PERSONAL EDUCATION

University of California, Berkeley
PhD, Biophysics

University of California, Davis
BS, Biochemistry

RESEARCH INTERESTS

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 their relative simplicity. This allows us to interrogate complex physiological 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

Facciotti M.T., Pang, W.L., Lo, F.Y., Whitehead, K., Koide, T., Masumura, K., Pan, M., Kaur, A., Larsen D.J., Reiss, D.J., Hoang, L., Kalisiak, E., Northern, T., Trauger, S.A., Siuzdak, G., and Baliga, N.S. Large scale physiological readjustment during growth in a simple batch culture. submitted.

Koide, T., Reiss, D.J., Bare, C.J., Facciotti, M.T., Schmid, A.K., Pan, M., Marzolf, B., Van, P.T., Lo, F., Pratrap, A., Deutsch, E.W., Peterson, A. Martin, D., Baliga, N.S. Interspersed regulatory logic within prokaryotic coding sequences. submitted.

Facciotti M.T. 2009. Training interdisciplinary scientists for systems biology. J. Invest. Medicine Feb;57(2):471-3

Benedyk M, Berglund L, Facciotti M, Mobley W, and Zucker D. 2009. Strategies for innovation and interdisciplinary translational research: research and career benefits and barriers. J. Invest. Medicine Feb;57(2):477-81.

Van, P., Schmid, A., King, N., Kaur, A., Pan, M., Whitehead, K., Koide, T., Facciotti, M.T., Goo, Y. A., Deutsch, E., Reiss, D., Mallick, P., Baliga, N.S. 2008. Halobacterium salinarum NRC-1 PeptideAtlas; towards strategies for target proteomics and improved proteome coverage. Journal of Proteome Research. published online July 25, 2008. PMID: 1865250

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.