In Press | Submitted | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 Undergraduate/High School Contributions - Bolded and Italicized Below
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| Submitted |
| Warnecke, T., Becker, E.A., Facciotti, M.T., Nislow, C. and Lehner, B. Nucleosome positions in eukaryotes and archaea primarily reflect rather than affect sequence evolution. |
| Wang, T., Facciotti, M.T. and Duan, Y. Schiff Base Switch II Precedes the Retinal Thermal Isomerization in the Photocycle of Bacteriorhodopsin. |
| Gilmore, S.F., Facciotti, M.T., Yao, A.I., Parikh, A.N. The role of squalene in the formation and organization of membrane domains of H. salinarum. |
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| 2013 |
| Wang, T., Sessions, A.O., Lunde, C.S., Rouhani, S., Glaeser, R.M., Duan, Y., and Facciotti, M.T. Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway. Structure. 21. 290-7. PMID:23394942. |
| Seitzer, P., Huynh, T. A., & Facciotti, M. T. (2013). JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. BMC Bioinformatics. 14(1). 18. doi:10.1186/1471-2105-14-18. PMID:23324080. |
| Yao, A.I., Fenton, T.A., Owsley, K., Seitzer, P., Larsen, D.J., Sit, H., Lau, J., Nair, A., Tantiongloc, J., Tagkopoulos, I., Facciotti, M.T. (2013). Promoter activity arising from the fusion of standard BioBrick™ parts. ACS Synthetic Biology. doi: 10.1021/sb300114d. 2(2), 111-120. Web Pub. |
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| 2012 |
| Köhler, S, Seitzer P, Facciotti M.T., & Ludäscher B. 2012. Improved Motif Detection in Large Sequence Sets with Random Sampling in a Kepler workflow. Procedia Computer Science. 9. 1999. |
| Seitzer P., Larsen D.J. Wilbanks E.G., and Facciotti M.T. A Monte Carlo-based framework to enhance the discovery and interpretation of regulatory sequence motifs. BMC Bioinformatics. 13(11). doi:10.1186. PMID: 23181585 |
| Tritt, A., Eisen, J.A., Facciotti, M.T. and Darling, A.E. 2012. A user-friendly pipeline for de novo assembly of microbial genomes. PLoS One. Sept 13. 7(9): e42304. PMID: 23028432 |
| Sun C., Alkhoury K., Wang Y.I., Foster G.A., Radecke C.E., Tam K., Edwards C.M., Facciotti M.T., Armstrong E.J., Knowlton A.A, Newman J.W., Passerini A.G., and Simon S.I. 2012. IRF-1 and miRNA126 modulate inflammatory VCAM-1 expression in response to a high fat meal. Circulation Research. Aug 8. PMID: 22874466 |
| Lynch, E.A., Langille, M.G.I, Darling, A.E., Wilbanks, E.G., Haitliner, C., Shao, K.S.Y., Starr, M.O., Teilling, C., Harkins, T., Edwards, R., Eisen, J.A., and Facciotti, M.T. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS One. Jul 24. PMID: 22848480. |
| Wilbanks, E.G., Larsen, D.J., Neches, R.Y.,Yao, A.I., Wu, C, Kjolby, R.S. and Facciotti, M.T. 2012. A workflow for genome-wide mapping of archaeal transcription factors with ChIP-Seq. Nucleic Acids Research. Feb 9. PMID: 22323522. |
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| 2011 |
| Yao A.I. and Facciotti M.T. Regulatory Multidimensionality of Gas Vesicle Biogenesis in Halobacterium salinarum NRC-1. 2011. Archaea. vol. 2011. Article ID 716456. Aug 7. PMID: 2022110395. |
| Darling A., Tritt A., Eisen J.A., and Facciotti M.T. 2011. Mauve Assembly Metrics. Bioinformatics. Aug 2. PMID: 21810901. |
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| 2010 |
| Wilbanks E.G., Facciotti M.T. 2010. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One. Jul;5(7):e11471 PMID:20628599 |
| 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. 2010. Large scale physiological readjustment during growth in a simple batch culture. BMC Systems Biology. May;14(4):64 PMID:20470417 |
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| 2009 |
| 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. 2009. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol. Syst. Biology. Jun;5:285 PMID:19536208 |
| Facciotti M.T. 2009. Training interdisciplinary scientists for systems biology. J. Invest. Medicine Feb;57(2):471-3 PMID:19174700 |
| 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. PMID:19174698 |
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| 2008 |
| 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 |
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| 2007 |
| 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 |
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| 2006 |
| 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 |
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| 2004 |
| 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 |
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| 2003 |
| 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 |
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| 2002 |
| 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. |
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| 2001 |
| 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 |
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| 2000 |
| 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 |
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| 1999 |
| 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 |
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| 1998 |
| Facciotti, M.T. and Yuan, L. 1998. Molecular dissection of the plant acyl-acyl carrier protein thioesterases. FETT Lipid. 100:4-5. 167-172. |
