User:JCAnderson

J. Christopher Anderson, Associate Professor, UC Berkeley

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John Christopher Anderson

Associate Professor
Department of Bioengineering, UC Berkeley
CSO, 20n Labs
JCAnderson at berkeley dot edu
Anderson Lab Home Page

Affiliations

SynBERC
Lawrence Berkeley National Lab
Clotho Core Development Team

Anderson Lab

My research interests are broad but all fit under the umbrella of Synthetic Biology. I'm primarily interested in foundational technologies including automated DNA fabrication and functional analysis, BioCAD tools, and new approaches to protein and promoter engineering. Additionally, my lab investigates new applications for synthetic biology including a primary focus on therapeutic bacteria for the treatment of cancer. We also have interests in diagnostics, new frontiers in small molecule biosynthesis, material production, and anything that expands the scope of synthetic biology to create new products and improve the human condition. Historically, I have been a wetlab experimentalist. However, in recent years my work has focused more on software tools and robotics-based wetlab experiments. Currently, I am a co-founder of the BioCAD company 20n and the non-for-profit Nona Research Foundation. I teach two courses at UC Berkeley, BioE 132 and BioE 140L, the content of which is available at http://synbiotrails.org. I have also mentored the Berkeley iGEM team 8 times.

Education

• 2014 Associate Professor, UC Berkeley, Department of Bioengineering
• 2007 Assistant Professor, UC Berkeley, Department of Bioengineering
• 2003-2007, Postdoctoral Fellow with Adam Arkin (UC Berkeley) and Christopher Voigt (UCSF)
• 2003, PhD, The Scripps Research Institute, Advisor Peter Schultz
• 1998, BS, University of North Carolina at Chapel Hill

Honors and Awards

• 2011 NSF CAREER Award
• 2011 The International Genetically Engineered Machine (iGEM) Competition (Instructor):
  • Best Poster, Americas

Best Poster, Americas

• 2009 The International Genetically Engineered Machine (iGEM) Competition (Instructor):
  • Best software award for tools team
• 2008 The International Genetically Engineered Machine (iGEM) Competition (Instructor):
  • Finalist for wet team
  • Best software award for tools team
• 2007 The International Genetically Engineered Machine (iGEM) Competition (Instructor):
  • Finalist
  • Best Poster Award
• 2007 Technology Review TR35 Award
• 2006 The International Genetically Engineered Machine (iGEM) Competition (Instructor):
  • 1st Place Best Part
  • 3rd Place Best Measurement and Part Characterization
• 2006 Synthetic Biology 2.0: Best Application Award
• 2003 Damon Runyon Cancer Research Foundation Postdoctoral Fellowship
• 1998-2001 NSF Graduate Research Fellowship
• 1998 Venable Medal
• 1996 Phi Beta Kappa
• 1995 Phi Eta Sigma
• 1995 Freshman Honors Program
• 1994-1998 Dean’s List

Publications and Conference Papers

1. DLENCA deep seq
2. Lopez G, Anderson JC. "Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain" ACS Synth Biol. 2015
3. Hsiau TH, Sukovich DJ, Elms P, Prince RN, Strittmatter T, Ruan P, Curry B, Anderson P, Sampson J, Anderson JC. "A method for multiplex gene synthesis employing error correction based on expression" PLoS One. 10(3):e0119927, 2015.
4. Sukovich DJ, Modavi C, de Raad M, Prince RN, Anderson JC. "A DNA-Linked Enzyme-Coupled Assay for Probing Glucosyltransferase Specificity" ACS Synth Biol. 2015
5. Galdzicki M, Wilson ML, Rodriguez CA, Oberortner E, Pocock M, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Huang H, Johnson JD, Kuchinsky A, Lux M, Misirli G, Myers CJ, Peccoud J, Plahar HA, Roehner N, Sirin E, Stan G-B, Villalobos A, Wipat A, Gennari JH, Sauro HM. SBOL: A community standard for communicating designs in synthetic biology. Nature Biotechnol., 32:545-550, 2014.
6. Hsiau TH, Anderson JC. "The Engineered DNA Sequence Syntax Inspector" ACS Synth. Biol. 2013
7. Xia Y, Diprimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weis DD, Anderson JC, Karanicolas J. "The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation" J. Am. Chem. Soc., 135(50):18840-9, 2013.
8. Oberortner, E., Bhatia, S., Densmore, D., Anderson, J. C. "Clotho 3.0: A Pattern-based Story on the Design of Clotho's New Architecture" 19th Conference on Pattern Languages of Programs, 2012.
9. Huh, J., Kittleson, J. T., Arkin, A. P., Anderson, J. C. "Modular Design of a Synthetic Payload Delivery Device" ACS Syn. Biol., 2(8):418-24, 2013.
10. Leguia, M., Brophy, J., Densmore, D., Asante, A., Anderson, J. C. "2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts" J. Biol. Eng. 7(1):2, 2013.
11. Kittleson, J. T., DeLoache, W., Cheng, H-Y. "Scalable Plasmid Transfer using Engineered P1-based Phagemids," ACS Syn. Biol., (12):583-9, 2012.
12. Srivastava, S., Kotker, J., Hamilton, S., Ruan, P., Tsui, J., Anderson, J. C., Bodik, R., Seshia, S. A. "Pathway Synthesis using the Act Ontology", Fourth International Workshop on Bio-Design Automation (IWBDA) 2012, San Francisco, June 2012.
13. Kittleson, J. T., Wu, G. C., Anderson, J. C. "Successes and failures in modular genetic engineering," Curr. Opin. Chem. Biol. 16(3-4):329-36, 2012.
14. Kittleson, J. T., Cheung, S., Anderson, J. C. "Rapid optimization of gene dosage in E. coli using DIAL strains," J. Biol. Eng. 5(1):10, 2011
15. Leguia M, Brophy J, Densmore D, Anderson JC. "Automated assembly of standard biological parts," Methods Enzymol. 498:363-97, 2011.
16. Xia B, Bhatia S, Bubenheim B, Dadgar M, Densmore D, Anderson JC. "Developer's and User's Guide to Clotho v2.0 A Software Platform for the Creation of Synthetic Biological Systems," Methods Enzymol. 498:97-135, 2011.
17. Bilitchenko, L, Liu, A., Cheung, S., Weeding, E., Xia, B., Leguia, M., Anderson, J. C., Densmore, D. "Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems" PLoS One, 2011.
18. Peccoud, J., Anderson, J. C., Chandran, D., Densmore, D., Galdzicki, M., Lux, M. W., Rodriguez, C. A., Stan, G. B., Sauro, H. M. "Essential information for synthetic DNA sequences," Nat Biotechnol., 29(1):22, 2011
19. Densmore, D., Kittleson, J. T., Bilitchennko, L., Liu, A., Anderson, J. C. "Rule Based Constraints for the Construction of Genetic Devices," IEEE International Symposium on Circuits and Systems (ISCAS) 2010, Paris France, May 2010.
20. Densmore, D., Hsiau T., Batten, C., Kittleson, J. T., DeLoache, W., Anderson, J. C. "Algorithms for Automated DNA Assembly" Nucleic Acids Res.38(8):2607-16, 2010 available online.
21. Anderson, J. C., Dueber, J. E., Leguia, M., Wu, G. C., Goler, J. A., Arkin, A. P., Keasling, J. D. "BglBricks: A flexible standard for biological part assembly" J. Biol. Eng., 4:1, 2010 available online.
22. Densmore, D., Anderson J. C., Combinational Logic Design in Synthetic Biology, IEEE International Symposium on Circuits and Systems (ISCAS) 2009, Taipei Taiwan, May 2009.
23. Czar, M. J., Anderson, J. C., Bader, J. S., Peccoud, J. "Gene synthesis demystified" Trends in Biotechnology, 27(2):63-72, 2009.
24. Anderson, J. C. "Cells By Design" Technology Review, 2007.
25. Guo, J., Wang, J., Anderson, J. C., Schultz, P. G. "Addition of an Alpha Hydroxy Acid to the Genetic Code of Bacteria" Angew. Chem. Int. Ed., 47(4) 722-725, 2007.
26. Cropp, T. A., Anderson, J. C., Chin, J. W. "Reprogramming the amino acid substrate specificity of orthogonal aminoacyl-tRNA-synthetases to expand the genetic code of eukaryotic cells" Nat Protoc. 2(10):2590-600, 2007.
27. Anderson, J. C., Voigt, C. A., Arkin, A. P.“Environmental signal integration by a modular AND gate” Mol. Sys. Biol., 3(133), Published online: 14 August 2007.
28. Anderson, J. C., Clarke, E. J., Arkin, A. P., Voigt, C. A. “Environmentally controlled invasion of cancer cells by engineered bacteria” J. Mol Biol., 355(4), 619-27, 2005.
29. Anderson, J. C., Wu, N., Santoro, S. W., Lakshman, V, King, D. S., Schultz, P.G. “An expanded genetic code with a functional quadruplet codon” Proc. Natl. Acad. Sci. U. S. A., 101(20), 7566-71, 2004
30. Santoro, S. W., Anderson, J. C., Lakshman, V., Schultz, P. G. “An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis in Escherichia coli” Nucleic Acids Res., 31(23), 6700-9, 2003.
31. Deiters, A., Cropp, T. A., Mukherji, M., Chin, J. W., Anderson, J. C., Schultz, P. G. “Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae” J. Am. Chem. Soc., 125(39), 11782-3, 2003.
32. Chin, J. W., Cropp, T. A., Anderson, J. C., Mukherji, M., Zhang, Z., Schultz, P. G. “An expanded eukaryotic genetic code” Science, 301(5635), 964-7, 2003.
33. Anderson, J. C., Schultz, P. G. “Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression” Biochemistry, 42(32), 9598-9608, 2003.
34. Mehl, R. A., Anderson, J. C., Santoro, S. W., Wang, L., Martin, A. B., King, D. S., Horn, D. M., Schultz, P. G. “Generation of a bacterium with a 21 amino acid genetic code” J. Am. Chem. Soc., 125(4), 935-939, 2003.
35. Anderson, J. C., Magliery, T. J., Schultz, P. G. “Exploring the limits of codon and anticodon size” Chem. Biol., 9(2), 237-244, 2002.
36. Magliery, T. J., Pastrnak, M., Anderson, J. C., Santoro, S. W., Herberich, B., Meggers, E. L., Wang, L. & Schultz, P. G. “In vitro tools and in vivo engineering: incorporation of unnatural amino acids into proteins” In Translation Mechanisms (ed. J. Lapointe and L. Brakier-Gingras), in press, 2001.
37. Magliery, T. J., Anderson, J. C., Schultz, P. G. “Expanding the genetic code: selection of efficient suppressors of four-base codons and identification of "shifty" four-base codons with a library approach in Escherichia coli” J. Mol. Biol., 307(3), 755-69, 2001.
38. Betts, D., Johnson, T., Anderson, J. C., DeSimone, J. M. “Controlled radical polymerization methods for the synthesis of non-ionic surfactants for CO2” Polym. Prepr., 38(1), 760-761, 1997.

Patents

1. Schultz, P. G., Wang, L., Anderson, J. C., Chin, J. W., Liu, D. R., Magliery, T. J., Meggers, E. L., Mehl, R. A., Pastrnak, M., Santoro, S. W., Zhang, Z. “Methods and compositions for the production of orthogonal tRNA-aminoacyl tRNA synthetase pairs” US Patent 7,083,970, 2006.
2. Schultz, P. G., Wang, L., Anderson, J. C., Chin, J. W., Liu, D. R., Magliery, T. J., Meggers, E. L., Mehl, R. A., Pastrnak, M., Santoro, S. W., Zhang, Z. “In vivo incorporation of unnatural amino acids” US Patent 7,045,337, 2006.