refs.bib

@article{	gibson09,
			Author="Gibson, Daniel G and Young, Lei and Chuang, Ray-Yuan and Venter, J Craig and Hutchison III, Clyde A and Smith, Hamilton O",
			Title="Enzymatic assembly of {DNA} molecules up to several hundred kilobases",
			Journal="Nature Methods",
			Volume="6",
			Year="2009",
			doi={10.1038/nmeth.1318}
}
			Pages="343-345",

@article{	venter10,
			Author="Gibson, Daniel G and Glass, John I and Lartigue, Carole and Noskov, Vladimir N and Chuang, Ray-Yuan and Algire, Mikkel A and Benders, Gwynedd A and Montague, Michael G and Ma, Li and Moodie, Monzia M and Merryman, Chuck and Vashee, Sanjay and Krishnakumar, Radha and Assad-Garcia, Nacyra and Segall-Shapiro, Thomas H and Calvey, Christopher H and Parmar, Prashanth P and Hutchison III, Clyde A and Smith, Hamilton O and Venter, J Craig",
			Title="Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome",
			Journal="Science",
			Volume="329",
			Number="5987",
			Year="2010",
			doi={10.1126/science.1190719}
}
			Pages="52-56",

@misc{rfc57,
  author="Collins, Bill and Copley, Hannah and Emmrich, Peter and Handley, Will and Hohmann, Anja and Knott, Emily and Masset, Paul and Reeve, Ben and Sanderson, Theo",
  title="{Assembly of BioBricks by the Gibson
Method}",
  series="Request for Comments",
  number="57",
  howpublished="RFC 57",
  publisher="BBF",
  organization="BioBrick Foundation",
  year=2010,
  month=oct,
  url="http://www.cambridgeigem.org/RFC57.pdf",
}

@article{canny,
	Author="Canny, John",
	Title="A computational approach to edge detection",
	Journal="IEEE Transactions on Pattern Analysis and Machine Intelligence",
	Volume="8",
	Year="1986",
	Month=nov,
	doi={10.1109/TPAMI.1986.4767851}
}
	Pages="679-698",

@article{berg84,
	Author="Berg, Howard C and Block, Steven M",
	Title="A Miniature Flow Cell Designed for Rapid Exchange of Media Under 
High-power Microscope Objectives",
	Journal="Journal of  General Microbiology",
	Volume="130",
	Year="1984",
	Month=may,
	doi={10.1099/00221287-130-11-2915}
}
	Pages="2915-2920",

@article{tsien98,
	Author="Tsien, Roger Y",
	Title="The Green Fluorescent Protein",
	Journal="Annual Review of Biochemistry",
	Volume="67",
	Year="1998",
	Month=jul,
	doi={10.1146/annurev.biochem.67.1.509}
}	
	Pages="509-544",


@article{nagai02,
	Author="Nagai, Takeharu and Ibata, Keiji and Park, Eun Sun and Kubota, Mei and Mikoshiba, Katsuhiko and Miyawaki, Atsushi",
	Title="A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications",
	Journal="Nature Biotechnology",
	Volume="20",
	Year="2002",
	Month=jan,
	doi={doi:10.1038/nbt0102-87}
}	
	Pages="87-90",


@article{vaknin07,
	Author="Vaknin, Andy and Berg, Howard C",
	Title="Physical Responses of Bacterial Chemoreceptors",
	Journal="Journal of Molecular Biology",
	Volume="366",
	Number="5",
	Year="2007",
	Month=mar,
	doi={10.1016/j.jmb.2006.12.024}
}
	Pages="1416-1423",

@article{hamadeh11,
	Author="Hamadeh, Abdullah and Roberts, Mark A J and Augus, Elias and McSharry, Patrick E and Maini, Philip K and Armitage, Judith P and Papachristodoulou, Antonis",
	Title="Feedback Control Architecture and the Bacterial Chemotaxis Network",
	Journal="PLoS Computational Biology",
	Volume="7",
	Number="5",
	Year="2011",
	Month=may,
	doi={10.1371/journal.pcbi.1001130}
}

@article{li04,
	Author="Li, Mingshan and Hazelbauer, Gerald L",
	Title="Cellular Stoichiometry of the Components of the Chemotaxis Signaling Complex",
	Journal="Journal of Bacteriology",
	Volume="168",
	Number="12",
	Year="2004",
	Month=jun,
	doi="10.1128/JB.186.12.3687-3694.2004"
}

@article{stock89,
	Author="Stock, Ann M and Mottonen, James M and Stock, Jeffry B and Schutt, Clarence E",
	Title="Three-dimensional structure of CheY, the response regulator of bacterial chemotaxis",
	Journal="Nature",
	Volume="337",
	Year="1989",
	Month=feb,
	doi="10.1038/337745a0"
}
	Pages="745-749",

@article{milligan87,
	Author="Miligan, Daniel L and Koshland Jr, Daniel E",
	Title="Site-directed Cross-linking: Establishing The Dimeric Structure Of The Aspartate Receptor Of Bacterial Chemotaxis",
	Journal="The Journal Of Biological Chemistry",
	Volume="263",
	Number="13",
	Pages="6268-6275",
	Year="1987",
	Month=may
}

@article{yi00,
	Author="Yi, Tau-Mu and Huang, Yun and Simon, Melvin I and Doyle, John",
	Title="Robust perfect adaptation in bacterial chemotaxis through integral feedback control",
	Journal="PNAS",
	Volume="97",
	Number="9",
	Year="2000",
	Month=apr,
	doi="10.1073/pnas.97.9.4649"
}
	Pages="4649-4653",

@article{lipkow06,
	Author="Lipkow, Karen",
	Title="Changing Cellular Location of CheZ Predicted by Molecular Simulations",
	Journal="PLoS Computational Biology",
	Volume="2",
	Number="4",
	Year="2006",
	Month=apr,
	doi={10.1371/journal.pcbi.0020039}
}	

Pages="301-310",


@article{greenfield09,
	Author="Greenfield, Derek and McEvoy, Ann L and Shroff, Hari and Crooks, Gavin E and Wingreen, Ned S and Betzig, Eric and Liphardt, Jan",
	Title="Self-Organization of the \ecolilong Chemotaxis Network Imaged with Super-Resolution Light Microscopy",
	Journal="PLoS Biology",
	Volume="7",
	Number="6",
	Year="2009",
	Month=jun,
	doi={10.1371/journal.pbio.1000137}
}

@article{hall11,
	Author="Hall, Benjamin A and Armitage, Judith P and Sansom, Mark S P",
	Title="Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling",
	Journal="PLoS Computational Biology",
	Volume="7",
	Number="10",
	Year="2011",
	Month=oct,
	doi={10.1371/journal.pcbi.1002204}
}

@article{kentner09,
	Author="Kentner, David and Sourjik, Victor",
	Title="Dynamic map of protein interactions in the \ecolilong chemotaxis pathway",
	Journal="Molecular Systems Biology",
	Volume="5",
	Number="238",
	Year="2009",
	doi={10.1038/msb.2008.77}
}

@article{wright06,
	Author="Wright, Stuart and Walia, Bharat and Parkinson, John S and Khan, Shahid",
	Title="Differential Activation of \ecolilong Chemoreceptors by Blue-Light Stimuli",
	Journal="Journal of Bacteriology",
	Volume="188",
	Number="11",
	Year="2006",
	Month=jun,
	doi={10.1128/JB.00149-06}
}	Pages="3962-3971",

@article{rittweger09,
	Author="Rittweger, Eva and Han, Kyu Young and Irvine, Scott E and Eggeling, Christian and Hell, Stefan W",
	Title="{S}{T}{E}{D} microscopy reveals crystal colour centres
with nanometric resolution",
	Journal="Nature Photonics",
	Volume="3",
	Year="2009",
	Month=mar,
	doi={10.1038/nphoton.2009.2}
}


@book{lakowicz,
	Author="Lakowicz, Joseph R",
	Title="Principles of Fluorescence Spectroscopy",
	Year="1999",
	Publisher="Springer",
	ISBN={978-0387312781}
}

@book{transform,
	Author="Sambrook, Joseph and Fritsch, E F and Maniatis, Tom",
	Title="Molecular Cloning: A Laboratory Manual",
	Year="1987",
	Publisher="Cold Spring Harbor Laboratory Press",
	ISBN={978-0879693091}
}
@article{micromanager,
	Author="Edelstein, Arthur and Amodaj, Nenad and Hoover, Karl and Vale, Ron and Stuurman, Nico",
	Title="Computer Control of Microscopes Using $\mu$Manager", 
	Journal="Current Protocols in Molecular Biology", 
	Year="2010",
	doi={10.10002/0471142727.mb1420s92}
}

@article{lipkowfigs,
	Author="Sewitz, Sven and Lipkow, Karen",
	Title="Simulating the bacterial chemotaxis pathway at high spatio-temporal detail",
	Journal="Current Chemical Biology",
	Year="2012",
	Note="In press"
}

@article{lipkow05,
	Author="Lipkow, Karen and Andrews, Steven S and Bray, Dennis",
	Journal="Journal of Bacteriology",
	Title={Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of \ecolilong},
	Year="2005",
	doi={10.1128/​JB.187.1.45-53.2005}
}

@article{zhou02,
	Author="Zhao, Rui and Collins, Edward J and Bourret, Robert B and Silversmith, Ruth E",
	Title={Structure and catalytic mechanism of the \ecoli chemotaxis phosphatase CheZ},
	Journal="Nature Structural Biology",
	Year="2002",
	doi={10.1038/nsb816}
}

@misc{jackson,
	Author="{Jackson ImmunoResearch}",
	Title="Recipe for Anti-fade Mounting Medium",
	Month="June",
	Year="2012",
	url={http://www.jacksonimmuno.com/technical/anti-fade.asp}
}

@misc{boiling,
	Author="Summers, Michael L",
	Title="\ecoli Boiling Lysis Plasmid Preparation",
	Year="2012",
	Month="June",
	url={http://www.csun.edu/~mls42367/Protocols/B_lysis_plas_prep.pdf}
}

@article{sourjik10,
	Author="Sourjik, Victor and Armitage, Judith P",
	Title="Spatial Organisation in Bacterial Chemotaxis",
	Journal="The EMBO Journal",
	Year="2010",
	Volume="29",
	doi={10:1038/emboj.2010.178}
}

@article{wadhams04,
	Author="Wadhams, George H and Armitage, Judith P",
	Title="Making sense of it all: bacterial chemotaxis",
	Journal="Nature Reviews Molecular Cell Biology",
	Year="2004",
	Volume="5",
	doi={10.1038/nrm1524}
}

@article{bray93,
	Author="Bray, Dennis and Bourret, Robert B and Simon, Melvin I",
	Title="Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis",
	Journal="Molecular Biology of th Cell",
	Year="1993",
	Volume="4",
	Number="5",
	Pages="469-482"
}

@article{miller10,
	Author="Miller, Jameson and Parker, Miles and Bourret, Robert B and Giddings, Morgan C",
	Title="An Agent-Based Model of Signal Transduction in Bacterial Chemotaxis",
	Journal="PLoS One",
	Year="2010",
	doi={10.1371/journal.pone.0009454}
}

@article{stock85,
	Author="Stock, Jeff and Kersulis, Greg and Koshland, Donald E",
	Title="Neither methylating nor demethylating enzymes are required for bacterial chemotaxis",
	Journal="Cell",
	Volume="42",
	Number="2",
	Year="1985",
	doi={10.1016/0092-8674(85)90125-4}
}

@article{blat98,
	Author="Blat, Yuval and Gillespie, Blake and Bren, Anat and Dahlquist, Frederick W and Eisenbach, Michael",
	Title="Regulation of phosphatase activity in bacterial chemotaxis",
	Journal="Journal of Molecular Biology",
	Volume="284",
	Number="4",
	Year="1998",
	doi={10.1006/jmbi.1998.2224}
}

@article{blat95,
	Author="Blat, Yuval and Eisenbach, Michael",
	Title="Oligomerization of the Phosphatase CheZ Upon Interaction with the Phosphorylated Form of CheY",
	Journal="Journal of Biological Chemistry",
	Volume="271",
	Number="2",
	Year="1995",
	doi={10.1074/jbc.271.2.1226}
}

@article{akrap11,
	Author="Akrap, Nina and Seidel, Thorsten and Barisas, B George",
	Title={F\"{o}rster distances for FRET between mCherry and other Visible Fluorescent Proteins},
	Year="2011",
	Journal="Anal Biochem",
	Volume="402",
	Number="1",
	doi={10.1016/j.ab.2010.03.026}
}

@article{sourjik00,
	Author="Sourjik, Victor and Berg, Howard C",
	Title="Localization of components of the chemotaxis machinery of \ecolilong using fluorescent protein fusions",
	Year="2000",
	Journal="Molecular Microbiology",
	Volume="37",
	Number="4",
	doi={10.1046/j.1365-2958.2000.02044.x}
}