User:Nikolai Eroshenko: Difference between revisions

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== Research ==
==Education==
[http://www.seas.harvard.edu/academics/graduate Harvard University] (2008-now) PhD candidate, Engineering Sciences: Bioengineering


I am building new technologies for basic and applied biology. Long-term research interests include:
[http://www.egr.vcu.edu/departments-centers/biomedical-engineering/ Virginia Commonwealth University] (2005-2008) BS, Biomedical Engineering
* fully synthetic (i.e. non-immunogenic) gene therapy vectors that integrate genes into a precise location on the genome
 
* cheaper, faster, and more accurate gene synthesis
==Contact==
* library vs. library screens which quantify the strength of protein-protein and protein-DNA interactions
eroshenkona AT gmail
 
77 Ave. Louis Pasteur<br>
NRB 238 <br>
Boston, MA 02115
 
[http://scholar.google.com/citations?user=FxBA_wQAAAAJ&hl=en Google Scholar page]
 
== Research Interests ==
synthetic evolution, gene therapy, gene synthesis, origins of life, protein design


== Publications ==
== Publications ==
6. '''Nikolai Eroshenko''', George Church (2013) [http://arep.med.harvard.edu/pdf/Eroshenko_rec_13.pdf Mutants of Cre recombinase with improved accuracy.] Nat Commun 4:2509
5. '''Nikolai Eroshenko'''*, Rukmani Ramachandran*, Vamsi Yadavalli, Raj R. Rao (2013) [http://www.jbioleng.org/content/pdf/1754-1611-7-7.pdf Effect of substrate stiffness on early human embryonic stem cell differentiation.] J Biol Eng 7:7
4. Shilpa Iyer, Ena Xiao, Khaled Alsayegh, '''Nikolai Eroshenko''', Marion J. Riggs, James P. Bennett. Jr & Raj R. Rao (2012) [https://dl.dropboxusercontent.com/u/5389110/gt2011134a.pdf Mitochondrial gene replacement in human pluripotent stem cell derived neural progenitors.] Gene Ther 19:469
3. '''Nikolai Eroshenko'''*, Sriram Kosuri*, Adam H. Marblestone, Nicholas Conway, George Church (2012) [http://dl.dropbox.com/u/5389110/GeneAssemblyFromChipSynthesizedOligonucleotides%20(1).pdf Gene assembly from chip-synthesized oligonucleotides.] Curr Prot Chem Biol 4:1
2. Sriram Kosuri*, '''Nikolai Eroshenko'''*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & George Church (2010) [http://dl.dropbox.com/u/5389110/nbt.1716.pdf Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips.] Nat Biotechnol 28:1295
1. Sheena Abraham, '''Nikolai Eroshenko''' & Raj R. Rao (2009) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756563/pdf/nihms-132034.pdf Role of bioinspired polymers in determination of pluripotent stem cell fate.] Regen Med 4:561
==Patents==
1. George Church, Sriram Kosuri, '''Nikolai Eroshenko''', [http://patentscope.wipo.int/search/docservicepdf_pct/id00000019172253.pdf Orthogonal amplification and assembly of nucleic acid sequences] International Patent Application No. PCT/US2011/05707 (Harvard)


<span style="font-size:115%">'''Gene assembly from chip-synthesized oligonucleotides''' ([http://dl.dropbox.com/u/5389110/GeneAssemblyFromChipSynthesizedOligonucleotides%20(1).pdf PDF])
== News ==
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2708.html Highly accurate Cre variants], Nature Methods, Oct. 30 2013


Nikolai Eroshenko*, Sriram Kosuri*, Adam H. Marblestone, Nicholas Conway, George Church, ''Current Protocols in Chemical Biology'' 4 (2012)
[http://www.biotechniques.com/news/Refining-a-Recombinase/biotechniques-347492.html#.UmV-fZSifTw Refining a Recombinase], BioTechniques, Oct. 20 2013, Jeffrey M. Perkel
* <span style="font-size:85%"> Gene Assembly by Subpool PCR (GASP) oligo design [https://bitbucket.org/skosuri/gasp/src/364d21def3ec/cleaned-up-scripts/gaspserver/ scripts] and [http://synbiosis.med.harvard.edu:8080/gaspserver.rpy server] </span>


<span style="font-size:115%"> Mitochondrial gene replacement in human pluripotent stem cell derived neural progenitors ([http://dl.dropbox.com/u/5389110/gt2011134a.pdf PDF])
[http://www.nature.com/nrg/journal/v12/n1/full/nrg2924.html Technology: Making more genes, better and for less], Nature Reviews Genetics, Jan. 2011, Louisa Flintoft


Shilpa Iyer, Ena Xiao, Khaled Alsayegh, Nikolai Eroshenko, Marion J. Riggs, James P. Bennett. Jr & Raj R. Rao, ''Gene Therapy'' AOP (2011)
[http://www.nature.com/scibx/journal/v4/n1/full/scibx.2011.28.html Gene construction using microchip-based DNA synthesis and PCR amplification], SciBX, Jan. 6 2011


<span style="font-size:115%">Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips ([http://dl.dropbox.com/u/5389110/nbt.1716.pdf PDF])
[http://www.biotechniques.com/news/Technology-for-the-everyman/biotechniques-307796.html Technology for the everyman], Biotechniques, Dec. 23 2010, Suzanne E. Winter
Sriram Kosuri*, Nikolai Eroshenko*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & George Church, ''Nature Biotechnology'' 28:1295 (2010)
* <span style="font-size:85%">[http://www.nature.com/nbt/journal/v28/n12/extref/nbt.1716-S1.pdf Supplementary Text and Figures] (.pdf)
* <span style="font-size:85%">[http://www.nature.com/nbt/journal/v28/n12/extref/nbt.1716-S2.xls Supplementary Sequences] (.xls)
* <span style="font-size:85%">[http://dl.dropbox.com/u/5389110/Science-2010-News%20Focus-1605-7.pdf Runner-up for Science 2011 Breakthrough of the Year]
* <span style="font-size:85%">Commentary: [http://dl.dropbox.com/u/5389110/nbt.1723.pdf Nature Biotechnology]; [http://dl.dropbox.com/u/5389110/nrg2924.pdf Nature Reviews Genetics]


<span style="font-size:115%">Role of bioinspired polymers in determination of pluripotent stem cell fate ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756563/pdf/nihms-132034.pdf PDF])
[http://www.nature.com/nbt/journal/v28/n12/full/nbt.1723.html Megabases for kilodollars], Nature Biotechnology, Dec. 07 2010, Mikkel Algire, Radha Krishnakumar & Chuck Merryman
Sheena Abraham, Nikolai Eroshenko & Raj R. Rao, ''Regenerative Medicine'' 4:561 (2009)

Revision as of 08:23, 26 August 2014

Education

Harvard University (2008-now) PhD candidate, Engineering Sciences: Bioengineering

Virginia Commonwealth University (2005-2008) BS, Biomedical Engineering

Contact

eroshenkona AT gmail

77 Ave. Louis Pasteur
NRB 238
Boston, MA 02115

Google Scholar page

Research Interests

synthetic evolution, gene therapy, gene synthesis, origins of life, protein design

Publications

6. Nikolai Eroshenko, George Church (2013) Mutants of Cre recombinase with improved accuracy. Nat Commun 4:2509

5. Nikolai Eroshenko*, Rukmani Ramachandran*, Vamsi Yadavalli, Raj R. Rao (2013) Effect of substrate stiffness on early human embryonic stem cell differentiation. J Biol Eng 7:7

4. Shilpa Iyer, Ena Xiao, Khaled Alsayegh, Nikolai Eroshenko, Marion J. Riggs, James P. Bennett. Jr & Raj R. Rao (2012) Mitochondrial gene replacement in human pluripotent stem cell derived neural progenitors. Gene Ther 19:469

3. Nikolai Eroshenko*, Sriram Kosuri*, Adam H. Marblestone, Nicholas Conway, George Church (2012) Gene assembly from chip-synthesized oligonucleotides. Curr Prot Chem Biol 4:1

2. Sriram Kosuri*, Nikolai Eroshenko*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & George Church (2010) Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol 28:1295

1. Sheena Abraham, Nikolai Eroshenko & Raj R. Rao (2009) Role of bioinspired polymers in determination of pluripotent stem cell fate. Regen Med 4:561

Patents

1. George Church, Sriram Kosuri, Nikolai Eroshenko, Orthogonal amplification and assembly of nucleic acid sequences International Patent Application No. PCT/US2011/05707 (Harvard)

News

Highly accurate Cre variants, Nature Methods, Oct. 30 2013

Refining a Recombinase, BioTechniques, Oct. 20 2013, Jeffrey M. Perkel

Technology: Making more genes, better and for less, Nature Reviews Genetics, Jan. 2011, Louisa Flintoft

Gene construction using microchip-based DNA synthesis and PCR amplification, SciBX, Jan. 6 2011

Technology for the everyman, Biotechniques, Dec. 23 2010, Suzanne E. Winter

Megabases for kilodollars, Nature Biotechnology, Dec. 07 2010, Mikkel Algire, Radha Krishnakumar & Chuck Merryman