Biographical Information

Education

Professional Experience

Honors and Awards

NSF CAREER Award, 2011

Elizabeth C. Crosby Research Award, University of Michigan, Fall 2007, 2011

Dean's Fund for Scholarly Travel, Princeton University, 2001

Ticona Assistant in Instruction (AI) Award, Princeton University, 2000-2001

Schowalter Travel Award, Princeton University, 2000

Dong Fellowship, Tsinghua University, 1995

Outstanding Student Awards, Tsinghua University, 1993, 1994, 1996

Research Interests

Integrating modeling and experiments at the interface of biology and engineering

Research in my research group aims to unearth fundamental mechanisms underlying the diverse and complex functions of biological networks, and to engineer them for developing biotechnologies, through integrated mathematical modeling, computer simulation and wet-lab experiments. Employing systems biology and synthetic biology approaches, we are focusing on three broad topics: i) system-level study and engineering of microbial communities; ii) mechanistic study and engineering of single-molecule biological switches; and iii) microbial engineering for bio-energy applications.

Recent Publications

Systems Biology and Synthetic Biology

1. 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).
2. 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).
3. 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)
4. 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).
5. 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.
6. 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).
7. 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).
8. 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).
9. 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).
10. Alissa Kerner, Jihyang Park, Audra Williams, and Xiaoxia Nina Lin. A programmable synthetic E. coli consortium via tunable symbiosis. Submitted.
11. Xiaoxia Lin*, Yuan Gao*, Yaoyun Shi, and George M. Church. *: Equal contributions. Biological switches arising from single protein multisite modifications. In revision.
12. 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.
13. Yu Chen  and Xiaoxia Nina Lin. A bioinformatics tool for automated generation of whole-cell metabolic networks from genomic data. To be submitted.
14. 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

1. 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).
2. 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).
3. 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).
4. 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).
5. 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).
6. 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).
7. 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).
8. 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).
9. 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).
10. 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).

Courses Taught at the University of Michigan

Undergraduate ChE Courses

ChE 330 - Chemical and Engineering Thermodynamics, Winter 2008, Winter 2009, Winter 2010
ChE 487 - Chemical Process Simulation and Design, Winter 2007

Graduate ChE Courses

ChE 696 - Mathematical Methods in Chemical and Biological Engineering, Fall 2008
ChE 696 - Mathematical Methods for Biological Network Analysis, Fall 2009, Fall 2010