Marc Tancredi Facciotti - Publications

Affiliations: 
University of California, Davis, Davis, CA 
 University of California, Berkeley, Berkeley, CA 
Area:
biophysics, systems biology, synthetic biology

63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Rodriguez-Medina J, Kim HG, Castro J, Contreras CM, Glon CL, Goyal A, Guo BY, Knowles S, Lin JC, McGuiness CL, Sorkin E, Stefani J, Yegireddi SJ, Chaganti S, Cui D, ... ... Facciotti MT, et al. Correction for Rodriguez-Medina et al., "Draft Genome Sequences of 16 Halophilic Prokaryotes Isolated from Diverse Environments". Microbiology Resource Announcements. 9. PMID 32273364 DOI: 10.1128/MRA.00239-20  1
2020 Rodriguez-Medina J, Kim HG, Castro J, Contreras CM, Glon CL, Goyal A, Guo BY, Knowles S, Lin JC, McGuiness CL, Sorkin E, Stefani J, Yegireddi SJ, Chaganti S, Cui D, ... ... Facciotti MT, et al. Draft Genome Sequences of 16 Halophilic Prokaryotes Isolated from Diverse Environments. Microbiology Resource Announcements. 9. PMID 32079635 DOI: 10.1128/MRA.01540-19  1
2018 Seitzer P, Jeanniard A, Ma F, Van Etten JL, Facciotti MT, Dunigan DD. Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. Viruses. 10. PMID 30347809 DOI: 10.3390/v10100576  1
2017 Becker EA, Easlon EJ, Potter SC, Guzman-Alvarez A, Spear JM, Facciotti MT, Igo MM, Singer M, Pagliarulo C. The Effects of Practice-Based Training on Graduate Teaching Assistants' Classroom Practices. Cbe Life Sciences Education. 16. PMID 29146664 DOI: 10.1187/cbe.16-05-0162  1
2017 Freund GS, O'Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB. Elucidating Substrate Promiscuity within the FabI Enzyme Family. Acs Chemical Biology. PMID 28820936 DOI: 10.1021/acschembio.7b00400  1
2016 Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KS, Yarov-Yarovoy V, Facciotti MT. A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site. Plos One. 11: e0156543. PMID 27327432 DOI: 10.1371/journal.pone.0156543  1
2016 Sánchez-Nieves R, Facciotti MT, Saavedra-Collado S, Dávila-Santiago L, Rodríguez-Carrero R, Montalvo-Rodríguez R. Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico Genomics Data. 7: 287-9. PMID 26981428 DOI: 10.1016/j.gdata.2016.02.004  1
2016 Sánchez-Nieves R, Facciotti MT, Saavedra-Collado S, Dávila-Santiago L, Rodríguez-Carrero R, Montalvo-Rodríguez R. Draft genome sequence of Halorubrum tropicale strain V5, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico. Genomics Data. 7: 284-6. PMID 26981427 DOI: 10.1016/j.gdata.2016.02.004  1
2015 Rudrappa D, Yao AI, White D, Pavlik BJ, Singh R, Facciotti MT, Blum P. Identification of an Archaeal Mercury Regulon by Chromatin Immunoprecipitation. Microbiology (Reading, England). PMID 26408318 DOI: 10.1099/mic.0.000189  1
2015 Rai N, Ferreiro A, Neckelmann A, Soon A, Yao A, Siegel J, Facciotti MT, Tagkopoulos I. RiboTALE: A modular, inducible system for accurate gene expression control. Scientific Reports. 5: 10658. PMID 26023068 DOI: 10.1038/srep10658  1
2015 Persson T, Battenberg K, Demina IV, Vigil-Stenman T, Vanden Heuvel B, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Cruz Hernandez MA, Mendoza Herrera A, Médigue C, Normand P, Pawlowski K, et al. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant. Plos One. 10: e0127630. PMID 26020781 DOI: 10.1371/journal.pone.0127630  1
2014 Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS. Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. Bmc Systems Biology. 8: 122. PMID 25394904 DOI: 10.1186/s12918-014-0122-2  1
2014 Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. Plos Genetics. 10: e1004784. PMID 25393412 DOI: 10.1371/journal.pgen.1004784  1
2014 Wang T, Oppawsky C, Duan Y, Tittor J, Oesterhelt D, Facciotti MT. Stable closure of the cytoplasmic half-channel is required for efficient proton transport at physiological membrane potentials in the bacteriorhodopsin catalytic cycle. Biochemistry. 53: 2380-90. PMID 24660845 DOI: 10.1021/bi4013808  1
2014 Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environmental Microbiology. 16: 3398-415. PMID 24428801 DOI: 10.1111/1462-2920.12388  1
2013 Warnecke T, Becker EA, Facciotti MT, Nislow C, Lehner B. Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution. Plos Computational Biology. 9: e1003373. PMID 24278010 DOI: 10.1371/journal.pcbi.1003373  1
2013 Facciotti MT. Thermodynamically inspired classifier for molecular phenotypes of health and disease. Proceedings of the National Academy of Sciences of the United States of America. 110: 19181-2. PMID 24204030 DOI: 10.1073/pnas.1317876110  1
2013 Wang T, Facciotti MT, Duan Y. Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin. Plos One. 8: e69882. PMID 23922839 DOI: 10.1371/journal.pone.0069882  1
2013 Gilmore SF, Yao AI, Tietel Z, Kind T, Facciotti MT, Parikh AN. Role of squalene in the organization of monolayers derived from lipid extracts of Halobacterium salinarum. Langmuir : the Acs Journal of Surfaces and Colloids. 29: 7922-30. PMID 23713788 DOI: 10.1021/la401412t  1
2013 Yao AI, Fenton TA, Owsley K, Seitzer P, Larsen DJ, Sit H, Lau J, Nair A, Tantiongloc J, Tagkopoulos I, Facciotti MT. Promoter element arising from the fusion of standard BioBrick parts. Acs Synthetic Biology. 2: 111-20. PMID 23656374 DOI: 10.1021/sb300114d  1
2013 Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, Facciotti MT. Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway Structure. 21: 290-297. PMID 23394942 DOI: 10.1016/j.str.2012.12.018  1
2013 Seitzer P, Huynh TA, Facciotti MT. JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. Bmc Bioinformatics. 14: 18. PMID 23324080 DOI: 10.1186/1471-2105-14-18  1
2012 Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT. A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. Bmc Bioinformatics. 13: 317. PMID 23181585 DOI: 10.1186/1471-2105-13-317  1
2012 Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. Plos One. 7: e42304. PMID 23028432 DOI: 10.1371/journal.pone.0042304  1
2012 Sun C, Alkhoury K, Wang YI, Foster GA, Radecke CE, Tam K, Edwards CM, Facciotti MT, Armstrong EJ, Knowlton AA, Newman JW, Passerini AG, Simon SI. IRF-1 and miRNA126 modulate VCAM-1 expression in response to a high-fat meal. Circulation Research. 111: 1054-64. PMID 22874466 DOI: 10.1161/CIRCRESAHA.112.270314  1
2012 Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. Plos One. 7: e41389. PMID 22848480 DOI: 10.1371/journal.pone.0041389  1
2012 Wilbanks EG, Larsen DJ, Neches RY, Yao AI, Wu CY, Kjolby RA, Facciotti MT. A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. Nucleic Acids Research. 40: e74. PMID 22323522 DOI: 10.1093/nar/gks063  1
2012 Köhler S, Seitzer P, Facciotti MT, Ludäscher B. Improved Motif Detection in Large Sequence Sets with Random Sampling in a Kepler workflow Procedia Computer Science. 9: 1999.  1
2011 Yao AI, Facciotti MT. Regulatory multidimensionality of gas vesicle biogenesis in Halobacterium salinarum NRC-1. Archaea (Vancouver, B.C.). 2011: 716456. PMID 22110395 DOI: 10.1155/2011/716456  1
2011 Darling AE, Tritt A, Eisen JA, Facciotti MT. Mauve assembly metrics. Bioinformatics (Oxford, England). 27: 2756-7. PMID 21810901 DOI: 10.1093/bioinformatics/btr451  1
2010 Wilbanks EG, Facciotti MT. Evaluation of algorithm performance in ChIP-seq peak detection. Plos One. 5: e11471. PMID 20628599 DOI: 10.1371/journal.pone.0011471  1
2010 Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, et al. Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. Bmc Systems Biology. 4: 64. PMID 20470417 DOI: 10.1186/1752-0509-4-64  1
2009 Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS. Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular Systems Biology. 5: 285. PMID 19536208 DOI: 10.1038/msb.2009.42  1
2009 Facciotti MT. Training interdisciplinary scientists for systems biology. Journal of Investigative Medicine : the Official Publication of the American Federation For Clinical Research. 57: 471-3. PMID 19174700 DOI: 10.231/JIM.0b013e31819825e3  1
2009 Benedyk M, Berglund L, Facciotti M, Mobley W, and Zucker D. Strategies for innovation and interdisciplinary translational research: research and career benefits and barriers J. Invest. Medicine. 57: 477-81. PMID 19174698  0.04
2008 Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of Proteome Research. 7: 3755-64. PMID 18652504 DOI: 10.1021/pr800031f  1
2008 Reiss DJ, Facciotti MT, Baliga NS. Model-based deconvolution of genome-wide DNA binding. Bioinformatics (Oxford, England). 24: 396-403. PMID 18056063 DOI: 10.1093/bioinformatics/btm592  1
2008 Larjo A, Lähdesmäki H, Facciotti MT, Baliga NS, Hli-Harja O, Shmulevich I. Active Learning of Bayesian Network Structure in a Realistic Setting Proceedings of the 5th International Workshop On Computational Systems Biology. 85-88.  1
2007 Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, et al. A predictive model for transcriptional control of physiology in a free living cell. Cell. 131: 1354-65. PMID 18160043 DOI: 10.1016/j.cell.2007.10.053  1
2007 Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS. General transcription factor specified global gene regulation in archaea. Proceedings of the National Academy of Sciences of the United States of America. 104: 4630-5. PMID 17360575 DOI: 10.1073/pnas.0611663104  1
2006 Kaur A, Pan M, Meislin M, Facciotti MT, El-Gewely R, Baliga NS. A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Research. 16: 841-54. PMID 16751342 DOI: 10.1101/gr.5189606  1
2006 Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology. 7: R36. PMID 16686963 DOI: 10.1186/gb-2006-7-5-r36  1
2006 Bonneau R, Reiss DJ, Shannon P, Facciotti MT, Hood L, Baliga NS, Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets de novo Genome Biology. 7: R36. PMID 16686963  1
2006 Lunde CS, Rouhani S, Facciotti MT, Glaeser RM. Membrane-protein stability in a phospholipid-based crystallization medium Journal of Structural Biology. 154: 223-231. PMID 16600634 DOI: 10.1016/j.jsb.2006.02.002  1
2004 Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Research. 14: 2221-34. PMID 15520287 DOI: 10.1101/gr.2700304  1
2004 Facciotti MT, Rouhani-Manshadi S, Glaeser RM. Energy transduction in transmembrane ion pumps Trends in Biochemical Sciences. 29: 445-451. PMID 15362229 DOI: 10.1016/j.tibs.2004.06.004  1
2004 Facciotti MT, Rouhani S, Glaeser RM. Crystal structures of bR(D85S) favor a model of bacteriorhodopsin as a hydroxyl-ion pump Febs Letters. 564: 301-306. PMID 15111113 DOI: 10.1016/S0014-5793(04)00208-X  1
2004 Facciotti MT, Cheung VS, Lunde CS, Rouhani S, Baliga NS, Glaeser RM. Specificity of Anion Binding in the Substrate Pocket of Bacteriorhodopsin Biochemistry. 43: 4934-4943. PMID 15109251 DOI: 10.1021/bi035757s  1
2004 Facciotti MT, Bonneau R, Hood L, Baliga NS. Systems biology experimental design - Considerations for building predictive gene regulatory network models for prokaryotic systems Current Genomics. 5: 527-544. DOI: 10.2174/1389202043348850  1
2004 Facciotti MT, Bonneau R, Hood L, Baliga NS. Systems Biology Experimental Design – Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems Current Genomics. 5: 527-544.  1
2003 Facciotti MT, Cheung VS, Nguyen D, Rouhani S, Glaeser RM. Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: Principles of ion pumping Biophysical Journal. 85: 451-458. PMID 12829500  1
2002 Rouhani S, Facciotti MT, Woodcock G, Cheung V, Cunningham C, Nguyen D, Rad B, Lin CT, Lunde CS, Glaeser RM. Crystallization of membrane proteins from media composed of connected-bilayer gels Biopolymers - Peptide Science Section. 66: 300-316. PMID 12539259 DOI: 10.1002/bip.10310  1
2002 Kennis JTM, Larsen DS, Ohta K, Facciotti MT, Glaeser RM, Fleming GR. Ultrafast protein dynamics of bacteriorhodopsin probed by photon echo and transient absorption spectroscopy Journal of Physical Chemistry B. 106: 6067-6080. DOI: 10.1021/jp014681b  1
2002 Kennis JTM, Larsen DS, Ohta K, Facciotti MT, Glaeser RM, Fleming GR. Ultrafast protein dynamics of bacteriorhodopsin probed by photon echo and transient absorption spectroscopy Journal of Physical Chemistry B. 106: 6067-6080.  1
2001 Facciotti MT, Rouhani S, Burkard FT, Betancourt FM, Downing KH, Rose RB, McDermott G, Glaeser RM. Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle. Biophysical Journal. 81: 3442-55. PMID 11721006 DOI: 10.1016/S0006-3495(01)75976-0  1
2001 Facciotti MT, Rouhani S, Burkard FT, Betancourt FM, Downing KH, Rose RB, McDermott G, Glaeser RM. Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle Biophysical Journal. 81: 3442-3455. PMID 11721006  1
2001 Rouhani S, Cartailler JP, Facciotti MT, Walian P, Needleman R, Lanyi JK, Glaeser RM, Luecke H. Crystal structure of the D85S mutant of bacteriorhodopsin: Model of an O-like photocycle intermediate Journal of Molecular Biology. 313: 615-628. PMID 11676543 DOI: 10.1006/jmbi.2001.5066  1
2001 Rouhani S, Cartailler J-P, Facciotti MT, Walian P, Needleman R, Lanyi JK, Glaeser RM, Luecke H. Crystal structure of the D85S mutant of bacteriorhodopsin: Model of an O-like photocycle intermediate Journal of Molecular Biology. 313: 615-628. PMID 11676543  1
2000 Glaeser R, Facciotti MT, Walian P, Rouhani S, Holton J, MacDowell A, Celestre R, Cambie D, Padmore H. Characterization of conditions required for X-ray diffraction experiments with protein microcrystals Biophysical Journal. 3178-3185. PMID 10827994  1
2000 Glaeser R, Facciotti M, Walian P, Rouhani S, Holton J, MacDowell A, Celestre R, Cambie D, Padmore H. Characterization of conditions required for x-ray diffraction experiments with protein microcrystals Biophysical Journal. 78: 3178-3185. PMID 10827994  1
1999 Facciotti MT, Bertain PB, Yuan L. Improved stearate phenotype in transgenic canola expressing a modified acyl-acyl carrier protein thioesterase. Nature Biotechnology. 17: 593-7. PMID 10385326 DOI: 10.1038/9909  1
1999 Facciotti MT, Bertain PB, and Yuan L. Improved stearate phenotype in transgenic canola expressing a modified acyl-acyl carrier protein thioesterase Nature Biotechnology. 17: 593-597. PMID 10385326  1
1998 Facciotti MT, Yuan, L. Molecular dissection of the plant acyl-acyl carrier protein thioesterases Fett Lipid. 100: 167-172.  0.01
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