Principal Investigator

Research Emphasis

• Adaptive Laboratory Evolution (ALE) - Supervises and leads the design, development, and implementation of an automated platform for ALE studies and a bioinformatics-driven mutational database
• Constraint-based Modeling and Reconstruction (COBRA): Major contributor to the field through model building, algorithm development, applied studies, and experimental validation
• Runs day-to-day operations of the Systems Biology Research Group including managing budgets and wet lab
• Serves as Research Advisor and Thesis Committee Member for numerous graduate students in the department of Bioengineering, as well as mentoring Post-docs and Undergraduate students


Research Scientist

July 2010 – present

Grants and Awards



  • Co-I - Agency: NIH - Focus: Systems biology targeting of antimicrobial resistance Project Description

  • Co-PI - Agency: Novo Nordisk Foundation - Focus: Network Reconstruction and in silico Biology


Key Selected Publications

  • Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM “The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology.” Metab Eng. 2019 Aug 8. pii: S1096-7176(19)30153-3. doi: 10.1016/j.ymben.2019.08.004

  • HG Lim, T Eng, D Banerjee, G Alarcon, AK Lau, MR Park, BA Simmons, BO Palsson, SW Singer, A Mukhopadhyay, Feist AM. Generation of Pseudomonas putida KT2440 strains with efficient utilization of xylose and galactose via adaptive laboratory evolution ACS Sustainable Chemistry & Engineering 9 (34), 11512-11523, 2021

  • Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM. Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. ACS Synth Biol. 2021 Dec 17;10(12):3379-3395. doi: 10.1021/acssynbio.1c00337.

  • Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. Commun Biol. 2021 Jun 25;4(1):793. doi: 10.1038/s42003-021-02339-z.

  • Mohamed ET, Werner AZ, Salvachúa D, Singer CA, Szostkiewicz K, Rafael Jiménez-Díaz M, Eng T, Radi MS, Simmons BA, Mukhopadhyay A, Herrgård MJ, Singer SW, Beckham GT, Feist AM. Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Metab Eng Commun. 2020 Aug 29;11:e00143. doi: 10.1016/j.mec.2020.e00143.

  • Guzmán GI, Sandberg TE, LaCroix RA, Nyerges A, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM “Enzyme promiscuity shapes adaptation to novel growth substrates” Mol Syst Biol. 2019 15: e8462 doi: 10.15252/msb.20188462

  • Phaneuf PV, Gosting D, Palsson BO, Feist AM. “ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.” Nucleic Acids Res. Oct 24. doi: 10.1093/nar/gky983. (2018)

  • McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. “Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.” Metab Eng. June 15. doi: 10.1016/j.ymben.2018.06.005 (2018)

  • LaCroix RA, Palsson BO, Feist AM “A Model for Designing Adaptive Laboratory Evolution Experiments.” Appl Environ Microbiol. Mar 31;83(8). pii: e03115-16. doi: 10.1128/AEM.03115-16 (2017)

  • Guzman GI, Utrilla J, Brunk E, Monk JM, Ebrahim A, Nurk S, Palsson BO, Feist A.M. "Model-driven discovery of underground metabolic functions in Escherichia coli." Proc Natl Acad Sci U S A. 112(3):929-34. (2015)

Google Scholar


Doctor of Philosophy in Bioengineering University of California - San Diego, December 2008

Master of Science in Bioengineering University of California - San Diego, December 2005

Bachelor of Science in Chemical Engineering University of Nebraska - Lincoln, May 2003, Honors Program Graduate

Previous Research Experience

GT Life Sciences, Inc., San Diego, CA (2009 - 2010)

Biological Process Development Facility / UNL - Protein Purification Laboratory (2002 - 2003)

Goodyear Inc., Lincoln, Nebraska - Co-Op Participant (2001 - 2002)

Research Experience for Undergraduates Program (REU) / Colorado State University (Summer 2001)

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Contact Information

Email Address:

Phone: (858) 534-9592

Mailing Address: 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412