User:Nikolai Eroshenko: Difference between revisions

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== Research ==
==Education==
[http://arep.med.harvard.edu/ Church lab, Harvard Medical School] (2014-currently) postdoc


I am building new technologies for basic and applied biology. Long-term research interests include:
[http://www.seas.harvard.edu/academics/graduate Harvard University] (2008-2014) PhD, Engineering Sciences: Bioengineering
* 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
[http://www.egr.vcu.edu/departments-centers/biomedical-engineering/ Virginia Commonwealth University] (2005-2008) BS, Biomedical Engineering
* library vs. library screens which quantify the strength of protein-protein and protein-DNA interactions
 
==Contact==
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==
2. '''Nikolai Eroshenko''', George Church (2014) [http://patentscope.wipo.int/search/en/WO2014158593 Mutants of cre recombinase] (Harvard)
1. George Church, Sriram Kosuri, '''Nikolai Eroshenko''' (2013) [http://patentscope.wipo.int/search/docservicepdf_pct/id00000019172253.pdf Orthogonal amplification and assembly of nucleic acid sequences] (Harvard)
== News ==
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2708.html Highly accurate Cre variants], Nature Methods, Oct. 30 2013
[http://www.biotechniques.com/news/Refining-a-Recombinase/biotechniques-347492.html#.UmV-fZSifTw Refining a Recombinase], BioTechniques, Oct. 20 2013, Jeffrey M. Perkel
[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


====Gene assembly from chip-synthesized oligonucleotides ([http://dl.dropbox.com/u/5389110/GeneAssemblyFromChipSynthesizedOligonucleotides%20(1).pdf PDF])====
[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
Nikolai Eroshenko*, Sriram Kosuri*, Adam H. Marblestone, Nicholas Conway, George Church, ''Current Protocols in Chemical Biology'' 4 (2012)
* <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>


====Mitochondrial gene replacement in human pluripotent stem cell derived neural progenitors ([http://dl.dropbox.com/u/5389110/gt2011134a.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
Shilpa Iyer, Ena Xiao, Khaled Alsayegh, Nikolai Eroshenko, Marion J. Riggs, James P. Bennett. Jr & Raj R. Rao, ''Gene Therapy'' AOP (2011)


====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.nature.com/nbt/journal/v28/n12/full/nbt.1723.html Megabases for kilodollars], Nature Biotechnology, Dec. 07 2010, Mikkel Algire, Radha Krishnakumar & Chuck Merryman
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)
* [http://www.nature.com/nbt/journal/v28/n12/extref/nbt.1716-S2.xls Supplementary Sequences] (.xls)
* [http://dl.dropbox.com/u/5389110/Science-2010-News%20Focus-1605-7.pdf Runner-up for Science 2011 Breakthrough of the Year]
* Commentary: [http://dl.dropbox.com/u/5389110/nbt.1723.pdf Nature Biotechnology]; [http://dl.dropbox.com/u/5389110/nrg2924.pdf Nature Reviews Genetics] </span>

Revision as of 18:53, 13 April 2015

Education

Church lab, Harvard Medical School (2014-currently) postdoc

Harvard University (2008-2014) PhD, 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

2. Nikolai Eroshenko, George Church (2014) Mutants of cre recombinase (Harvard)

1. George Church, Sriram Kosuri, Nikolai Eroshenko (2013) Orthogonal amplification and assembly of nucleic acid sequences (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