{"id":17,"date":"2013-02-26T20:32:40","date_gmt":"2013-02-26T20:32:40","guid":{"rendered":"http:\/\/faculty.engineering.ucdavis.edu\/template\/?page_id=17"},"modified":"2014-08-26T21:43:43","modified_gmt":"2014-08-26T21:43:43","slug":"publications","status":"publish","type":"page","link":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Facciotti M.T.<\/strong>, 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.<\/p>\n

Koide, T., Reiss, D.J., Bare, C.J.,\u00a0Facciotti, M.T.<\/strong>, 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.<\/p>\n

Facciotti M.T. 2009.<\/strong>\u00a0Training interdisciplinary scientists for systems biology. J. Invest. Medicine Feb;57(2):471-3<\/p>\n

Benedyk M, Berglund L,\u00a0Facciotti M<\/strong>, 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.<\/p>\n

Van, P., Schmid, A., King, N., Kaur, A., Pan, M., Whitehead, K., Koide, T.,\u00a0Facciotti, M.T.<\/strong>, 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<\/p>\n

Bonneau, R.,\u00a0Facciotti, M.T.<\/strong>, 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.\u00a0 PMID: 18160043<\/p>\n

Reiss, D.J.,\u00a0Facciotti M.T.<\/strong>, and Baliga, N.S. 2007. Model-based deconvolution of genome-wide DNA binding. Bioinformatics. PMID: 18056063<\/p>\n

Facciotti, M.T.<\/strong>, Reiss, D.J., Pan, M., Kaur, A., Vuthoori, M., Bonneau, R., Shannon, P., Srivastava, A., Donahoe, S.M., Hood, L., and Baliga, N.S.\u00a0 2007.\u00a0 Structure of a general transcription factor specified global gene regulatory network.\u00a0 PNAS. 104(11). 4630-4635.PMID: 117360575<\/p>\n

Kaur, A., Pan, M., Meislin, M.,\u00a0Facciotti, M.T.<\/strong>, El-Geweley, R. and Baliga, N.S.\u00a0 2006.\u00a0 A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Research. 16(7).\u00a0 841-854. PMID: 16751342<\/p>\n

Bonneau, R., Reiss, D.J., Shannon, P.\u00a0Facciotti, M.T.<\/strong>, Hood, L. Baliga, N.S., and Thorsson, V.\u00a0 2006.\u00a0 The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets de novo.\u00a0 Genome Biology. 7(6).\u00a0 R36. PMID: 16686963<\/p>\n

Lunde, C.S., Rouhani, S.,\u00a0Facciotti, M.T.<\/strong>, and Glaeser, R.M.\u00a0 2006. Membrane-Protein Stability in a Phospholipid-based Crystallization Medium.\u00a0 Journal of Structural Biology. 154(3). 223-231. PMID: 16600634<\/p>\n

Facciotti, M.T.<\/strong>, Bonneau, R., Hood, L., and Baliga, N.S.\u00a0 2004.\u00a0 Systems Biology Experimental Design \u2013 Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems.\u00a0 Current Genomics. 5(7).\u00a0 527-544.<\/p>\n

Baliga, N.S., Bonneau, R.\u00a0Facciotti, M.T.<\/strong>, 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.\u00a0 2004.\u00a0 Genome sequence of Haloarcula marismortui:\u00a0 A halophilic archaeon from the Dead Sea.\u00a0 Genome Research. 14(11).\u00a0 2221-2234. PMID: 15520287<\/p>\n

Facciotti, M.T.<\/strong>, Rouhani, S. and Glaeser, R.M.\u00a0 2004.\u00a0 Energy transduction in transmembrane ion pumps.\u00a0 Trends in Biochemical Sciences. 29(8). 445-451. PMID: 15362229<\/p>\n

Facciotti, M.T.<\/strong>, Rouhani, S. and Glaeser, R.M.\u00a0 2004.\u00a0 Crystal structures of bR(D85S) favor a model of bacteriorhodopsin as an hydroxyl-ion pump.\u00a0 FEBS Letters. 564(3). 301-306.PMID: 15111113<\/p>\n

Facciotti, M.T.<\/strong>, Cheung, V., Lunde, C.S., Rouhani, S., Baliga, N., and Glaeser, R.M.\u00a0 2004. Specificity of anion-binding in the substrate-pocket of bacteriorhodopsin.\u00a0 Biochemistry.43(17).\u00a0 4934-4943. PMID: 15109251<\/p>\n","protected":false},"excerpt":{"rendered":"

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, \u2026 Continue reading → <\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"template-twocolumns-left.php","meta":{"inline_featured_image":false,"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-17","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/pages\/17","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/comments?post=17"}],"version-history":[{"count":9,"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/pages\/17\/revisions"}],"predecessor-version":[{"id":255,"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/pages\/17\/revisions\/255"}],"wp:attachment":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/facciotti\/wp-json\/wp\/v2\/media?parent=17"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}