Tan, James Yi; Li, Jessica Du; Bahr, Auden; Lin, Xiaoxia Nina. Massively parallel metabarcoding of droplet co-cultures. 2025, bioRxiv. DOI: https://doi.org/10.1101/2025.01.14.633022
Jackman, Corine M.; Tan, James Y.; Lin, Xiaoxia Nina. Microdroplet-enabled high-throughput cultivation of vaginal bacteria using cervicovaginal fluids. 2023, bioRxiv. DOI: https://doi.org/10.1101/2023.09.26.559375
Tan, James Y.; Saleski, Tatyana E.; Lin, Xiaoxia Nina. The effect of droplet size on syntrophic dynamics in droplet-enabled microbial co-cultivation. PLOS ONE 2022, 17, e0266282. DOI: https://doi.org/10.1371/journal.pone.0266282
Krieger, Adam G.; Zhang, Jiahao; Lin, Xiaoxia Nina. Temperature regulation as a tool to program synthetic microbial community composition. Biotechnology and Bioengineering 2021, 118, 1381–1392. DOI: https://doi.org/10.1002/bit.27662
Smith, Derek J.; Tan, James Y.; Powers, McKenzie A.; Lin, Xiaoxia Nina; Davis, Timothy W.; Dick, Gregory J. Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time. Environmental Microbiology 2021, 23, 3020–3036. DOI: https://doi.org/10.1111/1462-2920.15514
Saleski, Tatyana E.; Chung, Meng Ting; Carruthers, David N.; Khasbaatar, Azzaya; Kurabayashi, Katsuo; Lin, Xiaoxia Nina. Optimized gene expression from bacterial chromosome by high-throughput integration and screening. Science Advances 2021, 7, eabe1767. DOI: https://doi.org/10.1126/sciadv.abe1767
Carruthers, David N.; Saleski, Tatyana E.; Scholz, Scott A.; Lin, Xiaoxia Nina. Random Chromosomal Integration and Screening Yields E. coli K-12 Derivatives Capable of Efficient Sucrose Utilization. ACS Synthetic Biology 2020, 9, 3311–3321. DOI: https://doi.org/10.1021/acssynbio.0c00392
Tan, James Y; Wang, Sida; Dick, Gregory J; Young, Vincent B; Sherman, David H; Burns, Mark A; Lin, Xiaoxia Nina. Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’. Integrative Biology 2020, 12, 263–274. DOI: https://doi.org/10.1093/intbio/zyaa021
Carruthers, David N.; Godwin, Casey M.; Hietala, David C.; Cardinale, Bradley J.; Lin, Xiaoxia Nina; Savage, Phillip E. Biodiversity Improves Life Cycle Sustainability Metrics in Algal Biofuel Production. Environmental Science & Technology 2019, 53, 9279–9288. DOI: https://doi.org/10.1021/acs.est.9b00909
Saleski, Tatyana E.; Kerner, Alissa R.; Chung, Meng Ting; Jackman, Corine M.; Khasbaatar, Azzaya; Kurabayashi, Katsuo; Lin, Xiaoxia Nina. Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries. Metabolic Engineering 2019, 54, 232–243. DOI: https://doi.org/10.1016/j.ymben.2019.04.007
Jackman, Corine M; Deans, Kyle W; Forney, Larry J; Lin, Xiaoxia Nina. Microdroplet co-cultivation and interaction characterization of human vaginal bacteria. Integrative Biology 2019, 11, 69–78. DOI: https://doi.org/10.1093/intbio/zyz006
Scholz, Scott A.; Diao, Rucheng; Wolfe, Michael B.; Fivenson, Elayne M.; Lin, Xiaoxia Nina; Freddolino, Peter L. High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription. Cell Systems 2019, 8, 212-225.e9. DOI: https://doi.org/10.1016/j.cels.2019.02.004
Scholz, Scott A.; Graves, Ian; Minty, Jeremy J.; Lin, Xiaoxia Nina. Production of cellulosic organic acids via synthetic fungal consortia. Biotechnology and Bioengineering 2017, 115, 1096–1100. DOI: https://doi.org/10.1002/bit.26509
Carruthers, David N.; Byun, Chang Kyu; Cardinale, Bradley J.; Lin, Xiaoxia Nina. Demonstration of transgressive overyielding of algal mixed cultures in microdroplets. Integrative Biology 2017, 9, 687–694. DOI: https://doi.org/10.1039/C6IB00241B
Wang, Sida; Sung, Ki-Joo; Lin, Xiaoxia Nina; Burns, Mark A. Bead mediated separation of microparticles in droplets. PLOS ONE2017, 12, e0173479. DOI: https://doi.org/10.1371/journal.pone.0173479
Saleski, Tatyana; Tan, James Yi; Lin, Xiaoxia Nina. Dissecting the Ecology of Microbes Using a Systems Toolbox. Cell Systems2017, 5, 442–444. DOI: https://doi.org/10.1016/j.cels.2017.11.009
Lin, Fengming; Ferguson, Kyle L.; Boyer, David R.; Lin, Xiaoxia Nina; Marsh, E. Neil G. 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, 10, 1137–1144. DOI: https://doi.org/10.1021/cb5008103
Minty, Jeremy J.; Lin, Xiaoxia N. 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 2015, 365–381. DOI: https://doi.org/10.1016/B978-0-444-59592-8.00018-X
Lin, Feng-Ming; Marsh, E. Neil G.; Lin, Xiaoxia Nina. Recent progress in hydrocarbon biofuel synthesis: Pathways and enzymes. Chinese Chemical Letters 2015, 26, 431–434. DOI: https://doi.org/10.1016/j.cclet.2015.03.018
Orfield, Nolan D.; Fang, Andrew J.; Valdez, Peter J.; Nelson, Michael C.; Savage, Phillip E.; Lin, Xiaoxia Nina; Keoleian, Gregory A. 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 2014, 2, 867–874. DOI:https://doi.org/10.1021/sc4004983
Shellman, Erin R.; Chen, Yu; Lin, Xiaoxia; Burant, Charles F.; Schnell, Santiago. Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Computational Biology and Chemistry2014, 53, 242–250. DOI: https://doi.org/10.1016/j.compbiolchem.2014.09.006
Valdez, Peter J.; Nelson, Michael C.; Faeth, Julia L.; Wang, Henry Y.; Lin, Xiaoxia Nina; Savage, Phillip E. Hydrothermal Liquefaction of Bacteria and Yeast Monocultures. Energy & Fuels 2013, 28, 67–75. DOI: https://doi.org/10.1021/ef401506u
Lin, Fengming; Chen, Yu; Levine, Robert; Lee, Kilho; Yuan, Yingjin; Lin, Xiaoxia Nina. Improving Fatty Acid Availability for Bio-Hydrocarbon Production in Escherichia coli by Metabolic Engineering. PLOS ONE 2013, 8, e78595. DOI: https://doi.org/10.1371/journal.pone.0078595
Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A.; Bae, Chang-Hoon; Ahn, Jung-Ho; Foster, Clifton E.; Liao, James C.; Lin, Xiaoxia Nina. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proceedings of the National Academy of Sciences 2013, 110, 14592–14597. DOI: https://doi.org/10.1073/pnas.1218447110. 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
Lin, Fengming; Das, Debasis; Lin, Xiaoxia N.; Marsh, E. Neil G. Aldehyde‐forming fatty acyl‐coA reductase from cyanobacteria: expression, purification and characterization of the recombinant enzyme. The FEBS Journal 2013, 280, 4773–4781. DOI: https://doi.org/10.1111/febs.12443
Nelson, Michael; Zhu, Lian; Thiel, Anne; Wu, Yan; Guan, Mary; Minty, Jeremy; Wang, Henry Y.; Lin, Xiaoxia Nina. Microbial utilization of aqueous co-products from hydrothermal liquefaction of microalgae Nannochloropsis oculata. Bioresource Technology2013, 136, 522–528. DOI: https://doi.org/10.1016/j.biortech.2013.03.074
Valdez, Peter J.; Nelson, Michael C.; Wang, Henry Y.; Lin, Xiaoxia Nina; Savage, Phillip E. Hydrothermal liquefaction of Nannochloropsis sp.: Systematic study of process variables and analysis of the product fractions. Biomass and Bioenergy 2012, 46, 317–331. DOI: https://doi.org/10.1016/j.biombioe.2012.08.009
Kerner, Alissa; Park, Jihyang; Williams, Audra; Lin, Xiaoxia Nina. A Programmable Escherichia coli Consortium via Tunable Symbiosis. PLOS ONE 2012, 7, e34032. DOI: https://doi.org/10.1371/journal.pone.0034032
Minty, Jeremy J; Lesnefsky, Ann A; Lin, Fengming; Chen, Yu; Zaroff, Ted A; Veloso, Artur B; Xie, Bin; McConnell, Catie A; Ward, Rebecca J; Schwartz, Donald R; Rouillard, Jean-Marie; Gao, Yuan; Gulari, Erdogan; Lin, Xiaoxia Nina. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microbial Cell Factories 2011, 10, . DOI: https://doi.org/10.1186/1475-2859-10-18
Park, Jihyang; Kerner, Alissa; Burns, Mark A.; Lin, Xiaoxia Nina. Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities. PLOS ONE 2011, 6, e17019. DOI: https://doi.org/10.1371/journal.pone.0017019
Marjan Varedi K., S.; Woolf, P.J.; Lin, Xiaoxia Nina. Minimum protein oscillator based on multisite phosphorylation/dephosphorylation. IET Systems Biology 2011, 5, 27–33. DOI: https://doi.org/10.1049/iet-syb.2009.0069
Varedi K., S. Marjan; Ventura, Alejandra C.; Merajver, Sofia D.; Lin, Xiaoxia Nina. Multisite Phosphorylation Provides an Effective and Flexible Mechanism for Switch-Like Protein Degradation. PLOS ONE 2010, 5, e14029. DOI: https://doi.org/10.1371/journal.pone.0014029
Minty, Jeremy J.; Varedi K, S. Marjan; Lin, Xiaoxia Nina. Network Benchmarking: A Happy Marriage between Systems and Synthetic Biology. Chemistry & Biology 2009, 16, 239–241. DOI: https://doi.org/10.1016/j.chembiol.2009.03.004
Prior to UM
Janak, Stacy L.; Lin, Xiaoxia; Floudas, Christodoulos A. A new robust optimization approach for scheduling under uncertainty: II. Uncertainty with known probability distribution. Computers & Chemical Engineering 2007, 31, 171–195. DOI: https://doi.org/10.1016/j.compchemeng.2006.05.035
Shendure, Jay; Porreca, Gregory J.; Reppas, Nikos B.; Lin, Xiaoxia; McCutcheon, John P.; Rosenbaum, Abraham M.; Wang, Michael D.; Zhang, Kun; Mitra, Robi D.; Church, George M. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 2005, 309, 1728–1732. DOI: https://doi.org/10.1126/science.1117389
Floudas, Christodoulos A.; Lin, Xiaoxia. Mixed Integer Linear Programming in Process Scheduling: Modeling, Algorithms, and Applications. Annals of Operations Research 2005, 139, 131–162. DOI: http://dx.doi.org/10.1007/s10479-005-3446-x
Lin, Xiaoxia; Floudas, Christodoulos A.; Kallrath, Josef. Global Solution Approach for a Nonconvex MINLP Problem in Product Portfolio Optimization. Journal of Global Optimization 2005, 32, 417–431. DOI: https://doi.org/10.1007/s10898-004-5903-5
Janak, Stacy L.; Lin, Xiaoxia; Floudas, Christodoulos A. 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 2004, 44, 426–426. DOI: https://doi.org/10.1021/ie048866r
Floudas, Christodoulos A.; Lin, Xiaoxia. Continuous-time versus discrete-time approaches for scheduling of chemical processes: a review. Computers & Chemical Engineering 2004, 28, 2109–2129. DOI: https://doi.org/10.1016/j.compchemeng.2004.05.002
Lin, Xiaoxia; Janak, Stacy L.; Floudas, Christodoulos A. A new robust optimization approach for scheduling under uncertainty: 1. bounded uncertainty. Computers & Chemical Engineering 2004, 28, 1069–1085. DOI: https://doi.org/10.1016/j.compchemeng.2003.09.020
Segrè, Daniel; Zucker, Jeremy; Katz, Jeremy; Lin, Xiaoxia; D’Haeseleer, Patrik; Rindone, Wayne P.; Kharchenko, Peter; Nguyen, Dat H.; Wright, Matthew A.; Church, George M. From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting. OMICS: A Journal of Integrative Biology 2003, 7, 301–316. DOI: https://doi.org/10.1089/153623103322452413
Lin, Xiaoxia; Floudas, Christodoulos A.; Wang, Ying; Broach, James R. Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data. Biotechnology and Bioengineering 2003, 84, 864–886. DOI: https://doi.org/10.1002/bit.10844
Lin, Xiaoxia; Chajakis, Emmanuel D.; Floudas, Christodoulos A. Scheduling of Tanker Lightering via a Novel Continuous-Time Optimization Framework. Industrial & Engineering Chemistry Research 2003, 42, 4441–4451. DOI: https://doi.org/10.1021/ie0205400
Lin, Xiaoxia; Floudas, Christodoulos A. A novel continuous-time modeling and optimization framework for well platform planning problems. Optimization and Engineering 2003, 4, 65–95. DOI: https://doi.org/10.1023/A:1021860330145
Lin, Xiaoxia; Floudas, Christodoulos A.; Modi, Sweta; Juhasz, Nikola M. Continuous-Time Optimization Approach for Medium-Range Production Scheduling of a Multiproduct Batch Plant. Industrial & Engineering Chemistry Research 2002, 41, 3884–3906. DOI: https://doi.org/10.1021/ie011002a
Lin, X; Floudas, C.A Design, synthesis and scheduling of multipurpose batch plants via an effective continuous-time formulation. Computers & Chemical Engineering 2001, 25, 665–674. DOI: https://doi.org/10.1016/S0098-1354(01)00663-9