Endy:PiP

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

WRITING

• Barry #1: A virtual machine for synthetic biology, or equivalent
  • Authors: Barry, Drew
  • Status: BC to discuss w/ various folks and propose scope of remaining work
  • Goal: Submit before the end of August 2008

• Jason #1: Measurement kits and reference standards for characterizing BioBrick promoters and ribosome binding sites
  • Authors: JK & DE
  • Status: submitted, awaiting comments and editorial decision
  • Goal: Accepted by June 27

• Jason #2: Programmed selection and preferential promotion of disadvantaged bacteria, or equivalent
  • Authors: JK & DE
  • Status: JK to propose scope of modeling work
  • Goal: Submit by June 27

• Reshma #1: A synthetic biology approach to reprogramming bacterial odor
  • Authors: RS & DE
  • Status: submitted, awaiting comments and editorial decision
  • Goal: Accepted by June 27, or revision underway

• Reshma #2: Signal levels, load, and error rates in engineered transcriptional devices
  • Authors: RS & DE
  • Status: RS to draft a first paragraph-level outline from most recent discussions with DE
  • Goal: Submit by June 27

• Samantha #1: Engineering phosphorylation-dependent post-translational protein devices
  • Authors: SS & DE
  • Status: SS and DE to discuss response to PLoS editors
  • Goal: Resubmit by June 4

• Samantha #2: Signals and specifications for a family of phosphorylation-dependent devices, or equivalent
  • Authors: SS & DE
  • Status: SS to draft paragraph level outline, pending resubmission of SS#1
  • Goal: Submit by June 27

• Ty #1: Tools for making systems biology models more scientific
  • Authors: TT, DE
  • Status: DE to edit, send to Roger for his comments, then to Ty, then final edits and submit
  • Goal: Submit by June 13

• Ty #2: Measurement and analysis of protein abundances suggests tradeoff between signaling system output and dynamic range
  • Authors: TT, DE
  • Status: DE to edit, send to Roger for his comments, then to Ty, then final edits and submit
  • Goal: Submit by June 13

• Ty #3: Mechanics, controls, and models of yeast mating response
  • Authors: TT, DE
  • Status: JT and TT to edit
  • Goal: Submit by June 27

• 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 June 27

• Drew #1: A Common Signal Carrier for Genetic Devices
  • Authors: Austin, Drew, Tom, Randy, Samantha
  • Status: DE to review
  • Goal: Submit by June 27

RESEARCH CONCLUDING

1. Deterministic cell fate selection during phage lambda infection
   • Francois,Drew
   • Status: FSP leading experiments
     • Bonus: consider what to do with right operator model paper

1. An engineered post-translational device
   • Samantha, Drew
   • Samantha finishing microscopy, gels; revising draft
2. Eau d'E.coli
   • iGEM 06
   • Status: Stephen drafting and finishing bananas characterization
3. PoPS toolkit
   • Jason and UROP army
   • Status: experiments completing, awaiting outline
4. Zinc-Finger Logic Gates
   • RS, TK, DE
   • Status: experiments completing, awaiting outline
5. M13.1
   • FM, BH, NK, DE
   • Status: awaiting synthetic DNA to test. Confirm completion of point mutants
6. Low abundance of Ste5 scaffold protein
   • KRB, TMT, ..., DE, RB
   • Status: TMT finishing modeling work, RY varying Ste5 abundances. Manuscript needs to be updated.

• Blank #1: Title, or equivalent
  • Authors: your names here
  • Status: your names here
  • Goal: Submit by some date

BOOKS

1. CoTS
   • Drew
   • Status: outlining
2. I2SB
   • Drew
   • Status: outlining