Patrick Shih

Patrick Shih

Position Title
Assistant Professor

  • Department of Plant Biology, College of Biological Sciences
2251 Life Sciences

Research Interests

Engineering and investigating the evolution of metabolic pathways using synthetic biology

The Shih lab focuses on two major areas of research: 1) developing synthetic biology approaches to enable complex engineering efforts in plant systems for applications in agriculture, sustainability, human health, and bioenergy and 2) leveraging genomics and molecular biology to investigate how the evolution of early microbial metabolisms (e.g., photosynthesis) shaped our planet over geological timescales.

Grad Group Affiliations

  • Plant Biology
  • Biochemistry, Molecular, Cellular and Developmental Biology
  • Integrative Genetics and Genomics
  • Chemistry

Specialties / Focus

  • Synthetic Biology
  • Molecular Biology and Biochemistry
  • Metabolic Engineering
  • Plant Biology
  • Microbiology
  • Evolutionary Biology

Honors and Awards

  • Packard Fellowship
  • Katherine Esau Junior Faculty Fellow Award
  • Alfred P. Sloan Fellowship in Computational & Evolutionary Molecular Biology
  • NIH K99 Award
  • Branco Weiss Fellowship
  • Life Sciences Research Foundation Fellowship
  • Lawrence Berkeley National Lab Director’s Award for Exceptional Early Scientific Career Achievement


    • Ph.D. in Plant Biology, University of California, Berkeley 
    • B.S. in Microbiology and B.A. in Political Science, University of California, San Diego

    Selected Publications

    Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E., Adams PD, Banfield JF, and Shih PM. (2020) Novel bacterial clade reveals origin of Form I Rubisco. Nature Plants, 6(9), 1158-1166.

    Calgaro-Kozina A, Vuu KM, Keasling JD, Loque D, Sattely ES, Shih PM. (2020) Engineering plant synthetic pathways for the biosynthesis of novel antifungals. ACS Central Science, 6(8):1394–1400.

    Belcher MS, Vuu KM, Zhou A, Mansoori N, Agosto Ramos A, Thompson MG, Scheller HV, Loque D, Shih PM. (2020) Design of orthogonal regulatory systems for modulating gene expression in plants. Nature Chemical Biology, 16(8):857-865.

    Shih PM. (2018) Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology. Plant Sci, 273:84-91.

    Shih PM, Ward LM, Fischer WW. (2017) Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi. Proc Nat Acad Sci, 114(40):10749-10754.

    Shih PM, Vuu K, Mansoori N, Ayad L, Louie K, Bowen BP, Northen TR, Loqué D. (2016) A robust gene stacking method utilizing yeast assembly for plant synthetic biology. Nature Commun, 7:13215.

    Shih PM, Occhialini A, Cameron JC, Andralojc PJ, Parry MAJ, Kerfeld CA. (2016) Biochemical characterization of predicted Precambrian RuBisCO. Nature Commun, 7:10382.

    Shih PM, Zarzycki J, Niyogi KK, Kerfeld CA. (2014) Introduction of a synthetic CO2-fixing photorespiratory bypass into a cyanobacterium. J Biol Chem, 289(14): 9493-500.

    Shih PM and Matzke NM. (2013) Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins. Proc Nat Acad Sci, 110 (30): 12355-360.

    Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Nat Acad Sci, 110 (3): 1053-58.