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The Fong Lab is interested in bridging the gap between fundamental understanding of biological systems and the novel applications of this knowledge for society's benefit.


Major areas of interest are:

Systems biology

Systems biology has returned systems-level perspectives to biology. This approach is based on the fundamental understanding that biological systems are complex and highly interconnected. Thus, studying single biological components in isolation is not sufficient to fully describe the functionality of the integrated system.

In practice, this discipline has been associated with high-throughput analytical tools that allow simultaneous analysis of all biological components. One of the great challenges in this area is interpretation and integration of these data.

Evolutionary biology

Using microorganisms with fast growth rates allows biological adaptation to be investigated experimentally. Experiments of this nature allow us to study fundamental aspects of biology such as how pathogens become resistant to antibiotics and the relationship between genotype and phenotype. In this area, our lab has studied:

  1. Computational methods for predicting growth behaviors of evolved E. coli
  2. Reproducibility and adaptability of E. coli evolution
  3. Molecular changes occurring during evolution using mRNA transcriptional profiling and metabolic flux analysis

Metabolic engineering

Metabolic engineering intends to intellegently alter the functionality of an organism for a desired purpose, often the production of a chemical of interest. Within a systems perspective, this is accomplished by analyzing how single modifications have effects on an entire biological system.

Progress in this area includes:

  1. Computational modeling and prediction of strain designs for chemical production.
  2. Construction and evolution of 3 strains of E. coli for production of lactic acid.
  3. Characterization of production strains using mRNA transcriptional profiling.

Novel solutions for sustainable production of biofuels

In the face of increasing energy demand, finite petroleum supplies, and urgent environmental concerns, it will be necessary to develop sustainable replacements for liquid petroleum fuels which can be quickly scaled for industrial production and incorporated into existing infrastructure. Our lab is working in a number of ways to address these issues.

Cellulosic ethanol

Cellulose makes up roughly 60% of the dry weight of all plant biomass on earth and therefore represents an extremely abundant and sustainable feedstock for the production of liquid fuels. Feedstocks such as switchgrass grown on marginal farmland, milled agricultural waste, and waste paper pulp can be biochemically converted to ethanol, thereby meeting a significant portion of the energy demand without affecting food supplies in the way that corn ethanol can.

We are working to develop cellulosic ethanol biotechnology by

  1. Optimizing biomass pretreatment processes to maximize enzyme accessibility and minimize chemical inhibition of downstream fermentation processes,
  2. Developing genome-scale constraint based models of a number of cellulolytic bacteria, including Clostridium thermocellum,
  3. Examining fermentation characteristics and gene regulation motifs in the cellulolytic bacterium Thermobifida fusca

Algal feedstocks for biofuel production


  1. Fong, S.S. "Evolutionary engineering of industrially important microbial phenotypes" in Metabolic Pathway Engineering Handbook. CRC press. In press. [FongCRC]
  2. Fong, S.S. "Genome-Scale Assessment of Phenotypic Changes during Adaptive Evolution" in Introduction to Systems Biology. Humana Press. In press.


  3. Apte AA, Cain JW, Bonchev DG, and Fong SS. . pmid:18304325. PubMed HubMed [Apte2008]
  4. Hua Q, Joyce AR, Palsson BØ, and Fong SS. . pmid:17513588. PubMed HubMed [Hua2007]
  5. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, and Palsson BO. . pmid:17088549. PubMed HubMed [Reed2006]
  6. Herrgård MJ, Fong SS, and Palsson BØ. . pmid:16839195. PubMed HubMed [Herrgard2006]
  7. Hua Q, Joyce AR, Fong SS, and Palsson BØ. . pmid:16807925. PubMed HubMed [Hua2006]
  8. Fong SS, Joyce AR, and Palsson BØ. . pmid:16408032. PubMed HubMed [Fong2005]
  9. Fong SS, Nanchen A, Palsson BO, and Sauer U. . pmid:16319065. PubMed HubMed [Fong2006]
  10. Fong SS, Joyce AR, and Palsson BØ. . pmid:16204189. PubMed HubMed [Fong2005b]
  11. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, and Palsson BO. . pmid:15962337. PubMed HubMed [Fong2005c]
  12. Fong SS and Palsson BØ. . pmid:15448692. PubMed HubMed [Fong2004]
  13. Fong SS, Marciniak JY, and Palsson BØ. . pmid:14563875. PubMed HubMed [Fong2003]
  14. Reed, J.L., Fong, S.S., Palsson, B.O. "Phenomics" in Microbial Diversity and Bioprospecting ASMPress 2003. (2003)


  15. Francis K, Palsson B, Donahue J, Fong S, and Carrier E. . pmid:12031652. PubMed HubMed [Francis2002]
  16. Lee GM, Fong SS, Oh DJ, Francis K, and Palsson BO. . pmid:11929001. PubMed HubMed [Lee2002]
  17. Lee, G.M., Fong, S., Francis, K., Oh, D.J., Palsson, B.O. In situ labeling of adherent cells with PKH26. In Vitro Cell. & Developmental Biology Animal. 36(1):4-6. (2000)


  18. Pazzano D, Mercier KA, Moran JM, Fong SS, DiBiasio DD, Rulfs JX, Kohles SS, and Bonassar LJ. . pmid:11027186. PubMed HubMed [Pazzano2000]
All Medline abstracts: PubMed HubMed
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