Michael R Connor
    Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
    Appl Microbiol Biotechnol 86:1155-64. 2010
    ..Investigation of the host's sensitivity to 3-methyl-1-butanol directed development of a two-phase fermentation process in which titers reached 9.5 g/L of 3-methyl-1-butanol with a yield of 0.11 g/g glucose after 60 h...
  66. pmc Regulation of nitric oxide consumption by hypoxic red blood cells
    Tae H Han
    Department of Chemical Engineering, University of California Los Angeles, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 100:12504-9. 2003
    ..Furthermore, accelerated NO consumption may exacerbate ischemia-mediated vasospasm and nitrate tolerance. Finally, this phenomenon may be an evolved mechanism to stabilize the vasculature in sepsis...
  67. ncbi request reprint Rhodopseudomonas palustris CGA009 has two functional ppsR genes, each of which encodes a repressor of photosynthesis gene expression
    Stephan Braatsch
    Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
    Biochemistry 45:14441-51. 2006
    ..This work shows that both the PpsR1 and PpsR2 proteins from R. palustris strain CGA009 function as oxygen-responsive transcriptional repressors...
  68. ncbi request reprint Control of acetate production rate in Escherichia coli by regulating expression of single-copy pta using lacI(Q) in multicopy plasmid
    Sun Gu Lee
    Department of Chemical and Biochemical Engineering, Pusan National University, Busan, 609 735, Korea
    J Microbiol Biotechnol 18:334-7. 2008
    ..The production rate of acetate was shown to be tightly controlled when varying the concentration of the inducer (IPTG) in the model system...
  69. ncbi request reprint Custom design of metabolism
    James C Liao
    Nat Biotechnol 22:823-4. 2004
  70. pmc Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions
    Mahesh S Joshi
    Department of Surgery, Louisiana State University Health Sciences Center, New Orleans, LA 70012, USA
    Proc Natl Acad Sci U S A 99:10341-6. 2002
    ..We conclude that the reaction of NO with hemoglobin under normoxic conditions results in consumption, rather than conservation, of NO...
  71. ncbi request reprint Blood feud: keeping hemoglobin from nixing NO
    James C Liao
    Nat Med 8:1350-1. 2002

Research Grants16

  1. Chemogenomic Analysis of E. coli Response to NO species
    James C Liao; Fiscal Year: 2010
    ..If hew TF targets are predicted, then the iteration continues. Otherwise, the predicted networks are verified using genetic and biochemical experiments. ..
  2. Nitric Oxide Interaction with Red Blood Cells
    James Liao; Fiscal Year: 2007
    ..Specific aim 2 will focus on the functional roles of this regulation using isolated porcine pulmonary and coronary microvessels. Together, these results will suggest clinical relevance and potential interventions. ..
  3. Engineering Large scale pathways from organisms to Escherichia coli
    James Liao; Fiscal Year: 2007
    ..In particular, selected projects proposed here will be used as modules in a workshop established by FRT at Ohio State and form the basis for a course (Metabolic Engineering) at UCLA. ..
  4. Chemogenomic Analysis of E. coli Response to NO species
    James Liao; Fiscal Year: 2007
    ..If hew TF targets are predicted, then the iteration continues. Otherwise, the predicted networks are verified using genetic and biochemical experiments. ..
  5. Automated Chip-Based Metabolomic Analysis
    James Liao; Fiscal Year: 2006
    ..abstract_text> ..
  6. NITRIC OXIDE DIFFUSION AND REACTION WITH ERTHROCYTES
    James Liao; Fiscal Year: 2003
    ..abstract_text> ..
  7. Nitric Oxide Interaction with Red Blood Cells
    James C Liao; Fiscal Year: 2010
    ..Specific aim 2 will focus on the functional roles of this regulation using isolated porcine pulmonary and coronary microvessels. Together, these results will suggest clinical relevance and potential interventions. ..