In the News

Publications

2018


Scholz, Scott A., et al. "Production of cellulosic organic acids via synthetic fungal consortia." Biotechnology and bioengineering 115.4 (2018): 1096-1100.

David N. Carruthers, Casey M. Godwin, David C. Hietala, Bradley J. Cardinale, Xiaoxia (Nina) Lin, Phillip E. Savage. Biodiversity enhances multifunctionality in a life cycle assessment of microalgal biofuel production. In Revision.

2017


Tatayana Saleski, James Y. Tan, Xiaoxia Nina Lin. Dissecting the Ecology of Microbes Using a Systems Toolbox. Cell Systems (2017). Invited commentary.

Scholz, Scott A., Graves, Ian, Minty J.J., Xiaoxia Nina Lin. Production of cellulosic organic acids via synthetic fungal consortia. Biotechnology and Bioengineering (2017).

David N. Carruthers, Chang Kyu Byun, Bradley J. Cardinale, Xiaoxia Nina Lin. Demonstration of transgressive overyielding of algal mixed cultures in microdroplets. Integrative Biology (2017).

Sida Wang, Ki-Joo Sung, Xiaoxia Nina Lin, Mark A. Burns. Bead mediated separation of microparticles in droplets. PLOS ONE (2017).

2015


Fengmin Lin, Kyle L. Ferguson, David R. Boyer, Xiaoxia Nina Lin, and E. Neil G. Marsh. Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic acid decarboxylase. ACS Chemical Biology (2015).

Alissa Kerner*, Jeremy Minty*, Sarah Kistler, Marc Singer, Ian Faulkner, Bruce Dale, Venkatesh Balan, and Xiaoxia Nina Lin. A synthetic E. coli consortium for efficient conversion of lignocellulose-derived hexose and pentose sugars to isobutanol. To be submitted (ACS Synthetic Biology).

Yu Chen, Tom Douce, Marc Singer, and Xiaoxia Nina Lin. In silico reconstruction and analysis of metagenome-wide metabolic networks of an acid mine drainage microbial consortium. In preparation.

Yu Chen and Xiaoxia Nina Lin. A bioinformatic pipeline for automated reconstruction of high-quality genome-scale metabolic networks using genome data. To be submitted.

Jihyang Park, Vincent B. Young, Mark A. Burns, and Xiaoxia Nina Lin. Oxygen gradient construction for co-cultivation of microbial communities in droplets. In revision.

S. Marjan Varedi K., Hangtian Song, Wendi A. Hale, Kristina Hakansson, and Xiaoxia Nina Lin. Multisite phosphorylation underlies ultrasensitive binding of Sic1 to Cdc4 in response to Cln2-Cdc28. In revision.

Gregory J. Boggy, Jeremy Minty, Marc E. Singer, Andrej-Nikolai Spiess, Xiaoxia Nina Lin, and Peter J. Woolf. Simplified measurement of multiple DNA targets with monochrome multiplex qPCR and mechanistic data analysis. PLoS One. In revision.

2014


Peter J. Valdez, Michael C. Nelson, Julia L. Faeth, Henry Y. Wang, Xiaoxia Nina Lin, and Phillip E. Savage. Hydrothermal liquefaction of bacteria and yeast monocultures. Energy & Fuels. 2(4): 867-874 (2014).

2013


Nolan D. Orfield, Andrew J. Fang, Peter J. Valdez, Michael C. Nelson, Philip E. Savage, Xiaoxia Nina Lin, and Gregory A. Keoleian. Life cycle design of an algal biorefinery featuring hydrothermal liquefaction: Effect of reaction conditions and an alternative pathway including microbial regrowth. ACS Sustainable Chemistry & Engineering, 2(4):867-874 (2013).

Fengming Lin, Yu Chen, Robert Levine, Kilho Lee, Yingjin Yuan, and Xiaoxia Nina Lin. Improving fatty acid availability for bio-hydrocarbon production in Escherichia coli by metabolic engineering. PLoS One, 8(10): e78595 (2013).

Jeremy J. Minty, Marc E. Singer, Scott Scholz, Chang Hoon Bae, JungHo Ahn, Cliff E. Foster, James C. Liao, and Xiaoxia Nina Lin. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. PNAS, 110(36): 14592-14597 (2013). Featured in U-Michigan College of Engineering press release: "Microbial team turns corn stalks and leaves into better biofuel", as well as in public media including Scientific American and Australian Broadcasting Corporation.

Fengming Lin, Debasis Das, Xiaoxia Nina Lin, and E. Neil G. Marsh. Aldehyde-forming fatty acyl-coA reductase from cyanobacteria: expression, purification and characterization of the recombinant enzyme. FEBS Journal, 280(19), 4773-4781 (2013).

Michael C. Nelson, Lian Zhu, Anne Thiel, Yan Wu, Mary Guan, Henry Y. Wang, and Xiaoxia Nina Lin. Microbial utilization of aqueous co-products from hydrothermal liquefaction of microalage Nannochloropsis oculata. Bioresource Technology, 136: 522-528 (2013).

2012


Peter J. Valdez, Michael C. Nelson, Henry Y. Wang, Xiaoxia Nina Lin, and Phillip E. Savage. Hydrothermal liquefaction of Nannochloropsis sp.: Systematic study of process variables and analysis of the product fractions. Biomass and Bioenergy, 46: 317-331 (2012).

Alissa Kerner, Jihyang Park, Audra Williams, and Xiaoxia Nina Lin. A programmable Escherichia coli consortium via tunable symbiosis. PLoS One, 7(3): e34032 (2012).

2011


Jeremy J Minty, Ann A Lesnefsky, Fengming Lin, Yu Chen, Ted A. Zaroff III, Artur B. Veloso, Bin Xie, Catie A. McConnell, Rebecca J. Ward, Donald R. Schwartz, Jean-Marie Rouillard, Yuan Gao, Erdogan Gulari, and Xiaoxia Nina Lin. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microbial Cell Factories, 10:18 (2011).

Jihyang Park, Alissa Kerner, Mark A. Burns, and Xiaoxia Nina Lin. Microdroplet-enabled highly parallel co-cultivation of microbial communities. PLoS One, 6(2): e17019 (2011).

S. Marjan Varedi K., Peter J. Woolf, and Xiaoxia Nina Lin. Minimum protein oscillator based on multisite phosphorylation/dephosphorylation. IET Systems Biology, 5, 27-33 (2011).

2010


S. Marjan Varedi K., Alejandra C. Ventura, Sofia D. Merajver, and Xiaoxia Nina Lin. Multisite phosphorylation provides an effective and flexible mechanism for switch-like protein degradation. PLoS One, 5(12):e14029 (2010).

Jeremy J. Minty, S. Marjan Varedi K., and Xiaoxia Nina Lin. Network benchmarking: a happy marriage between systems and synthetic Biology. Chemistry and Biology, 16, 239-241 (2009). Invited commentary.

2009 and Earlier


S. Marjan Varedi K., Peter J. Woolf, and Xiaoxia Nina Lin. Protein oscillator based on multisite phosphorylation/dephosphorylation. In Proceedings of the Third International Conference on Foundations of Systems Biology in Engineering, 137-140 (2009).

Jay Shendure, Gregory J. Porreca, Nikos B. Reppas, Xiaoxia Lin, John P. McCutcheon, Abraham M. Rosenbaum, Michael D. Wang, Kun Zhang, Robi D. Mitra, and George M. Church. Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-1732 (2005).

Daniel Segre, Jeremy Zucker, Jeremy Katz, Xiaoxia Lin, Patrik D’haeseleer, Wayne P. Rindone, Peter Kharchenko, Dat Nguyen, Matthew A. Wright, and George M. Church. From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics, 7, 301-316 (2003).

Xiaoxia Lin, Christodoulos A. Floudas, Ying Wang, and James R. Broach. Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data. Biotechnology and Bioengineering, 84, 864-886 (2003).

Stacy L. Janak, Xiaoxia Lin, and Christodoulos A. Floudas. A new robust optimization approach for scheduling under uncertainty: II. uncertainty with known probability distribution. Computers & Chemical Engineering, 31, 171-195 (2007).

Christodoulos A. Floudas and Xiaoxia Lin. Mixed integer linear programming in process scheduling: modeling, algorithms, and applications. Annals of Operations Research, 139, 131–162 (2005).

Xiaoxia Lin, Christodoulos A. Floudas, and Joseph Kallrath. Global solution approach for a nonconvex MINLP problem in product portfolio optimization. Journal of Global Optimization, 32, 417-431 (2005).

Christodoulos A. Floudas and Xiaoxia Lin. Continuous-time versus discrete-time approaches for scheduling of chemical processes: a review. Computers and Chemical Engineering, 28, 2109-2129 (2004).

Xiaoxia Lin, Stacy L. Janak, and Christodoulos A. Floudas. A new robust optimization approach for scheduling under uncertainty: 1. bounded uncertainty. Computers and Chemical Engineering, 28, 1069-1085 (2004).

Stacy L. Janak, Xiaoxia Lin and Christodoulos A. Floudas. An enhanced continuous-time unit-specific event based formulation for short-term scheduling of multipurpose batch Processes: resource constraints and mixed storage policies. Industrial and Engineering Chemistry Research, 43, 2516-2533 (2004).

Xiaoxia Lin, Emmanuel D. Chajakis and Christodoulos A. Floudas. Scheduling of tanker lightering via a novel continuous-time optimization framework. Industrial and Engineering Chemistry Research, 42, 4441-4451 (2003).

Xiaoxia Lin and Christodoulos A. Floudas. A novel continuous-time modeling and optimization framework for well platform planning problems. Optimization and Engineering, 4, 65-95 (2003).

Xiaoxia Lin and Christodoulos A. Floudas. Design, synthesis and scheduling of multipurpose batch plants via an effective continuous-time formulation. Computers and Chemical Engineering, 25, 665-674 (2001).