RESEARCH INTEREST
Our laboratory is interested in understanding how structures and
dynamics of gene regulatory networks have evolved to regulate complex
phenotypes. We focus primarily on microbial systems due to the
relative simplicity of microbial genomes, which allow us to
interrogate complex processes across a wide range of levels of
cellular complexity (e.g. from single proteins to comprehensive
systems-level analysis). We aim to develop tools that will allow the
rational engineering of gene regulatory networks at both the protein
and network-structure levels, and have application across species
boundaries.
RESEARCH PAPERS
Bonneau, R., Facciotti, M.T., Reiss, D.J., Schmid, A., Pan, M., Kaur, A., Thorsson, V., Shannon, P., Johnson M., Bare, C.J., Longabaugh, W., Vuthoori, M., Whitehead, K., Madar, A., Suzuki, L., Mori, T., Chang, D., DiRuggiero, J., Johnson, C., Hood, L. and Baliga N.S. 2007. A predictive model for transcriptional control of physiology in a free living cell. Cell. 131(7). 1354-1365. PMID: 18160043
Reiss, D.J., Facciotti M.T., and Baliga, N.S. 2007. Model-based deconvolution of genome-wide DNA binding. Bioinformatics. PMID: 18056063
Facciotti, M.T., Reiss, D.J., Pan, M., Kaur, A., Vuthoori, M., Bonneau, R., Shannon, P., Srivastava, A., Donahoe, S.M., Hood, L., and Baliga, N.S. 2007. Structure of a general transcription factor specified global gene regulatory network. PNAS. 104(11). 4630-4635. PMID: 117360575
Kaur, A., Pan, M., Meislin, M., Facciotti, M.T., El-Geweley, R. and Baliga, N.S. 2006. A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Research. 16(7). 841-854. PMID: 16751342
Bonneau, R., Reiss, D.J., Shannon, P. Facciotti, M.T., Hood, L. Baliga, N.S., and Thorsson, V. 2006. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets de novo. Genome Biology. 7(6). R36. PMID: 16686963
Lunde, C.S., Rouhani, S., Facciotti, M.T., and Glaeser, R.M. 2006. Membrane-Protein Stability in a Phospholipid-based Crystallization Medium. Journal of Structural Biology. 154(3). 223-231. PMID: 16600634
Facciotti, M.T., Bonneau, R., Hood, L., and Baliga, N.S. 2004. Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems. Current Genomics. 5(7). 527-544.
Baliga, N.S., Bonneau, R. Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., Shannon, P., Chiu, Y., Weng, R.S., Gan, R.R., Hung, P., Date, S.V., Marcotte, E., Hood, L., and Ng, W.V. 2004. Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea. Genome Research. 14(11). 2221-2234. PMID: 15520287
Facciotti, M.T., Rouhani, S. and Glaeser, R.M. 2004. Energy transduction in transmembrane ion pumps. Trends in Biochemical Sciences. 29(8). 445-451. PMID: 15362229
Facciotti, M.T., Rouhani, S. and Glaeser, R.M. 2004. Crystal structures of bR(D85S) favor a model of bacteriorhodopsin as an hydroxyl-ion pump. FEBS Letters. 564(3). 301-306. PMID: 15111113
Facciotti, M.T., Cheung, V., Lunde, C.S., Rouhani, S., Baliga, N., and Glaeser, R.M. 2004. Specificity of anion-binding in the substrate-pocket of bacteriorhodopsin. Biochemistry. 43(17). 4934-4943. PMID: 15109251
Facciotti, M.T., Cheung, V., Nguyen, D., Rouhani, S., and Glaeser, R.M. 2003. Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: principles of ion pumping. Biophysical Journal. 85. 451-458. PMID: 12829500
Rouhani, S., Facciotti, M.T., Woodcock, G., Cheung, V., Cunningham., Nguyen, D., Rad, B., Lin, C., Lunde, C.S., and Glaeser, R.M. 2002. Crystallization of membrane proteins from media composed of connected-bilayer gels. Biopolymers. 66. 300-316. PMID: 12539259
Kennis, J.T.M., Larsen, D.S., Ohta, K., Facciotti, M.T., Glaeser, R.M., and Fleming, G.R. 2002. Ultrafast protein dynamics of bacteriorhodopsin probed by photon echo and transient absorption spectroscopy. Journal of Physical Chemistry B. 106(23). 6067-6080.
Facciotti, M.T., Rouhani, S., Burkard, F.T., Betancourt, F.M., Downing, K.H., Rose, R.B., McDermott, G., and Glaeser, R.M. 2001. Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle. Biophysical Journal. 81. 3442-3455. PMID: 11721006
Rouhani, S., Cartailler, J-P., Facciotti, M.T., Walian, P., Needleman, R., Lanyi, J.K., Glaeser, R.M., and Luecke, H. 2001. Crystal structure of the D85S mutant of bacteriorhodopsin: Model of an O-like photocycle intermediate. Journal of Molecular Biology. 313. 615-628. PMID: 11676543
Glaeser, R., Facciotti, M.T., Walian, P., Rouhani, S., Holton, J., MacDowell, A., Celestre, R., Cambie, D., and Padmore, H. 2000. Characterization of conditions required for X-ray diffraction experiments with protein microcrystals. Biophysical Journal. 78. 3178-3185. PMID: 10827994
Facciotti, M.T., Bertain, P.B., and Yuan, L. 1999. Improved stearate phenotype in transgenic canola expressing a modified acyl-acyl carrier protein thioesterase. Nature Biotechnology. 17. 593-597. PMID: 10385326
Facciotti, M.T. and Yuan, L. 1998. Molecular dissection of the plant acyl-acyl carrier protein thioesterases. FETT Lipid. 100:4-5. 167-172.
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