Difference between revisions of "CH391L/S14/KeyPapers"

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(→‎This is a list of the key papers for the semester.)
(→‎This is a list of the key papers for the semester.)
 
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This will be updated throughout the semester to record the papers discussed and to provide a quick reference source for anyone looking back on the class.
 
This will be updated throughout the semester to record the papers discussed and to provide a quick reference source for anyone looking back on the class.
  
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+
===For Week III, February 3rd 2014===
 
*'''iGEM registry/parts:''' <biblio> Knight2003 T. Knight, “Idempotent Vector Design for Standard Assembly of Biobricks” (MIT, Cambridge, MA, 2003). </biblio>  
 
*'''iGEM registry/parts:''' <biblio> Knight2003 T. Knight, “Idempotent Vector Design for Standard Assembly of Biobricks” (MIT, Cambridge, MA, 2003). </biblio>  
 
*'''BioBricks:''' <biblio>#Endy2008 pmid=18612302</biblio>
 
*'''BioBricks:''' <biblio>#Endy2008 pmid=18612302</biblio>
 
*'''CAD systems:'''<biblio>#Sauro2009 pmid=19874625</biblio>
 
*'''CAD systems:'''<biblio>#Sauro2009 pmid=19874625</biblio>
 +
 +
 +
===For Week IV, February 10th 2014===
 
*'''Gibson assembly:'''<biblio>#Smith2009 pmid=19363495</biblio>
 
*'''Gibson assembly:'''<biblio>#Smith2009 pmid=19363495</biblio>
 
*'''Genome synthesis:'''<biblio>#Venter2010 pmid=20488990</biblio>
 
*'''Genome synthesis:'''<biblio>#Venter2010 pmid=20488990</biblio>
  
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 +
===For Week V, February 17th 2014===
 
*'''GFP  and    Ancestral Sequence Reconstruction:''' [combined for time and similarity] <biblio>#Matz2010 pmid=19793832</biblio>
 
*'''GFP  and    Ancestral Sequence Reconstruction:''' [combined for time and similarity] <biblio>#Matz2010 pmid=19793832</biblio>
  
  
 +
===For Week VI, February 24th 2014===
 
*'''Link to [http://www.tinkercell.com/downloads-2  Tinker Cell]'''
 
*'''Link to [http://www.tinkercell.com/downloads-2  Tinker Cell]'''
  
  
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===For Week VII, March 3rd 2014===
 
*'''Directed Protein Evolution:''' <biblio>#Liu2011 pmid=21478873</biblio>
 
*'''Directed Protein Evolution:''' <biblio>#Liu2011 pmid=21478873</biblio>
  
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*'''[http://www.synbiocyc.org/wiki/index.php/CH391L/S14/NucleicAcidsRiboswitches Reading for riboswitches (read before class on March 3rd)]'''
 
*'''[http://www.synbiocyc.org/wiki/index.php/CH391L/S14/NucleicAcidsRiboswitches Reading for riboswitches (read before class on March 3rd)]'''
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 +
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===For Week VIII, March 17th 2014===
 +
*'''Non-canonical Nucleotides:'''<biblio>#Benner2006 pmid=17074747</biblio>
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 +
*'''Stochastic Gene Expression:'''<biblio>#Swain2002 pmid=12183631</biblio>
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 +
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===For Week IX, March 24th 2014===
 +
*'''Motility and Taxis'''<biblio>#Voigt2006 pmid=16330045</biblio>
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*'''Optogenetics''' - Review article<biblio>#LaLumiere2011 pmid=21255749</biblio>
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*'''Quorum Sensing'''<biblio>#March2010 pmid=20534565</biblio>
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===For Week X, March 31st 2014===
 +
*'''Cell Counting and Memory'''<biblio>#Collins2009 pmid=19478183</biblio>
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*'''Oscillations'''<biblio>#Hasty2008 pmid=18971928</biblio>
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===For Week XI, April 7th 2014===
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*'''MAGE'''<biblio>#Church2011 pmid=21764749</biblio>
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*'''CRISPR'''<biblio>#Church2013 pmid=23287722</biblio>
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*'''GMO article from the NY Times.'''  Read the entirety of this article.  We will have a discussion relating to this and other GMO topics in class [http://www.nytimes.com/2014/01/05/us/on-hawaii-a-lonely-quest-for-facts-about-gmos.html?_r=1]
 +
 +
 +
*'''Amber-less E. coli [Led by Mike Hammerling.  Look over the paper, but you do not need to understand everything'''<biblio>#Isaacs2013 pmid=24136966</biblio>
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===For Week XII, April 14th 2014===
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*'''small RNAs'''<biblio>#Lee2013 pmid=23334451</biblio>
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===For Week XIII, April 21st 2014===
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*'''Bioremediation'''<biblio>#Apte2013 pmid=24140537</biblio>
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RECENT NATURE issue:  [http://http://www.nature.com/nature/research/research_by_type.html Synthetic Biology articles and news]
 +
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Recent Nature Biotech article on CRISPR: [http://www.nature.com/nbt/journal/v32/n4/full/nbt.2879.html?WT.ec_id=NBT-201404 GENOME engineering]

Latest revision as of 13:36, 16 April 2014

Contents

This is a list of the key papers for the semester.

This will be updated throughout the semester to record the papers discussed and to provide a quick reference source for anyone looking back on the class.

For Week III, February 3rd 2014

  • iGEM registry/parts:
    1. T. Knight, “Idempotent Vector Design for Standard Assembly of Biobricks” (MIT, Cambridge, MA, 2003). [Knight2003]
  • BioBricks:
    Error fetching PMID 18612302:
    1. Error fetching PMID 18612302: [Endy2008]
  • CAD systems:
    Error fetching PMID 19874625:
    1. Error fetching PMID 19874625: [Sauro2009]


For Week IV, February 10th 2014

  • Gibson assembly:
    Error fetching PMID 19363495:
    1. Error fetching PMID 19363495: [Smith2009]
  • Genome synthesis:
    Error fetching PMID 20488990:
    1. Error fetching PMID 20488990: [Venter2010]


For Week V, February 17th 2014

  • GFP and Ancestral Sequence Reconstruction: [combined for time and similarity]
    Error fetching PMID 19793832:
    1. Error fetching PMID 19793832: [Matz2010]


For Week VI, February 24th 2014


For Week VII, March 3rd 2014

  • Directed Protein Evolution:
    Error fetching PMID 21478873:
    1. Error fetching PMID 21478873: [Liu2011]
  • Biocontainment and Selections:
    Error fetching PMID 23662731:
    1. Error fetching PMID 23662731: [Guo2013]


For Week VIII, March 17th 2014

  • Non-canonical Nucleotides:
    Error fetching PMID 17074747:
    1. Error fetching PMID 17074747: [Benner2006]
  • Stochastic Gene Expression:
    Error fetching PMID 12183631:
    1. Error fetching PMID 12183631: [Swain2002]


For Week IX, March 24th 2014

  • Motility and Taxis
    Error fetching PMID 16330045:
    1. Error fetching PMID 16330045: [Voigt2006]
  • Optogenetics - Review article
    Error fetching PMID 21255749:
    1. Error fetching PMID 21255749: [LaLumiere2011]
  • Quorum Sensing
    Error fetching PMID 20534565:
    1. Error fetching PMID 20534565: [March2010]

For Week X, March 31st 2014

  • Cell Counting and Memory
    Error fetching PMID 19478183:
    1. Error fetching PMID 19478183: [Collins2009]
  • Oscillations
    Error fetching PMID 18971928:
    1. Error fetching PMID 18971928: [Hasty2008]

For Week XI, April 7th 2014

  • MAGE
    Error fetching PMID 21764749:
    1. Error fetching PMID 21764749: [Church2011]
  • CRISPR
    Error fetching PMID 23287722:
    1. Error fetching PMID 23287722: [Church2013]
  • GMO article from the NY Times. Read the entirety of this article. We will have a discussion relating to this and other GMO topics in class [1]


  • Amber-less E. coli [Led by Mike Hammerling. Look over the paper, but you do not need to understand everything
    Error fetching PMID 24136966:
    1. Error fetching PMID 24136966: [Isaacs2013]

For Week XII, April 14th 2014

  • small RNAs
    Error fetching PMID 23334451:
    1. Error fetching PMID 23334451: [Lee2013]


For Week XIII, April 21st 2014

  • Bioremediation
    Error fetching PMID 24140537:
    1. Error fetching PMID 24140537: [Apte2013]


RECENT NATURE issue: Synthetic Biology articles and news

Recent Nature Biotech article on CRISPR: GENOME engineering

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