User:Yun-Peng Xu

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[[Image:Peng.jpg|right|thumb]]
[[Image:Peng.jpg|right|thumb]]
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*Peng Xu ([http://openwetware.org/images/2/28/CV_11-3-2013_Academics.pdf Updated CV])
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*Peng Xu
*[http://bamel.scripts.mit.edu/gns/ Laboratory for Bioinformatics and Metabolic Engineering, 56-422]
*[http://bamel.scripts.mit.edu/gns/ Laboratory for Bioinformatics and Metabolic Engineering, 56-422]
*Department of Chemical Engieering, Massachusetts Institute of Technology
*Department of Chemical Engieering, Massachusetts Institute of Technology
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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 -->
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
Please refer to Google Scholar for [http://scholar.google.com/citations?user=vqLnxtEAAAAJ&hl=en complete list of publications and citations]
Please refer to Google Scholar for [http://scholar.google.com/citations?user=vqLnxtEAAAAJ&hl=en complete list of publications and citations]
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# Xu P, Wang W, Li L, Zhang F, Bhan N and Koffas MA. (2013) Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in E. coli. ACS Chemical Biology, Accepted.
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# '''Xu P''', Wang W, Li L, Zhang F, Bhan N and Koffas MA. (2013) [http://dx.doi.org/10.1021/cb400623m Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in ''E. coli'']. '''ACS Chemical Biology''', Accepted.
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# Wang W, Englaender J, Xu P, Linhardt RJ, Koffas MA. (2013) [http://dx.doi.org/10.1007/s12010-013-0415-8 Expression of low endotoxin 3-O-sulfotransferase in B. subtilis and B. megaterium]. Applied Biochemistry and Biotechnology, Accepted.
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# Wang W, Englaender J, '''Xu P''', Linhardt RJ, Koffas MA. (2013) [http://dx.doi.org/10.1007/s12010-013-0415-8 Expression of low endotoxin 3-O-sulfotransferase in B. subtilis and B. megaterium]. '''Applied Biochemistry and Biotechnology''', Accepted.
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# Xu P, Gu Q; Wang W, Wong L, Bower A, Collins CH and Koffas MA. (2013) [http://dx.doi.org/10.1038/ncomms2425 Modular optimization of multi-gene pathway for fatty acids production in ''E. coli'']. Nature Communications, 4: 1409.
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# '''Xu P''', Gu Q, Wang W, Wong L, Bower A, Collins CH and Koffas MA. (2013) [http://dx.doi.org/10.1038/ncomms2425 Modular optimization of multi-gene pathway for fatty acids production in ''E. coli'']. '''Nature Communications''', 4: 1409.
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# Bhan N, Xu P and Koffas MA. (2013) [http://dx.doi.org/10.1016/j.copbio.2013.02.019 Pathway and protein engineering approaches to produce novel and commodity small molecules]. Current Opinion in Biotechnology, Accepted.
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# Bhan N, '''Xu P''' and Koffas MA. (2013) [http://dx.doi.org/10.1016/j.copbio.2013.02.019 Pathway and protein engineering approaches to produce novel and commodity small molecules]. '''Current Opinion in Biotechnology''', Accepted.
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# Bhan N, Xu P, Khalidi O and Koffas MAG. (2013) [http://dx.doi.org/10.1016/j.ces.2012.10.009 Redirecting carbon flux into Malonyl-CoA to improve Resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework]. Chemical Engineering Science, Accepted manuscript, In press
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# Bhan N, '''Xu P''', Khalidi O and Koffas MAG. (2013) [http://dx.doi.org/10.1016/j.ces.2012.10.009 Redirecting carbon flux into Malonyl-CoA to improve Resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework]. '''Chemical Engineering Science''', 103, pp109-114.
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# Xu P and Koffas MA. (2013) [http://dx.doi.org/10.1007%2F978-1-62703-625-2_10 Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors]. Book chapter in Methods in Molecular Biology: Synthetic Biology.  
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# '''Xu P''' and Koffas MA. (2013) [http://dx.doi.org/10.1007%2F978-1-62703-625-2_10 Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors]. Book chapter in Methods in Molecular Biology: '''Synthetic Biology'''.  
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# Xu, Peng; Bhan, Namita; Koffas, Mattheos A.G. (2013) [http://dx.doi.org/10.1016/j.copbio.2012.08.010 Engineering plant metabolism into microbes: from systems biology to synthetic biology]. Current Opinion in Biotechnology, 24(2), pp 291-299. [http://koffasresearch.files.wordpress.com/2012/09/2012-08-010.pdf PDF]
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# '''Xu P''', Bhan N, Koffas MA. (2013) [http://dx.doi.org/10.1016/j.copbio.2012.08.010 Engineering plant metabolism into microbes: from systems biology to synthetic biology]. '''Current Opinion in Biotechnology''', 24(2), pp 291-299. [http://koffasresearch.files.wordpress.com/2012/09/2012-08-010.pdf PDF]
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# Xu, Peng; Vansiri, Amerin; Bhan, Namita; Koffas, Mattheos A.G. (2012) [http://dx.doi.org/doi:10.1021/sb300016b ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli]. ACS Synthetic Biology,1 (7), pp 256–266.[http://koffasresearch.files.wordpress.com/2012/07/epathbrick.pdf PDF]
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# '''Xu P''', Vansiri A, Bhan N, Koffas MA. (2012) [http://dx.doi.org/doi:10.1021/sb300016b ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli]. '''ACS Synthetic Biology''',1 (7), pp 256–266.[http://koffasresearch.files.wordpress.com/2012/07/epathbrick.pdf PDF]
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# Xu, Peng; Ranganathan, Sridhar; Fowler, Zachary; Maranas, Costas D.; Koffas, Mattheos A.G. (2011) [http://dx.doi.org/doi:10.1016/j.ymben.2011.06.008 Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA]. Metabolic Engineering, Volume: 13 Issue: 5 Pages: 578-587. [http://koffasresearch.files.wordpress.com/2012/07/malonyl-coa.pdf PDF]
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# '''Xu P''', Ranganathan S, Fowler ZL, Maranas CD, Koffas MA. (2011) [http://dx.doi.org/doi:10.1016/j.ymben.2011.06.008 Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA]. '''Metabolic Engineering''', Volume: 13 Issue: 5 Pages: 578-587. [http://koffasresearch.files.wordpress.com/2012/07/malonyl-coa.pdf PDF]
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# Xu, Peng; Koffas, Mattheos A. G. (2010) [http://dx.doi.org/doi:10.4155/bfs.10.13 Metabolic engineering of Escherichia coli for biofuel production], Biofuels, Volume: 1 Issue: 3 Pages: 493-504. [http://koffasresearch.files.wordpress.com/2012/07/biofuels.pdf PDF]
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# '''Xu P''', Koffas MA. (2010) [http://dx.doi.org/doi:10.4155/bfs.10.13 Metabolic engineering of Escherichia coli for biofuel production], '''Biofuels''', Volume: 1 Issue: 3 Pages: 493-504. [http://koffasresearch.files.wordpress.com/2012/07/biofuels.pdf PDF]
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# Zhang, Liang; Ding, Zhongyang; Xu, Peng; et al. (2011) [http://dx.doi.org/doi:10.1007/s12257-010-0345-z Methyl lucidenate F isolated from the ethanol-soluble-acidic components of Ganoderma lucidum is a novel tyrosinase inhibitor],Biotechnology and Bioprocess Engineering, Volume: 16 Issue: 3 Pages: 457-461. [https://docs.google.com/open?id=0B4wZIrGHL-wBZTU5YTQ1NDQtMzBlMy00NmRjLThlNjktMTdiNzY2OTY4YzM2 PDF]   
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# Zhang L, Ding Z, '''Xu P''' et al. (2011) [http://dx.doi.org/doi:10.1007/s12257-010-0345-z Methyl lucidenate F isolated from the ethanol-soluble-acidic components of Ganoderma lucidum is a novel tyrosinase inhibitor],'''Biotechnology and Bioprocess Engineering''', Volume: 16 Issue: 3 Pages: 457-461. [https://docs.google.com/open?id=0B4wZIrGHL-wBZTU5YTQ1NDQtMzBlMy00NmRjLThlNjktMTdiNzY2OTY4YzM2 PDF]   
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# Xu, Peng; Ding, ZY; Qian, Z; et al. (2008) [http://dx.doi.org/doi:10.1016/j.enzmictec.2007.10.016 Improved production of mycelial biomass and ganoderic acid by submerged culture of Ganoderma lucidum SB97 using complex media],  Enzyme and Microbial Technology, Volume: 42 Issue: 4 Pages: 325-331. [https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B4wZIrGHL-wBNmZhZTI1MDYtNzRkNS00ODczLTkwNTktZjM0ZmQxMmFhODE2&hl=en_US PDF]
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# '''Xu P''', Ding Z, Qian, Z et al. (2008) [http://dx.doi.org/doi:10.1016/j.enzmictec.2007.10.016 Improved production of mycelial biomass and ganoderic acid by submerged culture of Ganoderma lucidum SB97 using complex media],  '''Enzyme and Microbial Technology''', Volume: 42 Issue: 4 Pages: 325-331. [https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B4wZIrGHL-wBNmZhZTI1MDYtNzRkNS00ODczLTkwNTktZjM0ZmQxMmFhODE2&hl=en_US PDF]
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# Zhang, TX; Xu, P; Sun, J; et al. (2009) [http://dx.doi.org/doi:10.1094/ASBCJ-2008-1212-01 Identification of Biological Wort Turbidity Caused by Microbial Contamination of Gairdner Barley], Journal of the American Society of Brewing Chemists, Volume: 67 Issue: 1 Pages: 33-37
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# Zhang T, '''Xu P''', Sun J et al. (2009) [http://dx.doi.org/doi:10.1094/ASBCJ-2008-1212-01 Identification of Biological Wort Turbidity Caused by Microbial Contamination of Gairdner Barley], '''Journal of the American Society of Brewing Chemists''', Volume: 67 Issue: 1 Pages: 33-37
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# '''Xu P''', Qian Z, Zhao CX et al. (2008) Kinetic analysis of exo-polysaccharide and ganoderic acid production by submerged culture of Ganoderma lucidum. '''Chinese Journal of Applied & Environmental Biology''', 14(4): 562-565.
==Presentations==
==Presentations==

Current revision

Contents

Contact Info

I am a postdoctoral research associate in Stephanopoulos group at Massachusetts Institute of Technology.

Education

Short biography

Peng Xu, Ph.D., received his B.S. degree in biological engineering and M.S. degree in biochemical engineering from Jiangnan University (Wuxi, China). After that, he worked two years as a full-time instructor and researcher in Dalian Polytechnic University, where he lectured courses and conducted research on bioprocess and fermentation engineering. He then joined to the graduate program of Chemical and Biological engineering, the State University of New York at Buffalo. In January of 2011, he moved to the Chemical engineering department of Rensselaer Polytechnic Institute to continue his Ph.D. work. His Ph.D. project is mainly focused on the development of synthetic biology tools that support the design, construction and optimization of metabolic pathways. After completion of his Ph.D. degree, he moved to his current position as a postdoctoral research associate in the Department of Chemical Engineering, MIT, where he works on improving lipid biofuel production from Yarrowia lipolytica. Peng’s research work has led to 13 peer-reviewed scientific articles. He was awarded the Danisco Scholarship for Excellent Students in Biotechnology in 2006 and Chinese Government Scholarship for Outstanding Students Studying Abroad in 2012.

Research interests

  1. Metabolic engineering
  2. Synthetic biology
  3. Natural Products/Biofuels
  4. Biochemical/Bioprocess engineering

Publications

Please refer to Google Scholar for complete list of publications and citations

  1. Xu P, Wang W, Li L, Zhang F, Bhan N and Koffas MA. (2013) Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in E. coli. ACS Chemical Biology, Accepted.
  2. Wang W, Englaender J, Xu P, Linhardt RJ, Koffas MA. (2013) Expression of low endotoxin 3-O-sulfotransferase in B. subtilis and B. megaterium. Applied Biochemistry and Biotechnology, Accepted.
  3. Xu P, Gu Q, Wang W, Wong L, Bower A, Collins CH and Koffas MA. (2013) Modular optimization of multi-gene pathway for fatty acids production in E. coli. Nature Communications, 4: 1409.
  4. Bhan N, Xu P and Koffas MA. (2013) Pathway and protein engineering approaches to produce novel and commodity small molecules. Current Opinion in Biotechnology, Accepted.
  5. Bhan N, Xu P, Khalidi O and Koffas MAG. (2013) Redirecting carbon flux into Malonyl-CoA to improve Resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework. Chemical Engineering Science, 103, pp109-114.
  6. Xu P and Koffas MA. (2013) Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors. Book chapter in Methods in Molecular Biology: Synthetic Biology.
  7. Xu P, Bhan N, Koffas MA. (2013) Engineering plant metabolism into microbes: from systems biology to synthetic biology. Current Opinion in Biotechnology, 24(2), pp 291-299. PDF
  8. Xu P, Vansiri A, Bhan N, Koffas MA. (2012) ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synthetic Biology,1 (7), pp 256–266.PDF
  9. Xu P, Ranganathan S, Fowler ZL, Maranas CD, Koffas MA. (2011) Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metabolic Engineering, Volume: 13 Issue: 5 Pages: 578-587. PDF
  10. Xu P, Koffas MA. (2010) Metabolic engineering of Escherichia coli for biofuel production, Biofuels, Volume: 1 Issue: 3 Pages: 493-504. PDF
  11. Zhang L, Ding Z, Xu P et al. (2011) Methyl lucidenate F isolated from the ethanol-soluble-acidic components of Ganoderma lucidum is a novel tyrosinase inhibitor,Biotechnology and Bioprocess Engineering, Volume: 16 Issue: 3 Pages: 457-461. PDF
  12. Xu P, Ding Z, Qian, Z et al. (2008) Improved production of mycelial biomass and ganoderic acid by submerged culture of Ganoderma lucidum SB97 using complex media, Enzyme and Microbial Technology, Volume: 42 Issue: 4 Pages: 325-331. PDF
  13. Zhang T, Xu P, Sun J et al. (2009) Identification of Biological Wort Turbidity Caused by Microbial Contamination of Gairdner Barley, Journal of the American Society of Brewing Chemists, Volume: 67 Issue: 1 Pages: 33-37
  14. Xu P, Qian Z, Zhao CX et al. (2008) Kinetic analysis of exo-polysaccharide and ganoderic acid production by submerged culture of Ganoderma lucidum. Chinese Journal of Applied & Environmental Biology, 14(4): 562-565.

Presentations

  1. Xu P and Koffas MA. Engineering a synthetic malonyl-CoA controller for dynamic tuning metabolic flux in E. coli. 2013 AIChE annual meeting, San Francisco, CA (talk)
  2. Xu P. Engineering tailor-made microbial cell factories for phytochemical and fuels production. Invited by School of Engineering, Case Western Reserve University, Cleveland, OH. September 10, 2013 (talk)
  3. Xu P and Koffas MA. Expanding the synthetic biology toolbox for engineering metabolic pathways in E. Coli. 2012 AIChE annual meeting, Pittsburgh, PA (talk)
  4. Xu P and Koffas MA. ePathBrick directed modular pathway engineering for improved fatty acids production in E. Coli. 2012 AIChE annual meeting, Pittsburgh, PA (talk)
  5. Xu P, Ranganathan S, Maranas CD and Koffas MA. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. 2011 AIChE annual meeting, Minneapolis, MN (talk)
  6. Xu P and Koffas MA. Engineering synthetic malonyl-CoA sensor for dynamic tuning of metabolic flux in E. coli. The 1st Electrofuels Conference (2011), Society of Biological Engineering, Providence, RI (poster)
  7. Xu P, Ranganathan S, Koffas MA and Maranas CD. An integrated computational and experimental study to increase the production rate of flavanones in E. Coli. 2010 AIChE annual meeting, Salt Lake City, UT (talk)

Awards and honors

  1. Chinese Government Scholarship for Outstanding Self-financed Students Studying Abroad* 2012
  2. Travel grant for 1st Electrofuels Conference (Providence, RI), Society of Biological engineering 2011
  3. Danisco-Dupont Scholarship for Excellent Students in Biotechnology 2006

(*High distinction for top 0.3% Chinese PhD student studying in US). Media report

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