Sriram Kosuri

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[[Image:Sri Kosuri.jpg|thumb|right|Sri at work]]
[[Image:Sri Kosuri.jpg|thumb|right|Sri at work]]
===Bio===  
===Bio===  
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Since October, I have been working at a small Cambridge-area startup called Joule Biotechnologies. I am also on the Board of Directors for OpenWetWare.   I previously did a short postdoctoral stint in [http://laublab.mit.edu/ Mike Laub's lab] working on cell cycle in ''Caulobacter crescentus''. Prior to the Laub lab, I was a graduate student in [[Drew Endy]]'s lab and worked on understanding the development of a simple virus (T7) that infects ''E. coli''. As an undergraduate at [http://www.berkeley.edu UC Berkeley], I worked with [http://www.lbl.gov/~aparkin Adam Arkin], Dale Kaiser, and Roy Welch on modeling traveling wave formation in ''M. xanthus''.
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I am an Assistant Professor at [http://www.ucla.edu/ UCLA] in the [http://www.chemistry.ucla.edu/ Chemistry and Biochemistry Department]. I was previously a member of the [http://wyss.harvard.edu/viewpage/72/advanced-technology-team Advanced Technology Team] in the [http://wyss.harvard.edu/viewpage/101/synthetic-biology Synthetic Biology Platform] at the [http://wyss.harvard.edu/ Wyss Institute]. I was a postdoc in [[User:Geochurch|George Church]]'s [[Church Lab|lab]] in the [http://genetics.med.harvard.edu/ Department of Genetics] at Harvard Medical School and the Wyss Institute from 2009-2011.  From 2007-2009, I was the first employee of a biofuel startup called [http://jouleunlimited.com/ Joule Unlimited].  I got my ScD in [http://web.mit.edu/be/index.shtml Biological Engineering] at MIT in [[Drew Endy]]'s lab and worked on understanding the development of a simple virus (T7) that infects ''E. coli''. As an undergraduate in [http://bioeng.berkeley.edu/ Bioengineering] at UC Berkeley, I worked with [http://www.lbl.gov/~aparkin Adam Arkin], Dale Kaiser, and Roy Welch on modeling traveling wave formation in ''M. xanthus''. I also co-founded OpenWetWare. 
==Science==
==Science==
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===Interests===
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===Publications===
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*Understanding those aspects of biological design that allow for certain robust features of development in the face of large intrinsic and extrinsic variation specifically on non-evolutionary time-scales (I am currently giving up on the past. That may change in the future.).  
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'''Large-scale de novo DNA synthesis: technologies and applications'''<br>
 +
[[Sriram Kosuri]] & [[George_Church|George M Church]]<br>
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''Nature Biotechnology'', (2014) [http://dx.doi.org/10.1038/nmeth.2918 doi: 10.1038/nmeth.2918]
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*Enabling the design, construction, and use of biological organisms for the purposes of further scientific understanding; keeping extremely aware of the use of engineered biological organisms for other purposes.
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'''Causes and effects of N-terminal codon bias in bacterial genes'''<br>
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[[User:Daniel_Goodman|Daniel B Goodman]], [[George_Church|George M Church]], [[Sriram Kosuri]]<br>
 +
''Science'', (2013) [http://dx.doi.org/10.1126/science.1241934 doi:10.1126/science.1241934]
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*Property rights as related to biological information and organisms; understanding and reforming current and future frameworks; I really like these [http://sciencecommons.org people]
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'''Probing the Limits of Genetic Recoding in Essential Genes'''<br>
 +
Marc Lajoie*, [[Sriram Kosuri]]*, Joshua Mosberg, Christopher Gregg, Di Zhang, [[George_Church|George M Church]]<br>
 +
''Science'', (2013) [http://dx.doi.org/10.1126/science.1241460 doi:10.1126/science.1241460]  
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*Reforming the reward structures in biological sciences. -- more on this later, for now see [[Science 2.0]]
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'''Composability of regulatory sequences controlling transcription and translation in ''E. coli'''''<br>
 +
[[Sriram Kosuri]]*, [[User:Daniel_Goodman|Daniel B Goodman]]*, [[User:Guillaume_Cambray|Guillaume Cambray]], Vivek K Mutalik, Yuan Gao, [[User:Aparkin|Adam P. Arkin]], [[User:Endy|Drew Endy]], [[George_Church|George M Church]]<br>
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''PNAS'', (2013) [http://dx.doi.org/10.1073/pnas.1301301110 doi:10.1073/pnas.1301301110]
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*The energy problem.
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'''CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering'''<br>
 +
Prashant Mali, John Aach, P Benjamin Stranges, Kevin M Esvelt, Mark Moosburner, [[Sriram Kosuri]], Luhan Yang, [[George_Church|George M Church]]<br>
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''Nature Biotechnology'', (2013) [http://dx.doi.org/10.1038/nbt.2675 doi:10.1038/nbt.2675]
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*OpenWetWare of course!
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'''Next-Generation Digital Information Storage in DNA'''<br>
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George M. Church, Yuan Gao, [[Sriram Kosuri]]<br>
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''Science'' (2012) [http://dx.doi.org/10.1126/science.1226355 doi:10.1126/science.1226355]
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=== Past Projects ===
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'''When It Rains, It Pores'''<br>
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[[Sriram Kosuri]] & A. Michael Sismour<br>
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''ACS Synthetic Biology'' (2012) [http://dx.doi.org/10.1021/sb300015f doi:10.1021/sb300015f]
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[[Rebuilding T7]]
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'''Gene Assembly from Chip-Synthesized Oligonucleotides'''<br>
 +
[[User:Nikolai_Eroshenko|Nikolai Eroshenko]]*, [[Sriram Kosuri]]*, Adam H Marblestone, Nicholas Conway, & [[George_Church|George Church]]<br>
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''Current Protocols in Chemical Biology'' (2012) [http://dx.doi.org/10.1002/9780470559277.ch110190 doi:10.1002/9780470559277.ch110190]
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[[TABASCO]] -- A single molecule base-pair resolved gene expression simulator
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'''Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription'''<br>
 +
Feng Zhang*, Le Cong*, Simona Lodato, [[Sriram Kosuri]], [[George_Church|George Church]] & Paola Arlotta <br>
 +
''Nature Biotechnology'' (2011) [http://dx.doi.org/10.1038/nbt.1775 doi:10.1038/nbt.1775]
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Measure and Models of T7 Infection
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'''Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips'''<br>
 +
[[Sriram Kosuri]]*, [[User:Nikolai_Eroshenko|Nikolai Eroshenko]]*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & [[George_Church|George Church]]<br>
 +
''Nature Biotechnology'' (2010)  '''28''':1295  [http://dx.doi.org/10.1038/nbt.1716 doi:10.1038/nbt.1716]
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[http://dx.doi.org/10.1038/nbt.1723 News & Views], [http://www.nature.com/nbt/journal/v28/n12/covers/index.html Cover Art]
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[[How does T7 deal with Uncertainty]]
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'''TABASCO: A single molecule, base-pair resolved gene expression simulator'''<br>
 +
[[Sriram Kosuri]], [[Jason Kelly]] and [[Drew Endy]]<br>
 +
''BMC Bioinformatics 2007'', '''8''':480    doi:10.1186/1471-2105-8-480<br>
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[http://www.biomedcentral.com/1471-2105/8/480 URL]<br>
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[[User:Skosuri/T7.2 tests|T7.2 Tests]]
 
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===Publications===
 
'''Refactoring bacteriophage T7'''<br>
'''Refactoring bacteriophage T7'''<br>
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[[Leon Chan|Leon Y. Chan]], [[Sriram Kosuri]] and [[Drew Endy]]<br>
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[[Leon Chan|Leon Y. Chan]]*, [[Sriram Kosuri]]* and [[Drew Endy]]<br>
''Molecular Systems Biology'' 13 September 2005 DOI:10.1038/msb4100025<br>
''Molecular Systems Biology'' 13 September 2005 DOI:10.1038/msb4100025<br>
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html URL]
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html URL]
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[http://hdl.handle.net/1721.1/27501 October 2004 version]
[http://hdl.handle.net/1721.1/27501 October 2004 version]
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'''TABASCO: A single molecule, base-pair resolved gene expression simulator'''<br>
 
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[[Sriram Kosuri]], [[Jason Kelly]] and [[Drew Endy]]<br>
 
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''BMC Bioinformatics 2007'', '''8''':480    doi:10.1186/1471-2105-8-480<br>
 
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[http://www.biomedcentral.com/1471-2105/8/480 URL]<br>
 
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===Interesting Stuff===
 
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The beginnings of a [[/blog|blog]].
 
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See my [[Sriram Kosuri/Interesting Stuff|interesting stuff page]]
 
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[[Sriram Kosuri/Post-doctoral Fellowships|Post-doctoral Fellowships]]
 
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[[Media:CGR Research Plan.pdf|A failed Research Plan for a job at Harvard's CGR]]
 
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[http://hdl.handle.net/1721.1/35864 My Thesis!]
 
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[[Special:Contributions/Skosuri|My contributions to OWW]]
 
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[[Sriram Kosuri/temp]]
 
==Contact==
==Contact==
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'''Phone''': 617.253.3677<br>
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'''Phone''': 617-432-8283<br>
'''OWW users''': Post a message on my [[User talk:Skosuri|talk page]], or send me an [[Special:Emailuser/Skosuri|email]].<br>
'''OWW users''': Post a message on my [[User talk:Skosuri|talk page]], or send me an [[Special:Emailuser/Skosuri|email]].<br>
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'''Email''': [[Image:Sri Kosuri's Email.jpg|100px]]<br>
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'''Email''': [[Image:Sri Kosuri's Email.jpg|500px]]<br>
'''Postal''':<br>
'''Postal''':<br>
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31 Ames St.<br>
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Wyss Institute<br>
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68-611<br>
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CLSB 508-7<br>
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Cambridge, MA 02139<br>
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3 Blackfan Circle<br>
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Boston, MA 02115  USA <br>
[http://www.google.com/calendar/embed?src=skosuri%40gmail.com Calendar]
[http://www.google.com/calendar/embed?src=skosuri%40gmail.com Calendar]
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'''PGP Key: Use this is you have super secret information to send!'''
 
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==Who's Visiting==
==Who's Visiting==
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[[Category:Steering Committee member]]
[[Category:Steering Committee member]]
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[[Category:People at MIT]]
 

Current revision

Contents

Personal

Sri at work
Sri at work

Bio

I am an Assistant Professor at UCLA in the Chemistry and Biochemistry Department. I was previously a member of the Advanced Technology Team in the Synthetic Biology Platform at the Wyss Institute. I was a postdoc in George Church's lab in the Department of Genetics at Harvard Medical School and the Wyss Institute from 2009-2011. From 2007-2009, I was the first employee of a biofuel startup called Joule Unlimited. I got my ScD in Biological Engineering at MIT in Drew Endy's lab and worked on understanding the development of a simple virus (T7) that infects E. coli. As an undergraduate in Bioengineering at UC Berkeley, I worked with Adam Arkin, Dale Kaiser, and Roy Welch on modeling traveling wave formation in M. xanthus. I also co-founded OpenWetWare.

Science

Publications

Large-scale de novo DNA synthesis: technologies and applications
Sriram Kosuri & George M Church
Nature Biotechnology, (2014) doi: 10.1038/nmeth.2918

Causes and effects of N-terminal codon bias in bacterial genes
Daniel B Goodman, George M Church, Sriram Kosuri
Science, (2013) doi:10.1126/science.1241934

Probing the Limits of Genetic Recoding in Essential Genes
Marc Lajoie*, Sriram Kosuri*, Joshua Mosberg, Christopher Gregg, Di Zhang, George M Church
Science, (2013) doi:10.1126/science.1241460

Composability of regulatory sequences controlling transcription and translation in E. coli
Sriram Kosuri*, Daniel B Goodman*, Guillaume Cambray, Vivek K Mutalik, Yuan Gao, Adam P. Arkin, Drew Endy, George M Church
PNAS, (2013) doi:10.1073/pnas.1301301110

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
Prashant Mali, John Aach, P Benjamin Stranges, Kevin M Esvelt, Mark Moosburner, Sriram Kosuri, Luhan Yang, George M Church
Nature Biotechnology, (2013) doi:10.1038/nbt.2675

Next-Generation Digital Information Storage in DNA
George M. Church, Yuan Gao, Sriram Kosuri
Science (2012) doi:10.1126/science.1226355

When It Rains, It Pores
Sriram Kosuri & A. Michael Sismour
ACS Synthetic Biology (2012) doi:10.1021/sb300015f

Gene Assembly from Chip-Synthesized Oligonucleotides
Nikolai Eroshenko*, Sriram Kosuri*, Adam H Marblestone, Nicholas Conway, & George Church
Current Protocols in Chemical Biology (2012) doi:10.1002/9780470559277.ch110190

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription
Feng Zhang*, Le Cong*, Simona Lodato, Sriram Kosuri, George Church & Paola Arlotta
Nature Biotechnology (2011) doi:10.1038/nbt.1775

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
Sriram Kosuri*, Nikolai Eroshenko*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & George Church
Nature Biotechnology (2010) 28:1295 doi:10.1038/nbt.1716 News & Views, Cover Art

TABASCO: A single molecule, base-pair resolved gene expression simulator
Sriram Kosuri, Jason Kelly and Drew Endy
BMC Bioinformatics 2007, 8:480 doi:10.1186/1471-2105-8-480
URL

Refactoring bacteriophage T7
Leon Y. Chan*, Sriram Kosuri* and Drew Endy
Molecular Systems Biology 13 September 2005 DOI:10.1038/msb4100025
URL PDF reprint News & Views October 2004 version


Contact

Phone: 617-432-8283
OWW users: Post a message on my talk page, or send me an email.
Email:
Postal:
Wyss Institute
CLSB 508-7
3 Blackfan Circle
Boston, MA 02115 USA

Calendar


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