Endy:PiP

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(Ty #1: Tools for making systems biology models more scientific)
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===='''<font color="green">FSP #1</font>''': ''Deterministic cell fate selection during phage lambda infection''====
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===Research Manuscripts===
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*Authors: FSP, DE
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*Status: Experiments complete, FSP finalizing figures, DE and FSP drafting revision 
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*<font color="red">Goal</font>: Re-submit before the end of August 2008
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===='''<font color="green">Barry #1</font>''': ''Towards a biological virtual machine: an autoregulating network of RNA polymerases and ribosomes in Escherichia coli'', or equivalent====
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===='''<font color="green">Barry #1</font>''': ''Model-based forward engineering of autocatalytic, self-regulating, and orthogonal gene expression systems in Escherichia coli''====
*Authors: Barry, Drew
*Authors: Barry, Drew
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*Status: RNA work underway, Barry praying for good RNA data, Barry coordinating getting some micrographs and perhaps cytometer data
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*Status: Drew drafting for PNAS
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*Writing: First outline complete and under revision, Figures discussed
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*Writing: On Google Docs
*[[User:Barry Canton/Notebook/T7 RNAP transcription of rRNA | Project page]] & [[Endy:Chassis engineering/Paper|Paper page]].
*[[User:Barry Canton/Notebook/T7 RNAP transcription of rRNA | Project page]] & [[Endy:Chassis engineering/Paper|Paper page]].
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*<font color="red">Goal</font>: Submit by September 15
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*<font color="red">Goal</font>: Submit June 2009
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===='''<font color="green">Jason #1</font>''': ''Measurement kits and reference standards for characterizing BioBrick promoters and ribosome binding sites''====
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*Authors: JK & DE
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*Status: reviews received, JK and DE struggling through standards theory
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*<font color="red">Goal</font>: Resubmit by end of August
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===='''<font color="green">Jason #2</font>''': ''Programmed selection and preferential promotion of disadvantaged bacteria in a microfluidic sortostat,'' or equivalent====
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===='''<font color="green">Jason #2</font>''': ''Programmed selection and preferential promotion of microbes using a selectostat''====
*Authors: JK & DE
*Authors: JK & DE
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*Status: Modeling scope, data analysis and writing needs to be completed
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*Status: Endy drafting for PNAS
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*Main Text on Google Docs
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*Figures
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*Supplement
*[[Endy:Notebook/Sortostat_Paper | OWW Page]]
*[[Endy:Notebook/Sortostat_Paper | OWW Page]]
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*<font color="red">Goal</font>: Submit by end of August
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*<font color="red">Goal</font>: Submit June 2009
===='''<font color="green">Reshma #1</font>''': ''Using genetically encoded odorant reporters to engineer bacteria that smell like wintergreen and banana''====
===='''<font color="green">Reshma #1</font>''': ''Using genetically encoded odorant reporters to engineer bacteria that smell like wintergreen and banana''====
*Authors: RS & DE
*Authors: RS & DE
*Status: reviews received, revision complete, sent to RC3 for his comments
*Status: reviews received, revision complete, sent to RC3 for his comments
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*<font color="red">Goal</font>: Resubmit by end of August
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*<font color="red">Goal</font>: submitted
===='''<font color="green">Reshma #2</font>''': ''Signal levels, load, and error rates in engineered transcriptional devices''====
===='''<font color="green">Reshma #2</font>''': ''Signal levels, load, and error rates in engineered transcriptional devices''====
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*<font color="red">Goal</font>: Submit by end of August
*<font color="red">Goal</font>: Submit by end of August
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==='''<font color="green">Ty #2</font>''': ''Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range''===
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===='''<font color="green">Ty #2</font>''': ''Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range''====
*Authors: TT, DE
*Authors: TT, DE
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*Status: sent to RB and TT for final review and approval
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*Status: Submitted to MSB
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*<font color="red">Goal</font>: Submit by end of August
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*<font color="red">Goal</font>: Get published ASAP.
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==='''<font color="green">Ty #3</font>''': ''Mechanics, Controls, and Modeling of Mating Pheromone-Initiated Signaling in the Yeast Saccharomyces cerevisiae:  A Comprehensive Analysis''===
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===='''<font color="green">Ty #3</font>''': ''Mechanics, Controls, and Modeling of Mating Pheromone-Initiated Signaling in the Yeast Saccharomyces cerevisiae:  A Comprehensive Analysis''====
*Authors: TT, DE
*Authors: TT, DE
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*Status: JT and TT to edit
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*Status: JT and TT to edit (not working well, what should DE do?)
*<font color="red">Goal</font>: Submit by ???
*<font color="red">Goal</font>: Submit by ???
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==='''<font color="green">Sri #1</font>''': ''Measures & models of phage T7 mRNA''===
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===='''<font color="green">Sri #1</font>''': ''Measures & models of phage T7 mRNA''====
*Authors: HK, DE, SK
*Authors: HK, DE, SK
*Status: Sri needs to provide Fig 4, Drew needs to edit
*Status: Sri needs to provide Fig 4, Drew needs to edit
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*<font color="red">Goal</font>: Submit by June 27
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*<font color="red">Goal</font>: Submit by end of August
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==='''<font color="green">Drew #1</font>''': ''A common signal carrier for genetic devices''===
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===='''<font color="green">Drew #1</font>''': ''A common signal carrier for genetic devices''====
*Authors: Austin, Drew, Tom, Randy, Samantha
*Authors: Austin, Drew, Tom, Randy, Samantha
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*Status: DE to rewrite
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*Status: DE to expand and rewrite
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*<font color="red">Goal</font>: Submit by June 27
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*<font color="red">Goal</font>: Submit by end of August
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==='''<font color="green">Drew #2</font>''': ''Free as in phosphoramidites'', or equivalent===
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===='''<font color="green">Drew #2</font>''': ''Free as in phosphoramidites'', or equivalent====
*Authors: DG and DE
*Authors: DG and DE
*Status: DE to write
*Status: DE to write
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*<font color="red">Goal</font>: Submit by June 7
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*<font color="red">Goal</font>: Submit by end of August
===BOOKS===
===BOOKS===
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*'''<font color="green">DE #1</font>''':CoTS
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===='''<font color="green">DE #1</font>''':CoTS====
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**Authors: DE
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*Authors: DE
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**Status: DE outlining
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*Status: DE outlining
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**<font color="red">Goal</font>: ??
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*<font color="red">Goal</font>: Proposal by end of August
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*'''<font color="green">DE #2</font>''':I2SB
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**Authors: DE
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===='''<font color="green">DE #2</font>''':I2SB====
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**Status: DE outlining
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*Authors: DE
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**<font color="red">Goal</font>: ??
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*Status: DE outlining
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*<font color="red">Goal</font>: Outline by end of August
===BLANK===
===BLANK===
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*'''<font color="green">Blank #1</font>''': ''Title,'' or equivalent
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===='''<font color="green">Blank #1</font>''': ''Title,'' or equivalent====
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**Authors: your names here
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*Authors: your names here
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**Status: your names here
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*Status: your names here
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**<font color="red">Goal</font>: Submit by some date
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*<font color="red">Goal</font>: Submit by some date
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Current revision

Home        Lab Members        Research        Notebooks        Publications        Internal        Contact       


This page is for keeping track of the status of papers in the Endy writing queue.


Contents

Research Manuscripts

Barry #1: Model-based forward engineering of autocatalytic, self-regulating, and orthogonal gene expression systems in Escherichia coli

  • Authors: Barry, Drew
  • Status: Drew drafting for PNAS
  • Writing: On Google Docs
  • Project page & Paper page.
  • Goal: Submit June 2009

Jason #2: Programmed selection and preferential promotion of microbes using a selectostat

  • Authors: JK & DE
  • Status: Endy drafting for PNAS
  • Main Text on Google Docs
  • Figures
  • Supplement
  • OWW Page
  • Goal: Submit June 2009

Reshma #1: Using genetically encoded odorant reporters to engineer bacteria that smell like wintergreen and banana

  • Authors: RS & DE
  • Status: reviews received, revision complete, sent to RC3 for his comments
  • Goal: submitted

Reshma #2: Signal levels, load, and error rates in engineered transcriptional devices

  • Authors: RS & DE
  • Status: RS working on figures
  • Goal: Submit by end of August

Samantha #1: Controlling cellular location by engineering phosphorylation

  • Authors: SS & DE
  • Status: In review at PLoS Biology
  • Goal: Have in press in 2008

Samantha #2: Signals and specifications for a family of phosphorylation-dependent devices, or equivalent

  • Authors: SS & DE
  • Status: Outline and structure finalized, SS leading writing
  • Goal: Submit by end of August

Ty #1: Tools for making systems biology models more scientific

  • Authors: TT, DE
  • Status: DE to do final edit, send to RB and TT for final approval
  • Goal: Submit by end of August

Ty #2: Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range

  • Authors: TT, DE
  • Status: Submitted to MSB
  • Goal: Get published ASAP.

Ty #3: Mechanics, Controls, and Modeling of Mating Pheromone-Initiated Signaling in the Yeast Saccharomyces cerevisiae: A Comprehensive Analysis

  • Authors: TT, DE
  • Status: JT and TT to edit (not working well, what should DE do?)
  • Goal: Submit by ???

Sri #1: Measures & models of phage T7 mRNA

  • Authors: HK, DE, SK
  • Status: Sri needs to provide Fig 4, Drew needs to edit
  • Goal: Submit by end of August

Drew #1: A common signal carrier for genetic devices

  • Authors: Austin, Drew, Tom, Randy, Samantha
  • Status: DE to expand and rewrite
  • Goal: Submit by end of August

Drew #2: Free as in phosphoramidites, or equivalent

  • Authors: DG and DE
  • Status: DE to write
  • Goal: Submit by end of August

BOOKS

DE #1:CoTS

  • Authors: DE
  • Status: DE outlining
  • Goal: Proposal by end of August

DE #2:I2SB

  • Authors: DE
  • Status: DE outlining
  • Goal: Outline by end of August

BLANK

Blank #1: Title, or equivalent

  • Authors: your names here
  • Status: your names here
  • Goal: Submit by some date
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