User:JCAnderson

J. Christopher Anderson, Associate Professor, UC Berkeley

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John Christopher Anderson

Associate Professor
Department of Bioengineering, UC Berkeley
JCAnderson at berkeley dot edu

Affiliations

EBRC
SynBERC
Lawrence Berkeley National Lab
Clotho Core Development Team
20n Labs
Synvivia

Research History and Current Interests

My research interests are broad but all fit under the umbrella of Synthetic Biology. My PhD research with Peter Schultz focused on the site-specific incorporation of unnatural amino acids in living cells. This research was spun out as the startup Ambrx which develops site-specifically modified therapeutic proteins. In my postdoctoral work with Adam Arkin and Chris Voigt I worked to develop anti-cancer bacteria. I also began a foray into foundational tool development with new standard assembly methods and a set of constitutive promoter parts now referred to as the Anderson Promoter library, or J23100 series. In 2007, I began my UC Berkeley professorship continuing the therapeutic bacteria work and expanding into foundational technologies. Initially focused on automated assembly and selection methods for protein engineering, I expanded into BioCAD tool development, biosafety containment methods, amongst other new technologies. Some of this work was done within the iGEM program, which I mentored in the competition 8 times. In 2015 I went on leave for the startup 20n with DARPA and YCombinator support. For 2 years I worked as a founder and CSO of 20n, which was a software focused metabolic engineering company. We performed biochemical analyses to other companies and DARPA, and developed chemical producing strains through "lab in the cloud" outsourced experimentation. Much of this work focused on producing acetaminophen biologically. In 2016, a graduate student, Gabe Lopez, spun out a second YC company, Synvivia, which is commercializing the synthetic auxotrophy technology we developed at UCB. In 2017 I returned to UC Berkeley full time. My current research consists of BioCAD tool development to support a concurrent wetlab project to produce gram quantities of unstudied biochemical products.

Options for training

I accept students, postdocs, and visiting scholars for research in computational projects, wetlab, or combinations of the two. I am primarily focused on undergraduate and masters student training through hands-on research experience-based courses (BioE 140L and BioE 134) as well as independent and small group projects.

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. Ataii, N., Bakshi, S., Chen, Y., Fernandez, M., Shao, Z., Scheftel, Z., et al. "Enabling AI in synthetic biology through Construction File specification." PLoS ONE. 18(11):e0294469, 2023. https://doi.org/10.1371/journal.pone.0294469
2. Raad, M., Modavi, C., Sukovich, D. J., Anderson, J. C. "Observing Biosynthetic Activity Utilizing Next Generation Sequencing and the DNA Linked Enzyme Coupled Assay" ACS Chem Biol. 2017 Jan 20;12(1):191-199
3. Lopez, G., Anderson, J. C. "Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain" ACS Synth Biol. 2015
4. Hsiau, T. H., Sukovich, D. J., Elms, P., Prince, R. N., Strittmatter, T., Ruan, P., Curry, B., Anderson, P., Sampson, J., Anderson, J. C. "A method for multiplex gene synthesis employing error correction based on expression" PLoS One. 10(3):e0119927, 2015.
5. Sukovich, D. J., Modavi, C., de Raad, M., Prince, R. N., Anderson, J. C. "A DNA-Linked Enzyme-Coupled Assay for Probing Glucosyltransferase Specificity" ACS Synth Biol. 2015
6. 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.
7. Hsiau TH, Anderson JC. "The Engineered DNA Sequence Syntax Inspector" ACS Synth. Biol. 2013
8. 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.
9. 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.
10. 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.
11. 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.
12. Kittleson, J. T., DeLoache, W., Cheng, H-Y. "Scalable Plasmid Transfer using Engineered P1-based Phagemids," ACS Syn. Biol., (12):583-9, 2012.
13. 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.
14. 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.
15. 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
16. Leguia M, Brophy J, Densmore D, Anderson JC. "Automated assembly of standard biological parts," Methods Enzymol. 498:363-97, 2011.
17. 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.
18. 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.
19. 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
20. 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.
21. 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.
22. 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.
23. Densmore, D., Anderson J. C., Combinational Logic Design in Synthetic Biology, IEEE International Symposium on Circuits and Systems (ISCAS) 2009, Taipei Taiwan, May 2009.
24. Czar, M. J., Anderson, J. C., Bader, J. S., Peccoud, J. "Gene synthesis demystified" Trends in Biotechnology, 27(2):63-72, 2009.
25. Anderson, J. C. "Cells By Design" Technology Review, 2007.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. Anderson, J. C., Magliery, T. J., Schultz, P. G. “Exploring the limits of codon and anticodon size” Chem. Biol., 9(2), 237-244, 2002.
37. 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.
38. 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.
39. 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

From PhD with Peter Schultz

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.

Additional patents are omitted for brevity including: US7527943B2, DK1456360T3, AU2007251897B2, US7993872B2, US20060160175A1, US7527943B2, US8669073B2, AU2002256292A1, US7794978B2, US8445446B2, AU2002256292C1, WO2009064416A2, AU2013201487B2, AU2007251897B2, ES2348487T3

From 20n

1. Anderson, J. C., Srivastava, S., Daly, M. T., Poon, P. , Revak, T. “Biosynthetic production of acetaminophen, p-aminophenol, and p-aminobenzoic acid” US Patent US20170211104A1, 2017.
2. Anderson, J. C., Srivastava, S., Daly, M. “Biosynthetic production of carnosine and beta-alanine” US Patent US20170211105A1, 2017.
3. Anderson, J. C., Srivastava, S., Daly, M. “Biosynthetic production of choline, ethanolamine, phosphoethanolamine, and phosphocholine” US Patent US20170211103A1, 2017.

From UCB professorship

1. Anderson, J. C., Lopez, G. “Synthetic auxotrophs with ligand dependent essential genes for biosafety” WIPO Patent WO2016191757A1, 2016.
2. Anderson, J. C., Hsiau, T., Srivastava, S., Ruan, P., Prakash, J., Bodik, R., Seshia, S. A. “Method for Biosynthesis of Acetaminophen” WIPO Patent WO2016069155A2, 2016.
3. Anderson, J. C., Sukovich, D. J., Modavi, C., De Raad, M. “Dna-linked enzyme-coupled assays” US Patent US20170240952A1, 2017.
4. Anderson, J. C., Curry, B., Hsiau, T. “One-pot multiplex gene synthesis” US Patent US20170218358A1, 2017.
5. Anderson, J. C., Hsiau, T., Srivastava, S., Ruan, P., Prakash, J., Bodik, R., Seshia, S. A. “Method for Biosynthesis of Acetaminophen” US Patent US20170260555A1, 2017.
6. Anderson, J. C., Lopez, G. “Synthetic auxotrophs with ligand dependent essential genes for biosafety” US Patent US20180155711A1, 2018.
7. Anderson, J. C., Lopez, G. “Synthetic auxotrophs with ligand dependent essential genes for biosafety” European Patent EP3303581A4, 2018.
8. Anderson, J. C., Lopez, G. “Synthetic auxotrophs with ligand dependent essential genes for biosafety” Japanese Patent JP2018516568A, 2018.