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Marc T. Facciotti, Ph.D. - Publications

Affiliations: 
1997-2002 University of California, Berkeley, Berkeley, CA, United States 
 2003-2007 Institute for Systems Biology, Seattle, WA, United States 
 2008- University of California, Davis, Davis, CA 
Area:
biophysics, systems biology, synthetic biology
Website:
https://bme.ucdavis.edu/people/marc-facciotti
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50 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 Seitzer P, Yao AI, Cisneros A, Facciotti MT. The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances. Microorganisms. 8. PMID 33266086 DOI: 10.3390/microorganisms8121900  0.782
2020 Furrow RE, Kim HG, Abdelrazek SMR, Dahlhausen K, Yao AI, Eisen JA, Goldman MS, Albeck JG, Facciotti MT. Combining Microbial Culturing With Mathematical Modeling in an Introductory Course-Based Undergraduate Research Experience. Frontiers in Microbiology. 11: 581903. PMID 33250873 DOI: 10.3389/fmicb.2020.581903  0.358
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  0.788
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  0.739
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  0.761
2016 Sánchez-Nieves R, Facciotti M, 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.2016.02.005  0.381
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  0.375
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  0.353
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  0.306
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  0.748
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  0.589
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  0.772
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  0.757
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  0.773
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  0.31
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  0.772
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  0.516
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  0.788
2013 Yao AI, Fenton TA, Owsley K, Seitzer P, Larsen DJ, Sit H, Lau J, Nair A, Tantiongloc J, Tagkopoulos I, Facciotti MT. Correction to Promoter Element Arising from the Fusion of Standard BioBrick Parts Acs Synthetic Biology. 2: 351-351. DOI: 10.1021/Sb400031E  0.739
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  0.776
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  0.53
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  0.806
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  0.776
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. DOI: 10.1016/j.procs.2012.04.219  0.748
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  0.534
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  0.759
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  0.62
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  0.633
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  0.548
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  0.615
2008 Johnson MH, Facciotti MT, Reiss DJ, Whitehead K, Schmid A, Kaur A, Pan M, Shannon P, Tenenbaum D, Bonneau R, Baliga NS. QS437. Integrated Biological and Computational Analysis of Important But Largely Under-Studied Organisms Journal of Surgical Research. 144: 441. DOI: 10.1016/J.Jss.2007.12.695  0.56
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  0.667
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  0.67
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  0.549
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  0.66
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  0.522
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  0.708
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  0.685
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  0.565
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  0.677
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  0.615
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 DOI: 10.1016/S0006-3495(03)74490-7  0.562
2003 Kennis JTM, Larsen DS, Ohta K, Facciotti MT, Glaeser RM, Fleming GR. Protein dynamics of bacteriorhodopsin probed by photon echo and transient absorption spectroscopy Springer Series in Chemical Physics. 71: 646-648.  0.442
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  0.515
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  0.523
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  0.513
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  0.523
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 DOI: 10.1016/S0006-3495(00)76854-8  0.495
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  0.455
1998 Facciotti MT, Yuan L. Molecular dissection of the plant acyl-acyl carrier protein thioesterases Lipid - Fett. 100: 167-172. DOI: 10.1002/(Sici)1521-4133(19985)100:4/5<167::Aid-Lipi167>3.0.Co;2-1  0.312
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