James Y. Tan, Tatyana E. Saleski, Xiaoxia Nina Lin. The effect of droplet size on syntrophic dynamics in microdropTan JY, Saleski TE, Lin XN (2022) The effect of droplet size on syntrophic dynamics in droplet-enabled microbial co-cultivation. PLOS ONE 17(3): e0266282.

Adam G. Krieger, Jiahao Zhang, Xiaoxia Nina Lin. Temperature regulation as a tool to program synthetic microbial community composition. Biotechnology and Bioengineering, 118, 1381–1392 (2021).

Derek J. Smith, James Y. Tan, McKenzie A. Powers, Xiaoxia N. Lin, Timothy W. Davis, Gregory J. Dick. Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time. Environmental Microbiology 23(6), 3020– 3036 (2021).

Tatyana E. Saleski, Meng Ting Chung, David N. Carruthers, Azzaya Khasbaatar, Katsuo Kurabayashi, Xiaoxia Nina Lin.  Optimized gene expression from bacterial chromosome by high-throughput integration and screening. Science Advances, eabe1767 (2021).

David N. Carruthers, Tatyana E. Saleski, Scott A. Scholz, and Xiaoxia Nina Lin. Random chromosomal integration and screening yields E. coli K-12 derivatives capable of efficient sucrose utilization. ACS Synthetic Biology, 9, 12, 3311–3321 (2020).

James Y. Tan, Sida Wang, Gregory J. Dick, Vincent B. Young, David H. Sherman, Mark A. Burns, Xiaoxia Nina Lin, Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’. Integrative Biology, 12, 11, 263–274 (2020).

David N. Carruthers, Casey M. Godwin, David C. Hietala, Bradley J. Cardinale, Xiaoxia Nina Lin*, Phillip E. Savage*. *: Corresponding authors. Biodiversity improves life cycle sustainability metrics in algal biofuel production. Environmental Science & Technology, 53,15, 9279-9288 (2019).

Tatyana E. Saleski, Alissa R. Kerner, Meng Ting Chung, Corine M. Jackman, Azzaya Khasbaatar, Katsuo Kurabayashi, Xiaoxia Nina Lin. Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries. Metabolic Engineering, 54, 232-243 (2019).

Corine M. Jackman, Kyle W. Deans, Larry J. Forney, Xiaoxia Nina Lin. Microdroplet co-cultivation and interaction characterization of human vaginal bacteria. Integrative Biology, 11, 69-78 (2019).

Scott Scholz, Rucheng Diao, Elayne Fivenson, Xiaoxia Nina Lin*, Peter Freddolino*. *: Corresponding authors. High-resolution mapping of the Escherichia coli chromosome reveals positions of high and low transcription. Cell Systems, 8(3), 212-225.e9 (2019).

Scott Scholz, Ian Graves, Jeremy Minty, Xiaoxia Nina Lin. Production of cellulosic organic acids via synthetic fungal consortia. Biotechnology and Bioengineering, 115(4):1096-1100 (2018).

David N. Carruthers, Chang Kyu Byun, Bradley J. Cardinale, Xiaoxia Nina Lin. Demonstration of transgressive overyielding of algal mixed cultures in microdroplets. Integrative Biology, 9, 687-694 (2017).

Sida Wang, Ki-Joo Sung, Xiaoxia Nina Lin, Mark A. Burns. Bead mediated separation of microparticles in droplets, PLoS One, 12(3): e0173479(2017).

Tatyana Saleski, James Yi Tan, and Xiaoxia Nina Lin. Dissecting the ecology of microbes using a systems toolbox. Cell Systems, 5(5) 442-444 (2017). Invited preview.

Fengming Lin, Kyle Ferguson, David Boyer, Xiaoxia Lin*, and E. Neil Marsh*. *: Corresponding authors. 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 10, 1137-1144 (2015).

Jeremy J. Minty, and Xiaoxia Nina Lin. Engineering synthetic microbial consortia for consolidated bioprocessing of ligonocellulosic biomass into valuable fuels and chemicals. Chapter 18 in Direct Microbial Conversion of Biomass to Advanced Biofuels, edited by Michael Himmel. Elsevier (2015).

Fengming Lin, and E. Neil G. Marsh, Xiaoxia Nina Lin. Recent progress in hydrocarbon biofuel synthesis: pathways and enzymes. Chinese Chemical Letters 26, 431–434 (2015).

Nolan D. Orfield, Andrew J. Fang, Peter J. Valdez, Michael C. Nelson, Phillip 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, 867-874 (2014).

Erin R. Shellman, Yu Chen, Xiaoxia Lin, Charles F. Burant, and Santiago Schnell. Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Computational Biology and Chemistry 53, 242–250 (2014).

Peter Valdez, Michael Nelson, Julia Faeth, Henry Wang, Xiaoxia Nina Lin, and Phillip Savage. Hydrothermal liquefaction of bacteria and yeast monocultures. Energy & Fuels, 28, 67−75 (2014).

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. Proc Natl Acad Sci USA, 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 such as Scientific American and Australian Broadcasting Corporation.  

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

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

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).

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).

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 & Biology, 16, 239–241 (2009). Invited preview.

Prior to UM

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).

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).

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).

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 & Engineering Chemistry Research, 43, 2516–2533 (2004).

Christodoulos A. Floudas and Xiaoxia Lin. Continuous-time versus discrete-time approaches for scheduling of chemical processes: a review. Computers & 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 & Chemical Engineering, 28, 1069–1085 (2004).

Daniel Segrè, 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).

Xiaoxia Lin, Emmanuel D. Chajakis, and Christodoulos A. Floudas. Scheduling of tanker lightering via a novel continuous-time optimization framework. Industrial & 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, Christodoulos A. Floudas, Sweta Modi, and Nikola M. Juhasz. Continuous-time optimization approach for medium-range production scheduling of a multi-product batch plant. Industrial & Engineering Chemistry Research, 41, 3884–3906 (2002).

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