User:Jerome Bonnet

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==Contact Info==
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[[Image:Jerome1.png|thumb|right|]]
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[[Image:OWWEmblem.png|thumb|right|Jerome Bonnet (an artistic interpretation)]]
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==Research interests==
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*Jerome Bonnet, Stanford University, Department of Bioengineering.
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Developing and applying tools to program living cells like computers.  
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Y2E2-B007, MC4201
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473 Via Ortega
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Starting my lab in January 2014 at the [http://www.cbs.cnrs.fr/spip.php?rubrique298 Centre de Biochimie Structurale], Montpellier, France.
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Stanford, CA 94305
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I was a post-doc in the [http://openwetware.org/wiki/Endy:Lab Endy Lab] at Stanford University from 2008 to 2013. I was a fellow from the [http://longevity.stanford.edu/ Stanford Center on Longevity] from 2009-2012.<br>
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I have been working on the engineering of the [http://www.ncbi.nlm.nih.gov/pubmed/22615351 first rewritable DNA memory] and the [http://www.ncbi.nlm.nih.gov/pubmed/23539178 first complete logic gates collection operating in single cells] and capable of signal amplification via a genetic transistor-like architecture, the [http://en.wikipedia.org/wiki/Transcriptor Transcriptor].<br>
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Lab. (650) 721-5721
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Both systems use the powerful serine integrases recombinases from bacteriophages. These enzymes can operate in numerous species, enabling our devices to be widely re-applied to various model systems. We [https://biobricks.org/bpa/contributions/57/ contributed] the Boolean Integrase Logic (BIL) Gates family in the public domain via the [https://biobricks.org/bpa/ BioBrick Public Agreement].
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email: bonnet[at]stanford.edu
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We hope that the tools we developed to program living cells will revolutionize the study and the engineering of biological systems. For example, our genetic memory devices could be combined as described [http://www.sciencedirect.com/science/article/pii/S1877050912005893 here] by [[User:Pakpoom Subsoontorn|Pakpoom Subsoontorn]] to build  a cell cycle counter. By allowing cells to report the number of time they divided, such a counter would enable high-resolution monitoring of aging and developmental processes.
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==Contact==
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I work in the [http://openwetware.org/wiki/Endy:Lab Endy Lab] at Stanford University on the engineering of genetically encoded memory systems. One application of this genetic memory devices is a cell cycle counter, which would allow cells to report the number of time they divided. Such a counter would be useful to monitor the aging process with high resolution. I'm a fellow of the Stanford Center on Longevity.
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Jerome Bonnet<br>
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Synthetic Biology Group <br>
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Centre de Biochimie Structurale<br>
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29 rue de Navacelles<br>
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34090 Montpellier, France<br>
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email: bonnet[at]cbs.cnrs.fr <br>
==Education==
==Education==
<!--Include info about your educational background-->
<!--Include info about your educational background-->
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* 2007, PhD in cell and molecular biology, CRBM-CNRS, University of Montpellier, france
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2007, PhD in cell and molecular biology, University of Montpellier (CRBM-CNRS UMR5237), France. <br>
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* 2003, MS in Biological science and health, University of Montpellier.
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2003, MS in Biological science and health, University of Montpellier.<br>
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* 2001, BS in Biochemistry, University of Montpellier.
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2001, BS in Biochemistry, University of Montpellier.<br>
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==Publications==
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==Research interests==
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'''Amplifying genetic logic gates'''<br>
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<!-- Feel free to add brief descriptions to your research interests as well -->
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''Science,'' 28 March 2013, doi: 10.1126/science.1232758 <br>
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Synthetic Biology, Systems Biology, Aging,
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'''Jérôme Bonnet''', Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, Drew Endy <br>
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Evolutionary Biology,
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[http://www.ncbi.nlm.nih.gov/pubmed/23539178 Abstract]  [[Media:Science-2013-Bonnet-599-603.pdf|PDF]] [http://www.npr.org/2013/03/29/175604770/tiny-dna-switches-aim-to-revolutionize-cellular-computing NPR] [http://youtu.be/ahYZBeP_r5U YouTube primer] News and views in [http://www.sciencemag.org/content/340/6132/554.long ''Science''] and [http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2501.html?WT.ec_id=NMETH-201306 ''Nature Methods''] <br>
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Origins of Life.
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*See my [http://openwetware.org/wiki/User:Jerome_Bonnet/Notebook lab notebooks]
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'''Switches, switches, every where, In any drop we drink''' <br>
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''Molecular cell,'' 2013, Jan 24;49(2):232-3. Preview on [http://www.ncbi.nlm.nih.gov/pubmed/23246436 Hatfull lab's paper] <br>
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'''Jérôme Bonnet''' and Drew Endy <br> 
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[http://www.ncbi.nlm.nih.gov/pubmed/23352244 URL] [[Media:Molecular_Cell_2013_Bonnet.pdf|PDF]]
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'''Rewritable digital data storage in live cells via engineered control of recombination directionality'''<br>
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''PNAS,'' 2012, 109(23):8884-8889<br>
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'''Jérôme Bonnet''', Pakpoom Subsoontorn and Drew Endy. <br>
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[http://www.ncbi.nlm.nih.gov/pubmed/22615351 Abstract]  [[Media:Bonnet_PNAS_2012.pdf|PDF]]
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'''Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila'''<br>
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''Cell,'' 2011 144 (2) pp. 214-226 <br>
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Frédéric Bantignies, Virginie Roure, Itys Comet, Benjamin Leblanc, Bernd Schuettengruber, '''Jerome Bonnet''', Vanessa Tixier, André Mas, and Giacomo Cavalli. <br>
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[http://www.ncbi.nlm.nih.gov/pubmed/21241892 Abstract]
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==Publications==
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'''Targeting Kinases and Phosphatases that regulate Cell Cycle Progression''' <br>
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<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed -->
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''Trends in cell cycle research,'' 2008.<br>
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<biblio>
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'''Jérôme Bonnet''', Johanna Scheper, Gilles Divita and May C. Morris <br>
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#Paper1 pmid=18604163
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[http://www.ressign.com/UserBookDetail.aspx?bkid=797&catid=175 URL]<br>
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#Paper2 pmid=18384749
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#Review Bonnet J, Scheper J, Divita G. and Morris MC (2008) ''Targeting Kinases and Phosphatases that regulate Cell Cycle Progression''. Trends in cell cycle research, ed. Yoshida K., Research signpost.
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'''Characterization of centrosomal localization and dynamics of Cdc25C phosphatase in mitosis'''<br>
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''Cell Cycle,'' 2008, 7:13, 1991-1998 <br>
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'''Jérôme Bonnet''', Peter Coopman and May C. Morris <br>
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[http://www.ncbi.nlm.nih.gov/pubmed/18604163 Abstract]  [[Media:Cell_Cycle_2008_Bonnet.pdf‎|PDF]]
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</biblio>
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'''Differential phosphorylation of Cdc25C in mitosis''' <br>
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''Biochemical and Biophysical research communication,'' 2008, 370, 483–488 <br>
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'''Jérôme Bonnet,''' Pauline Mayonove, and May C. Morris <br>
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[http://www.ncbi.nlm.nih.gov/pubmed/18384749 Abstract]  [[Media:BBRC_2008_Bonnet.pdf‎|PDF]]
==Useful links==
==Useful links==
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*[http://fold.it/portal/ Foldit!]
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* [http://fold.it/portal/ Foldit!]
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* [http://longevity.stanford.edu/ Stanford Center on Longevity (SCL)]]
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* [http://eterna.cmu.edu/web/ eteRNA]
* [http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=101999&ver=1 Bionumbers]
* [http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=101999&ver=1 Bionumbers]
* [http://openwetware.org/wiki/E._coli_genotypes E. coli genotypes]
* [http://openwetware.org/wiki/E._coli_genotypes E. coli genotypes]
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*[[OpenWetWare:Welcome|Introductory tutorial]]
 
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*[[Help|OpenWetWare help pages]]
 
== other interests ==
== other interests ==
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* music
 
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West African traditional Mandingo music.
 
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http://profile.myspace.com/index.cfm?fuseaction=user.viewprofile&friendid=322568465
 
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Donaba, French site, with a lot of videos: http://www.donaba.net/videoAfrique.php?service=surleWeb&categorie=&pays=&page=1
 
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Hibernating member of [http://profile.myspace.com/index.cfm?fuseaction=user.viewprofile&friendid=322568465 Yakasseme] (West African traditional Mandingo music).
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*[[life as a scientist]]
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See more on [http://www.donaba.net/videoAfrique.php?service=surleWeb&categorie=&pays=&page=1 Donaba], French site with a lot of music videos.

Current revision

Contents

Research interests

Developing and applying tools to program living cells like computers.

Starting my lab in January 2014 at the Centre de Biochimie Structurale, Montpellier, France.

I was a post-doc in the Endy Lab at Stanford University from 2008 to 2013. I was a fellow from the Stanford Center on Longevity from 2009-2012.

I have been working on the engineering of the first rewritable DNA memory and the first complete logic gates collection operating in single cells and capable of signal amplification via a genetic transistor-like architecture, the Transcriptor.

Both systems use the powerful serine integrases recombinases from bacteriophages. These enzymes can operate in numerous species, enabling our devices to be widely re-applied to various model systems. We contributed the Boolean Integrase Logic (BIL) Gates family in the public domain via the BioBrick Public Agreement.

We hope that the tools we developed to program living cells will revolutionize the study and the engineering of biological systems. For example, our genetic memory devices could be combined as described here by Pakpoom Subsoontorn to build a cell cycle counter. By allowing cells to report the number of time they divided, such a counter would enable high-resolution monitoring of aging and developmental processes.

Contact

Jerome Bonnet
Synthetic Biology Group

Centre de Biochimie Structurale
29 rue de Navacelles
34090 Montpellier, France

email: bonnet[at]cbs.cnrs.fr

Education

2007, PhD in cell and molecular biology, University of Montpellier (CRBM-CNRS UMR5237), France.
2003, MS in Biological science and health, University of Montpellier.
2001, BS in Biochemistry, University of Montpellier.

Publications

Amplifying genetic logic gates
Science, 28 March 2013, doi: 10.1126/science.1232758
Jérôme Bonnet, Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, Drew Endy
Abstract PDF NPR YouTube primer News and views in Science and Nature Methods

Switches, switches, every where, In any drop we drink
Molecular cell, 2013, Jan 24;49(2):232-3. Preview on Hatfull lab's paper
Jérôme Bonnet and Drew Endy
URL PDF

Rewritable digital data storage in live cells via engineered control of recombination directionality
PNAS, 2012, 109(23):8884-8889
Jérôme Bonnet, Pakpoom Subsoontorn and Drew Endy.
Abstract PDF

Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
Cell, 2011 144 (2) pp. 214-226
Frédéric Bantignies, Virginie Roure, Itys Comet, Benjamin Leblanc, Bernd Schuettengruber, Jerome Bonnet, Vanessa Tixier, André Mas, and Giacomo Cavalli.
Abstract

Targeting Kinases and Phosphatases that regulate Cell Cycle Progression
Trends in cell cycle research, 2008.
Jérôme Bonnet, Johanna Scheper, Gilles Divita and May C. Morris
URL

Characterization of centrosomal localization and dynamics of Cdc25C phosphatase in mitosis
Cell Cycle, 2008, 7:13, 1991-1998
Jérôme Bonnet, Peter Coopman and May C. Morris
Abstract PDF

Differential phosphorylation of Cdc25C in mitosis
Biochemical and Biophysical research communication, 2008, 370, 483–488
Jérôme Bonnet, Pauline Mayonove, and May C. Morris
Abstract PDF

Useful links

other interests

Hibernating member of Yakasseme (West African traditional Mandingo music).

See more on Donaba, French site with a lot of music videos.

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