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 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).
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. Xiaoxia Lin*, Yuan Gao*, Yaoyun Shi, and George M. Church. *: Equal contributions. The sound of silence: biological switches through single protein multisite modifications. In revision.
5. Nikos Reppas*, Xiaoxia Lin*, Jay Shendure, Gregory J. Porreca, and George M. Church. *: Equal contributions. Evolution of microbial symbiosis: a synthetic system of two cross-feeding E. coli auxotrophs. In preparation.
6. Aaron Brandes*, Xiaoxia Lin*, Jeremy Zucker, and George M. Church. *: Equal contributions. In silico reconstruction of metabolic networks from annotated genomes: a new MILP based approach and its application to marine cyanobacterium Prochlorococcus. In preparation.
Chemical Process Systems Engineering
7. 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).
8. 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 and Engineering Chemistry Research, 41, 3884–3906 (2002).
9. 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).
10. 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).
11. 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).
12. 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).
13. 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).
14. 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).
15. 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).