Now showing items 1-10 of 10

    • Common principles and best practices for engineering microbiomes 

      Lawson, C.E.; Harcombe, W.R.; Hatzenpichler, R.; Noguera, D.R.; McMahon, K.D.; Lindemann, S.R.; Loffler, F.E.; O'Malley, M.A.; Garcia-Martin, H.; Pfleger, B.F.; Raskin, L.; Venturelli, O.S.; Weissbrodt, D.G. (2019)
      Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue hat structuring research ...
    • A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630 

      Roell, G.W.; Carr, R.R.; Campbell, T.; Shang, Z.; Henson, W.R.; Czajka, J.J.; Garcia-Martin, H.; Zhang, F.; Foston, M.; Dantas, G.; Moon, T.S.; Tang, Y.J. (2019-06)
      Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, ...
    • The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization 

      Morrell, W.C.; Birkel, G.W.; Forrer, M.; Lopez, T.; Backman, T.W.H.; Dussault, M.; Petzold, C.J.; Baidoo, E.E.K.; Costello, Z.; Ando, D.; Alonso-Gutierrez, J.; George, K.W.; Mukhopadhyay, A.; Vaino, I.; Keasling, J.D.; Adams, P.D.; Hillson, N.J.; Garcia-Martin, H. (2017-09-30)
      Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large ...
    • Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism 

      Shymansky, C.M.; Wang, G.; Baidoo, E.E.K.; Gin, J.; Apel, A.R.; Mukhopadhyay, A.; Garcia-Martin, H.; Keasling, J.D. (2017-05-31)
      13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference ...
    • The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism 

      Birkel, G.W.; Ghosh, A.; Kumar, V.S.; Weaver, D.; Ando, D.; Backman, T.W.H.; Arkin, A.P.; Keasling, J.D.; Garcia-Martin, H. (2017-01-01)
      Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ...
    • Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning 

      Opgenorth, P.; Costello, Z.; Okada, T.; Goyal, G.; Chen, Y.; Gin, J.; Benites, V.; de Raad, M.; Northen, T.R.; Deng, K.; Deutsch, S.; Baidoo, E.E.K.; Petzold, C.J.; Hillson, N.J.; Garcia-Martin, H.; Beller, H.R. (2019-01-01)
      The Design–Build–Test–Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient ...
    • A Machine Learning Approach to Predict Metabolic Pathway Dynamics from Time Series Multiomics Data 

      Costello, Z.; Garcia-Martin, H. (2018-05)
      New synthetic biology capabilities hold the promise of dramatically improving our ability to engineer biological systems. However, a fundamental hurdle in realizing this potential is our inability to accurately predict ...
    • Machine learning framework for assessment of microbial factory performance 

      Oyetunde, T.; Liu, D.; Garcia-Martin, H.; Tang, Y.J. (2019-01-01)
      Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance (including product titer or rate) under suboptimal metabolism and complex bioprocess ...
    • Microbial production of advanced biofuels 

      Keasling, J.; Garcia Martin, H.; Lee, T; Mukhopadhyay, A.; Singer, S.; Sundstrom, E. (2021)
      Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels are biofuels produced from a renewable carbon source using engineered ...
    • Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation 

      Carbonell, P.; Radivojevic, T.; Garcia-Martin, H. (2019-07)
      Our inability to predict the behavior of biological systems severely hampers progress in bioengineering and biomedical applications. We cannot predict the effect of genotype changes on phenotype, nor extrapolate the ...