PhD ChE ’03
BS ChE ’97
BS Computer Science and Technology ’97
Professor Lin’s research lies at the intersection of biology and engineering with a focus on microbial systems, particularly microbial communities, using systems biology and synthetic biology approaches. Her lab aims to employ engineering tools and skills such as microfluidics and quantitative modeling to help unlock mysteries of complex natural microbial communities, especially those closely associated with environment and health issues (e.g. human microbiome). In parallel, the research group exploits design principles nature utilizes and develops synthetic microbial consortia technologies to address critical needs faced by our society such as sustainable biofuel and chemical production.
University of Michigan
Chemical Engineering Department
Ann Arbor, Michigan
Associate Professor, 2014-
Assistant Professor, 2006 –
Harvard Medical School
Department of Genetics
Postdoctoral Fellow, 2003-2006
ChE 330 – Chemical and Engineering Thermodynamics, Winter 2008, Winter 2009, Winter 2010
ChE 466 – Process Dynamics and Control
ChE 487 – Chemical Process Simulation and Design, Winter 2007
ChE 496 – Product Design and Development
ChE 696 – Mathematical Methods in Chemical and Biological Engineering, Fall 2008
ChE 696 – Mathematical Methods for Biological Network Analysis, Fall 2009, Fall 2010
NSF CAREER Award, 2011
National Science Foundation
Elizabeth C. Crosby Research Award, Fall 2007, 2011
University of Michigan
Dean’s Fund for Scholarly Travel, 2001
Ticona Assistant in Instruction (AI) Award, 2000-2001
Schowalter Travel Award, 2000
Dong Fellowship, 1995
Outstanding Student Awards, 1993, 1994, 1996
Systems Biology and Synthetic Biology
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).
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).
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)
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).
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 commentary.
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).
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).
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).
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).
Alissa Kerner, Jihyang Park, Audra Williams, and Xiaoxia Nina Lin. A programmable synthetic E. coli consortium via tunable symbiosis. Submitted.
Xiaoxia Lin*, Yuan Gao*, Yaoyun Shi, and George M. Church. *: Equal contributions. Biological switches arising from single protein multisite modifications. In revision.
Nikos B. Reppas*, Xiaoxia Lin*, Jay Shendure, Yuan Gao, Jeremy Minty, and George M. Church. *: Equal contributions. Evolution of microbial symbiosis: a synthetic system of two cross-feeding E. coli auxotrophs. To be submitted.
Yu Chen and Xiaoxia Nina Lin. A bioinformatics tool for automated generation of whole-cell metabolic networks from genomic data. To be submitted.
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. To be submitted.
Process Systems Engineering
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).
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. A novel continuous-time modeling and optimization framework for well platform planning problems. Optimization and Engineering, 4, 65–95 (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, 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).
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).
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).
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. Mixed integer linear programming in process scheduling: modeling, algorithms, and applications. Annals of Operations Research, 139, 131–162 (2005).
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).