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News & Media : Scientific Publications
Selected Scientific Publications: Publications by Topic
Verenium feels the communication of scientific information through journal publications and presentations at scientific meetings is an important way to share knowledge. Information will be made publicly available through these means as intellectual property and business concerns are satisfied. We look forward to making you aware of advances in our ground breaking technology.
Applications
Discovery, development, and mill application of a thermostable xylanase for prebleaching of kraft pulp
Esteghlalian, A.R., Blum, D.L., Kazaoka, M., Wu, D., Cruz, D.M., Varvak, A., Healey, S., Janssen, G., Weiner, D.P., and Hazlewood, G.
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005, BIOT-332. 2005
Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric
Solbak, A.I., Richardson, T.H., McCann, R.T., Kline, K.A., Bartnek, F., Tomlinson, G., Tan, X., Parra-Gessert, L., Frey, G.J., Podar, M., Luginbuehl, P., Gray, K.A., Mathur, E.J., Robertson, D.E., Burk, M.J., Hazlewood, G.P., Short, J.M., and Kerovuo, J.
Journal of Biological Chemistry, 280(10):9431-9438. 2005
Chemoenzymatic approaches to the dynamic kinetic asymmetric synthesis of aromatic amino acids
Chaplin, J.A., Levin, M.D., Morgan, B., Farid, N., Li, J., Zhu, Z., McQuaid, J., Nicholson, L.W., Rand, C.A., and Burk, M.J.
Tetrahedron: Asymmetry, 15(18):2793-2796. 2004
Enhancing the thermal tolerance and gastric performance of a microbial phytase for use as a phosphate-mobilizing monogastric-feed supplement
Garrett, J.B., Kretz, K.A., O'Donoghue, E., Kerovuo, J., Kim, W., Barton, N.R., Hazlewood, G.P., Short, J.M., Robertson, D.E., and Gray, K.A.
Applied and Environmental Microbiology, 70(5):3041-3046. 2004
Development of an efficient, scalable, aldolase-catalyzed process for enantioselective synthesis of statin intermediates
Greenberg, W.A., Varvak, A., Hanson, S.R., Wong, K., Huang, H., Chen, P., and Burk, M.J.
Proceedings of the National Academy of Sciences of the United States of America, 101(16):5788-5793. 2004
Epoxide Hydrolase-Catalyzed Enantioselective Synthesis of Chiral 1,2-Diols via Desymmetrization of meso-Epoxides
Zhao, L., Han, B., Huang, Z., Miller, M., Huang, H., Malashock, D.S., Zhu, Z., Milan, A., Robertson, D.E., Weiner, D.P., and Burk, M.J.
Journal of the American Chemical Society, 126(36):11156-11157. 2004
An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives
DeSantis, G., Zhu, Z., Greenberg, W.A., Wong, K., Chaplin, J., Hanson, S.R., Farwell, B., Nicholson, L.W., Rand, C.L., Weiner, D.P., Robertson, D.E., and Burk, M.J.
Journal of the American Chemical Society, 124(31):9024-9025. 2002
A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase
Richardson, T.H., Tan, X., Frey, G., Callen, W., Cabell, M., Lam, D., Macomber, J., Short, J.M., Robertson, D.E., and Miller, C.
J.Biol.Chem., 277(29):26501-26507. 2002
Creation of a Productive, Highly Enantioselective Nitrilase through Gene Site Saturation Mutagenesis (GSSM)
DeSantis, G., Wong, K., Farwell, B., Chatman, K., Zhu, Z., Tomlinson, G., Huang, H., Tan, X., Bibbs, L., Chen, P., Kretz, K., and Burk, M.J.
Journal of the American Chemical Society, 125(38):11476-11477. 2003
Biodesulfurization of fossil fuels
Gray, K.A., Mrachko, G.T., and Squires, C.H.
Current Opinion in Microbiology, 6(3):229-235. 2003
Rapid evolution of reversible denaturation and elevated melting temperature in a microbial haloalkane dehalogenase
Gray, K.A., Richardson, T.H., Kretz, K., Short, J.M., Bartnek, F., Knowles, R., Kan, L., Swanson, P.E., and Robertson, D.E.
Advanced Synthesis & Catalysis, 343(6+7):607-617. 2001
Discovery
Environmental whole-genome amplification to access microbial populations in contaminated sediments
Abulencia, C.B., Wyborski, D.L., Garcia, J.A., Podar, M., Chen, W., Chang, S.H., Chang, H.W., Watson, D., Brodie, E.L., Hazen, T.C., and Keller, M.
Applied and Environmental Microbiology, 72(5):3291-3301. 2006
Capturing the uncultivated majority
Green, B.D. and Keller, M.
Current Opinion in Biotechnology, 17(3):236-240. 2006
A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution
Mathur, E., Toledo, G., Green, B.D., Podar, M., Richardson, T.H., Kulwiec, M., and Chang, H.C.
Industrial Biotechnology, 1(4):283-287. 2005
Discovery, development, and mill application of a thermostable xylanase for prebleaching of kraft pulp
Esteghlalian, A.R., Blum, D.L., Kazaoka, M., Wu, D., Cruz, D.M., Varvak, A., Healey, S., Janssen, G., Weiner, D.P., and Hazlewood, G.
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005, BIOT-332. 2005
Evolution of a microbial nitrilase gene family: A comparative and environmental genomics study
Podar, M., Eads, J.R., and Richardson, T.H.
BMC Evolutionary Biology, 5. 2005
Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric
Solbak, A.I., Richardson, T.H., McCann, R.T., Kline, K.A., Bartnek, F., Tomlinson, G., Tan, X., Parra-Gessert, L., Frey, G.J., Podar, M., Luginbuehl, P., Gray, K.A., Mathur, E.J., Robertson, D.E., Burk, M.J., Hazlewood, G.P., Short, J.M., and Kerovuo, J.
Journal of Biological Chemistry, 280(10):9431-9438. 2005
Global proteome discovery using an online three-dimensional LC-MS/MS
Wei, J., Sun, J., Yu, W., Jones, A., Oeller, P., Keller, M., Woodnutt, G., and Short, J.
Journal of Proteome Research, 4(3):801-808. 2005
New methods to access microbial diversity for small molecule discovery
Zengler, K., Paradkar, A., and Keller, M.
Natural Products, 275-293. 2005
Unusual microbial xylanases from insect guts
Brennan, Y., Callen, W.N., Christoffersen, L., Dupree, P., Goubet, F., Healey, S., Hernandez, M., Keller, M., Li, K., Palackal, N., Sittenfeld, A., Tamayo, G., Wells, S., Hazlewood, G.P., Mathur, E.J., Short, J.M., Robertson, D.E., and Steer, B.A.
Applied and Environmental Microbiology, 70(6):3609-3617. 2004
Development of an efficient, scalable, aldolase-catalyzed process for enantioselective synthesis of statin intermediates
Greenberg, W.A., Varvak, A., Hanson, S.R., Wong, K., Huang, H., Chen, P., and Burk, M.J.
Proceedings of the National Academy of Sciences of the United States of America, 101(16):5788-5793. 2004
Tapping into microbial diversity
Keller, M. and Sengler, K.
Nature Reviews Microbiology, 2(2):141-150. 2004
GigaMatrix: an ultra high-throughput tool for accessing biodiversity
Lafferty, M. and Dycaico, M.J.
JALA, 9(4):200-208. 2004
GigaMatrix: A novel ultrahigh throughput protein optimization and discovery platform
Lafferty, M. and Dycaico, M.J.
Methods in Enzymology, 388(Protein Engineering):119-134. 2004
Recent progress in biocatalyst discovery and optimization
Robertson, D.E. and Steer, B.A.
Current Opinion in Chemical Biology, 8(2):141-149. 2004
Exploring nitrilase sequence space for enantioselective catalysis
Robertson, D.E., Chaplin, J.A., DeSantis, G., Podar, M., Madden, M., Chi, E., Richardson, T., Milan, A., Miller, M., Weiner, D.P., Wong, K., McQuaid, J., Farwell, B., Preston, L.A., Tan, X., Snead, M.A., Keller, M., Mathur, E., Kretz, P.L., Burk, M.J., and Short, J.M.
Applied and Environmental Microbiology, 70(4):2429-2436. 2004
Epoxide Hydrolase-Catalyzed Enantioselective Synthesis of Chiral 1,2-Diols via Desymmetrization of meso-Epoxides
Zhao, L., Han, B., Huang, Z., Miller, M., Huang, H., Malashock, D.S., Zhu, Z.,
Milan, A., Robertson, D.E., Weiner, D.P., and Burk, M.J.
Journal of the American Chemical Society, 126(36):11156-11157. 2004
An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives
DeSantis, G., Zhu, Z., Greenberg, W.A., Wong, K., Chaplin, J., Hanson, S.R., Farwell, B., Nicholson, L.W., Rand, C.L., Weiner, D.P., Robertson, D.E., and Burk, M.J.
Journal of the American Chemical Society, 124(31):9024-9025. 2002
A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase
Richardson, T.H., Tan, X., Frey, G., Callen, W., Cabell, M., Lam, D., Macomber, J., Short, J.M., Robertson, D.E., and Miller, C.
J.Biol.Chem., 277(29):26501-26507. 2002
Cultivating the uncultured
Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E.J., Short, J.M., and Keller, M.
Proceedings of the National Academy of Sciences of the United States of America, 99(24):15681-15686. 2002
Bacterial group II introns in a deep-sea hydrothermal vent environment
Podar, M., Mullineaux, L., Huang, H.R., Perlman, P.S., and Sogin, M.L.
Appl.Environ.Microbiol., 68(12):6392-6398. 2002
Soil-based gene discovery: a new technology to accelerate and broaden biocatalytic applications
Gray, K.A., Richardson, T.H., Robertson, D.E., Swanson, P.E., and Subramanian, M.V.
Advances in Applied Microbiology, 52:1-27, 3. 2003
cDNA library construction for the Lambda ZAP-based vectors
Snead, M.A., Alting-Mees, M.A., and Short, J.M.
Nucleic Acid Protocols Handbook, 355-365. 2000
Advances in enzyme discovery technology: capturing diversity
Miller, C.
Inform, 11(5):489-2000
Panning microbial diversity for novel catalytic activities
Kretz, K., Mathur, E., Robertson, D., Swanson, R., and Short, J.
Developments in Industrial Microbiology Series, 34:61-64. 1997
Recombinant approaches for accessing biodiversity
Short, J.M.
Nature Biotechnology, 15(13):1322-1323. 1997
Opimization
Engineering stability into Escherichia coli secreted Fabs leads to increased functional expression
Demarest, S.J., Chen, G., Kimmel, B.E., Gustafson, D., Wu, J., Salbato, J., Poland, J., Elia, M., Tan, X., Wong, K., Short, J., and Hansen, G.
Protein Engineering, Design & Selection, 19(7):325-336. 2006
A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution
Mathur, E., Toledo, G., Green, B.D., Podar, M., Richardson, T.H., Kulwiec, M., and Chang, H.C.
Industrial Biotechnology, 1(4):283-287. 2005
Discovery, development, and mill application of a thermostable xylanase for prebleaching of kraft pulp
Esteghlalian, A.R., Blum, D.L., Kazaoka, M., Wu, D., Cruz, D.M., Varvak, A., Healey, S., Janssen, G., Weiner, D.P., and Hazlewood, G.
Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005, BIOT-332. 2005
Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric
Solbak, A.I., Richardson, T.H., McCann, R.T., Kline, K.A., Bartnek, F., Tomlinson, G., Tan, X., Parra-Gessert, L., Frey, G.J., Podar, M., Luginbuehl, P., Gray, K.A., Mathur, E.J., Robertson, D.E., Burk, M.J., Hazlewood, G.P., Short, J.M., and Kerovuo, J.
Journal of Biological Chemistry, 280(10):9431-9438. 2005
Enhancing the thermal tolerance and gastric performance of a microbial phytase for use as a phosphate-mobilizing monogastric-feed supplement
Garrett, J.B., Kretz, K.A., O'Donoghue, E., Kerovuo, J., Kim, W., Barton, N.R., Hazlewood, G.P., Short, J.M., Robertson, D.E., and Gray, K.A.
Applied and Environmental Microbiology, 70(5):3041-3046. 2004
Gene site saturation mutagenesis: A comprehensive mutagenesis approach
Kretz, K.A., Richardson, T.H., Gray, K.A., Robertson, D.E., Tan, X., and Short, J.M.
Methods in Enzymology, 388(Protein Engineering):3-11. 2004
GigaMatrix: A novel ultrahigh throughput protein optimization and discovery platform
Lafferty, M. and Dycaico, M.J.
Methods in Enzymology, 388(Protein Engineering):119-134. 2004
An evolutionary route to xylanase process fitness
Palackal, N., Brennan, Y., Callen, W.N., Dupree, P., Frey, G., Goubet, F., Hazlewood, G.P., Healey, S., Kang, Y.E., Kretz, K.A., Lee, E., Tan, X., Tomlinson, G.L., Verruto, J., Wong, V.W.K., Mathur, E.J., Short, J.M., Robertson, D.E., and Steer, B.A.
Protein Science, 13(2):494-503. 2004
Recent progress in biocatalyst discovery and optimization
Robertson, D.E. and Steer, B.A.
Current Opinion in Chemical Biology, 8(2):141-149. 2004
A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase
Richardson, T.H., Tan, X., Frey, G., Callen, W., Cabell, M., Lam, D., Macomber, J., Short, J.M., Robertson, D.E., and Miller, C.
J.Biol.Chem., 277(29):26501-26507. 2002
Creation of a Productive, Highly Enantioselective Nitrilase through Gene Site Saturation Mutagenesis (GSSM)
DeSantis, G., Wong, K., Farwell, B., Chatman, K., Zhu, Z., Tomlinson, G., Huang, H., Tan, X., Bibbs, L., Chen, P., Kretz, K., and Burk, M.J.
Journal of the American Chemical Society, 125(38):11476-11477. 2003
Rapid evolution of reversible denaturation and elevated melting temperature in a microbial haloalkane dehalogenase
Gray, K.A., Richardson, T.H., Kretz, K., Short, J.M., Bartnek, F., Knowles, R., Kan, L., Swanson, P.E., and Robertson, D.E.
Advanced Synthesis & Catalysis, 343(6+7):607-617. 2001
Antibody Engineering
Engineering stability into Escherichia coli secreted Fabs leads to increased functional expression
Demarest, S.J., Chen, G., Kimmel, B.E., Gustafson, D., Wu, J., Salbato, J., Poland, J., Elia, M., Tan, X., Wong, K., Short, J., and Hansen, G.
Protein Engineering, Design & Selection, 19(7):325-336. 2006
Bioinformatics
Environmental whole-genome amplification to access microbial populations in contaminated sediments
Abulencia, C.B., Wyborski, D.L., Garcia, J.A., Podar, M., Chen, W., Chang, S.H., Chang, H.W., Watson, D., Brodie, E.L., Hazen, T.C., and Keller, M.
Applied and Environmental Microbiology, 72(5):3291-3301. 2006
Evolution of a microbial nitrilase gene family: A comparative and environmental genomics study
Podar, M., Eads, J.R., and Richardson, T.H.
BMC Evolutionary Biology, 5. 2005
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
Waters, E., Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., Podar, M., Richardson, T., Sutton, G.G., Simon, M., Soell, D., Stetter, K.O., Short, J.M., and Noordewier, M.
Proceedings of the National Academy of Sciences of the United States of America, 100(22):12984-12988. 2003
Unfolding the secrets of the Salmonella genome to aid drug development
Noordewier, M. and Brown, J.
Trends in Pharmacological Sciences, 23(9):397-399. 2002
Streptomyces genetics: a genomic perspective
Paradkar, A., Trefzer, A., Chakraburtty, R., and Stassi, D.
Critical Reviews in Biotechnology, 23(1):1-27. 2003
A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes
Podar, M., Haddock, S.H.D., Sogin, M.L., and Harbison, G.R.
Molecular Phylogenetics and Evolution, 21(2):218-230. 2001
The complete genome of the hyperthermophilic bacterium Aquifex aeolicus
Deckert, G., Warren, P.V., Gaasterland, T., Young, W.G., Lenox, A.L., Graham, D.E., Overbeek, R., Snead, M.A., Keller, M., Aujay, M., Huber, R., Feldman, R.A., Short, J.M., Olsen, G.J., and Swanson, R.V.
Nature (London), 392(6674):353-358. 1998
Biodiversity
Environmental whole-genome amplification to access microbial populations in contaminated sediments
Abulencia, C.B., Wyborski, D.L., Garcia, J.A., Podar, M., Chen, W., Chang, S.H., Chang, H.W., Watson, D., Brodie, E.L., Hazen, T.C., and Keller, M.
Applied and Environmental Microbiology, 72(5):3291-3301. 2006
Capturing the uncultivated majority
Green, B.D. and Keller, M.
Current Opinion in Biotechnology, 17(3):236-240. 2006
Bioprospecting ethics & benefits: A model for effective benefit-sharing
Christoffersen, L. and Mathur, E.
Industrial Biotechnology, 1(4):255-259. 2005
A biodiversity-based approach to development of performance enzymes: Applied metagenomics and directed evolution
Mathur, E., Toledo, G., Green, B.D., Podar, M., Richardson, T.H., Kulwiec, M., and Chang, H.C.
Industrial Biotechnology, 1(4):283-287. 2005
New methods to access microbial diversity for small molecule discovery
Zengler, K., Paradkar, A., and Keller, M.
Natural Products, 275-293. 2005
Unusual microbial xylanases from insect guts
Brennan, Y., Callen, W.N., Christoffersen, L., Dupree, P., Goubet, F., Healey, S., Hernandez, M., Keller, M., Li, K., Palackal, N., Sittenfeld, A., Tamayo, G., Wells, S., Hazlewood, G.P., Mathur, E.J., Short, J.M., Robertson, D.E., and Steer, B.A.
Applied and Environmental Microbiology, 70(6):3609-3617. 2004
Tapping into microbial diversity
Keller, M. and Sengler, K.
Nature Reviews Microbiology, 2(2):141-150. 2004
GigaMatrix: an ultra high-throughput tool for accessing biodiversity
Lafferty, M. and Dycaico, M.J.
JALA, 9(4):200-208. 2004
Cultivating the uncultured
Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E.J., Short, J.M., and Keller, M.
Proceedings of the National Academy of Sciences of the United States of America, 99(24):15681-15686. 2002
Hydrogen-sulfur oxidoreductase complex from Pyrodictium abyssi
Keller, M. and Dirmeier, R.
Methods in Enzymology, 331(Hyperthermophilic Enzymes, Part B):442-451. 2001
Where are the limits of life?
Rusterholtz, K. and Pohlschroder, M.
Cell (Cambridge, Massachusetts), 96(4):469-470. 1999
Recombinant approaches for accessing biodiversity
Short, J.M.
Nature Biotechnology, 15(13):1322-1323. 1997
Regulatory
Safety evaluation of a phytase, expressed in Schizosaccharomyces pombe, intended for use in animal feed
Ciofalo, V., Barton, N., Kretz, K., Baird, J., Cook, M., and Shanahan, D.
Regul.Toxicol.Pharmacol., 37(2):286-292. 2003
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The communication of scientific information through journal publications and presentations at scientific meetings is an important way to share knowledge.
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