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Publications

1. Achyuthan, K. E., A. M. Achyuthan, et al. (2010). "Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to Cost-Effective Lignocellulosic Biofuels." Molecules 15(12): 8641-8688.
2. Achyuthan, K. E., P. D. Adams, et al. (2010). "Hitherto Unrecognized Fluorescence Properties of Coniferyl Alcohol." Molecules 15(3): 1645-1667.
3. Achyuthan, K. E., P. D. Adams, et al. (2009). "Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products." Molecules 14(11): 4758-4778.
4. Bates, J. T., D. Chivian, et al. (2011). "GLAMM: Genome-Linked Application for Metabolic Maps." Nucleic Acids Research 39(Web Server issue): W400-405.
5. Bharadwaj, R., Z. Chen, et al. (2010). "Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion." Analytical Chemistry 82(22): 9513–9520.
6. Bharadwaj, R., A. Wong, et al. (2011). "High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration." Bioresource Technology 102(2): 1329-1337.
7. Blanch, H. W. (2011). "Bioprocessing for biofuels." Current Opinion in Biotechnology 23: 1-6.*
8. Blanch, H. W., P. D. Adams, et al. (2008). "Addressing the need for alternative transportation fuels: The Joint BioEnergy Institute." ACS Chemical Biology 3(1): 17-20.
9. Cao, P. J., K. H. Jung, et al. (2010). "A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes." Bioenergy Research 3(2): 108-114.
10. Cetinkol, O. P., D. C. Dibble, et al. (2010). "Understanding the impact of ionic liquid pretreatment on eucalyptus." Biofuels 1(1): 33-46.
11. Chandrasekaran, A., R. Bharadwaj, et al. (2010). "A Microscale Platform For Integrated Cell-Free Expression And Activity Screening Of Cellulases." Journal of Proteome Research 9(11): 5677-5683.
12. Chhabra, S. R., G. Butland, et al. (2011). "Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio vulgaris Genome." Applied and Environmental Microbiology 77(21): 7595-7604.
13. Chhabra, S. R., M. P. Joachimiak, et al. (2011). "Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough." PLoS One 6(6): e21470.
14. Cong, Y., M. L. Baker, et al. (2010). "4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement." Proceedings of the National Academy of Sciences 107(11): 4967-4972.
15. Dehal, P. S., M. P. Joachimiak, et al. (2010). "MicrobesOnline: an integrated portal for comparative and functional genomics." Nucleic Acids Research 38: D396-D400.
16. Dibble, D., C. Li , et al. (2011). "A facile method for the recovery of ionic liquid and lignin from biomass pretreatment." Green Chemistry 13(11): 3255-3264.
17. Dougherty, M. J. and F. H. Arnold (2009). "Directed evolution: new parts and optimized function." Current Opinion in Biotechnology 20(4): 486-491.
18. Dueber, J. E., G. C. Wu, et al. (2009). "Synthetic protein scaffolds provide modular control over metabolic flux." Nature Biotechnology 27(8): 753-U107.
19. Dunlop, M. J., Z. Y. Dossani, et al. (2011). "Engineering microbial biofuel tolerance and export using efflux pumps." Molecular Systems Biology 7: 487.
20. Eudes, A., E. E. Baidoo, et al. (2011). "Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae." Applied Microbiology and Biotechnology 89(4): 989-1000.
21. Garcia, D. E., E. E. Baidoo, et al. (2008). "Separation and mass spectrometry in microbial metabolomics." Current Opinion in Microbiology 11(3): 233-239.
22. George, A., K. Tran, et al. (2011). "The effect of ionic liquid cation and anion combinations on the macromolecular structure of lignins." Green Chemistry.*
23. Han, J., S. Singh, et al. (2010). "Chemical profiling of the plant cell wall through Raman microspectroscopy in 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro." IEEE ISBI: 1273-1276.
24. Harper, J. C., S. M. Brozik, et al. (2009). "Fabrication and testing of a microneedles sensor array for p-cresol detection with potential biofuel applications." ACS Applied Materials & Interfaces 1(7): 1591-1598.
25. Heazlewood, J. L. and C. J. Petzold (2011). Proteomics - Applications in Biology. Rijeka, Croatia, InTech.*
26. Ito, J., T. S. Batth, et al. (2011). "Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism." Journal of Proteome Research 10(4): 1571-1582.
27. Ito, J., C. J. Petzold, et al. (2010). "The Role of Proteomics in the Development of Cellulosic Biofuels." Current Proteomics 7(2): 121-134.
28. Joshua, C. J., R. Dahl, et al. (2011). "Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius." Journal of Bacteriology 193(6): 1293-1301.
29. Juminaga, D., E. E. Baidoo, et al. (2011). "Modular Engineering of L-Tyrosine Production in Escherichia coli." Applied and Environmental Microbiology.*
30. Kent, M. S., G. Cheng, et al. (2010). "Study of Enzymatic Digestion of Cellulose by Small Angle Neutron Scattering." Biomacromolecules 11(2): 357-368.
31. Li, C., B. Knierim, et al. (2010). "Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification." Bioresource Technology 101(13): 4900-4906.
32. Liu, H., J. H. Pereira, et al. (2010). "Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A." FEBS Letters 584(15): 3431-3435.
33. Ma, S. M., D. E. Garcia, et al. (2011). "Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases." Metabolic Engineering 13(5): 588-597.
34. McAndrew, R. P., P. P. Peralta-Yahya, et al. (2011). "Structure of a Three-Domain Sesquiterpene Synthase: A Prospective Target for Advanced Biofuels Production." Structure 19: 1-9.*
35. Mukhopadhyay, A., A. M. Redding, et al. (2008). "Importance of systems biology in engineering microbes for biofuel production." Current Opinion in Biotechnology 19(3): 228-234.
36. Ouellet, M., P. D. Adams, et al. (2009). "A rapid and inexpensive labeling method for microarray gene expression analysis." BMC Biotechnology 9: 97.
37. Ouellet, M., S. Datta, et al. (2011). "Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production." Green Chemistry 13(10): 2743-2749.
38. Parsons, H. T., J. Ito, et al. (2011). The current state of the Golgi proteomes. Proteomics - Applications in Biology. J. L. Heazlewood and C. J. Petzold. Rijeka, Croatia, InTech.*
39. Pereira, J. H., Z. Chen, et al. (2010). "Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima." Journal of Structural Biology 172(3): 372-379.
40. Pereira, J. H., R. Sapra, et al. (2009). "Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius." Acta Crystallographica Section D Biological Crystallography 65(Pt 8): 744-750.
41. Petzold, C. J. and J. D. Keasling (2010). Metabolic engineering of E.coli for the production of a precursor to artemisinin, an anti-malarial drug. The Manual of Industrial Microbiology and Biotechnology. R. Balz. Washington, DC, ASM Press: 364-379.
42. Rautengarten, C., B. Ebert, et al. (2011). "The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis." Plant Cell 23(4): 1373-1390.
43. Redding-Johanson, A. M., T. S. Batth, et al. (2011). "Targeted proteomics for metabolic pathway optimization: Application to terpene production." Metabolic Engineering 13(2): 194-203.
44. Reindl, W., K. Deng, et al. (2011). "Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities." Energy & Environmental Science 4(8): 2884-2893.
45. Rutherford, B. J., R. H. Dahl, et al. (2010). "Functional genomic study of exogenous n-butanol stress in Escherichia coli." Applied and Environmental Microbiology 76(6): 1935-1945.
46. Sarkar, P., E. Bosneaga, et al. (2009). "Plant cell walls throughout evolution: towards a molecular understanding of their design principles." Journal of Experimental Botany 60(13): 3615-3635.
47. Shaikh, A. S., Y. J. Tang, et al. (2010). "Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein." Biotechnology Progress 26(1): 52-56.
48. Shui, W., L. Sheu, et al. (2008). "Membrane proteomics of phagosomes suggests a connection to autophagy." Proceedings of the National Academy of Sciences 105(44): 16952-16957.
49. Steen, E. J., R. Chan, et al. (2008). "Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol." Microbial Cell Factories 7: 36.
50. Tang, Y. J., H. G. Martin, et al. (2009). "Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism." Biotechnology and Bioengineering 102(4): 1161-1169.
51. Varanasi, P., L. Sun, et al. (2011). Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research. Biofuel's Engineering Process Technology. M. A. dos Santos Bernades, InTech: 493-520.
52. Yin, L., Y. Verhertbruggen, et al. (2011). "The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal Arabidopsis Development." Molecular Plant 4(6): 1024-1037.
53. Yu, E., S. P. Gaucher, et al. (2010). "Probing conformational changes in Ape1 during the progression of base excision repair." Biochemistry 49(18): 3786-3796.
54. Yu, E. T. and M. Z. Hadi (2010). "Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function." Mutation Research 722(2): 140-146.