User:Jerome Bonnet: Difference between revisions
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==Research interests== | |||
Developing and applying tools to program living cells like computers. | |||
Presently at the [http://www.cbs.cnrs.fr/index.php/en/ Centre de Biochimie Structurale], Montpellier, France. | |||
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> | |||
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> | |||
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]. | |||
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. | |||
==Contact== | |||
Jerome Bonnet<br> | |||
Synthetic Biology Group <br> | |||
Centre de Biochimie Structurale<br> | |||
29 rue de Navacelles<br> | |||
34090 Montpellier, France<br> | |||
email: bonnet[at]cbs.cnrs.fr <br> | |||
==Education== | ==Education== | ||
<!--Include info about your educational background--> | <!--Include info about your educational background--> | ||
2007, PhD in cell and molecular biology, University of Montpellier (CRBM-CNRS UMR5237), France. <br> | |||
2003, MS in Biological science and health, University of Montpellier.<br> | |||
2001, BS in Biochemistry, University of Montpellier.<br> | |||
==Publications== | |||
'''Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates'''<br> | |||
''Science Translational Medicine'', 2015 May 27;7(289):289ra83<br> | |||
Alexis Courbet, Drew Endy, Eric Renard, Franck Molina, and '''Jérôme Bonnet''' <br> | |||
[http://www.ncbi.nlm.nih.gov/pubmed/26019219 Abstract] [[Media:Courbet_STM.pdf|PDF]]<br> | |||
[[Media:Courbet_STM_SM.pdf|Supplementary Materials]] | |||
'''Amplifying genetic logic gates'''<br> | |||
''Science,'' 28 March 2013, doi: 10.1126/science.1232758 <br> | |||
'''Jérôme Bonnet''', Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, Drew Endy <br> | |||
[http://www.ncbi.nlm.nih.gov/pubmed/23539178 Abstract] [[Media:Science-2013-Bonnet-599-603.pdf|PDF]] <br> [[Media:Bonnet_SM(1).pdf|Supplementary Materials]]<br> | |||
[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> | |||
'''Switches, switches, every where, In any drop we drink''' <br> | |||
< | ''Molecular cell,'' 2013, Jan 24;49(2):232-3. Preview on [http://www.ncbi.nlm.nih.gov/pubmed/23246436 Hatfull lab's paper] <br> | ||
'''Jérôme Bonnet''' and Drew Endy <br> | |||
[http://www.ncbi.nlm.nih.gov/pubmed/23352244 URL] [[Media:Molecular_Cell_2013_Bonnet.pdf|PDF]] | |||
'''Rewritable digital data storage in live cells via engineered control of recombination directionality'''<br> | |||
''PNAS,'' 2012, 109(23):8884-8889<br> | |||
'''Jérôme Bonnet''', Pakpoom Subsoontorn and Drew Endy. <br> | |||
[http://www.ncbi.nlm.nih.gov/pubmed/22615351 Abstract] [[Media:Bonnet_PNAS_2012.pdf|PDF]] | |||
'''Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila'''<br> | |||
''Cell,'' 2011 144 (2) pp. 214-226 <br> | |||
Frédéric Bantignies, Virginie Roure, Itys Comet, Benjamin Leblanc, Bernd Schuettengruber, '''Jerome Bonnet''', Vanessa Tixier, André Mas, and Giacomo Cavalli. <br> | |||
[http://www.ncbi.nlm.nih.gov/pubmed/21241892 Abstract] | |||
'''Targeting Kinases and Phosphatases that regulate Cell Cycle Progression''' <br> | |||
http:// | ''Trends in cell cycle research,'' 2008.<br> | ||
'''Jérôme Bonnet''', Johanna Scheper, Gilles Divita and May C. Morris <br> | |||
[http://www.ressign.com/UserBookDetail.aspx?bkid=797&catid=175 URL]<br> | |||
'''Characterization of centrosomal localization and dynamics of Cdc25C phosphatase in mitosis'''<br> | |||
''Cell Cycle,'' 2008, 7:13, 1991-1998 <br> | |||
'''Jérôme Bonnet''', Peter Coopman and May C. Morris <br> | |||
[http://www.ncbi.nlm.nih.gov/pubmed/18604163 Abstract] [[Media:Cell_Cycle_2008_Bonnet.pdf|PDF]] | |||
'''Differential phosphorylation of Cdc25C in mitosis''' <br> | |||
< | ''Biochemical and Biophysical research communication,'' 2008, 370, 483–488 <br> | ||
< | '''Jérôme Bonnet,''' Pauline Mayonove, and May C. Morris <br> | ||
[http://www.ncbi.nlm.nih.gov/pubmed/18384749 Abstract] [[Media:BBRC_2008_Bonnet.pdf|PDF]] | |||
// | |||
[[ | |||
==Useful links== | ==Useful links== | ||
*[[ | |||
*[[ | * [http://fold.it/portal/ Foldit!] | ||
* [http://eterna.cmu.edu/web/ eteRNA] | |||
* [http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=101999&ver=1 Bionumbers] | |||
* [http://openwetware.org/wiki/E._coli_genotypes E. coli genotypes] | |||
== other interests == | |||
Hibernating member of [http://profile.myspace.com/index.cfm?fuseaction=user.viewprofile&friendid=322568465 Yakasseme] (West African traditional Mandingo music). | |||
See more on [http://www.donaba.net/videoAfrique.php?service=surleWeb&categorie=&pays=&page=1 Donaba], French site with a lot of music videos. | |||
Latest revision as of 01:09, 2 June 2015
Research interests
Developing and applying tools to program living cells like computers.
Presently 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
Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates
Science Translational Medicine, 2015 May 27;7(289):289ra83
Alexis Courbet, Drew Endy, Eric Renard, Franck Molina, and Jérôme Bonnet
Abstract PDF
Supplementary Materials
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
Supplementary Materials
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.
