PUBLICATIONS

Select publications from group members, 2004-2005:

Bommarius, A.S. and Riebel, B.R.
Biocatalysis - fundamentals and applications.
Wiley-VCH, 1st edition (2004).

Desai, S.K. and Gallivan, J.P.
Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation.
J. Amer. Chem. Soc. 2004; 126, 13247-13254.

Dubey, A., Realff, M.J., Lee, J.H. and Bommarius, A.S.
Support vector machines for learning to identify the critical positions
of a protein.
J. Theor. Biol. 2005; 234, 351-361.

Gao, R. and Lynn, D.G.
Environmental pH sensing: resolving the VirA/VirG two-component system inputs for Agrobacterium pathogenesis.
J. Bacteriol. 2005; 187, 2182-2189.

Geddie, M.L. and Matsumura, I.
Rapid evolution of beta-glucuronidase specificity by saturation mutagenesis of an active site loop.
J. Biol. Chem. 2004; 279, 26462-26468.

Geddie, M.L., Rowe, L.A., Alexander, O.B. and Matsumura, I.
High throughput microplate screens for directed protein evolution.
Methods Enzymol. 2004; 388, 134-145.

Gerth, M.L., Patrick, W.M. and Lutz, S.
A second-generation system for unbiased reading frame selection.
Protein Eng. Des. Sel. 2004; 17, 595-602.

Hud, N.V. and Lynn, D.G.
From life's origins to a synthetic biology - editorial overview.
Curr. Opin. Chem. Biol. 2004; 8, 627-628.

Jain, S.S., Anet, F.A.L., Stahle, C.J. and Hud, N.V.
Enzymatic behavior by intercalating molecules in a template-directed ligation reaction.
Angew. Chem. Int. Ed. Eng. 2004; 43, 2004-2008.

Kim, W.Y., George, A., Evans, M. and Conticello, V.P.
Cotranslational incorporation of a structurally diverse series of proline analogues in an Escherichia coli expression system.
ChemBioChem 2004; 5, 928-936.

Lutz, S. and Patrick, W.M.
Novel methods for directed evolution of enzymes: quality, not quantity.
Curr. Opin. Biotechnol. 2004; 15, 291-297.

Mukhopadhyay, A., Gao, R. and Lynn, D.G.
Integrating input from multiple signals: the VirA/VirG two-component system of Agrobacterium tumefaciens.
ChemBioChem 2004; 5, 1535-1542.

Schwimmer, L.J., Rohatgi, P., Azizi, B., Seley, K.L. and Doyle, D.F.
Creation and discovery of ligand-receptor pairs for transcriptional
control with small molecules.
Proc. Natl Acad. Sci. USA 2004; 101, 14707-14712.

Watt, T.J. and Doyle, D.F.
ESPSearch: a program for finding exact sequences and patterns in
DNA, RNA, or protein.
Biotechniques 2005; 38, 109-115.

Yokoyama, S. and Takenaka, N.
The molecular basis of adaptive evolution of squirrelfish rhodopsins.
Mol. Biol. Evol. 2004; 21, 2071-2078.

Yokoyama, S. and Takenaka, N.
Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates.
Mol. Biol. Evol. 2005; 22, 968-975.

Zimenkov, Y., Conticello, V.P., Guo, L. and Thiyagarajan, P.
Rational design of a nanoscale helical scaffold derived from self-assembly of a dimeric coiled coil motif.
Tetrahedron 2004; 60, 7237-7246.