For a current list, click here or here.


29. Spahn, P., Lewis, N.E.‡ Systems glycomics for glycoengineering. Current Opinion in Biotechnology, accepted.

28. Hefzi, H., Lewis, N.E.‡ From random mutagenesis to systems biology in metabolic engineering of mammalian cells. Pharmaceutical Bioprocessing, accepted.

27. Kumar, A., Harrelson, T., Lewis, N.E., Gallagher, E., LeRoith, D., Shiloach, J., Betenbaugh, M.J. Multi-tissue computational modeling analyzes pathophysiology of Type 2 Diabetes in MKR mice. PLoS One, 9(7): e102319. DOI: 10.1371/journal.pone.0102319

26. Bordbar, A., Nagarajan, H., Lewis, N.E., Schellenberger, J., Latif, H., Federowicz, S., Ebrahim, A., Palsson, B.O. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Molecular Systems Biology, 10:737 (2014). DOI: 10.15252/msb.20145243

25. Robasky, K.*, Lewis, N.E.‡*, Church, G.M. The Role of Replicates for Error Mitigation in Next-Generation Sequencing. Nature Reviews Genetics. 15:56–62 (2014). DOI: 10.1038/nrg3655
corresponding author, * equal contribution



24. Lewis, N.E.‡, Abdel-Haleem, A.M. The evolution of genome-scale models of cancer metabolism. Front. Physiol. 4:237 (2013). DOI: 10.3389/fphys.2013.00237
corresponding author

23. Lewis, N.E.*, Liu, X.*, Li, Y.*, Nagarajan, H.*, Yerganian, G., O'Brien, E., Bordbar, A., Roth, A.M., Rosenbloom, J., Bian, C., Xie, M., Chen, W., Li, N., Baycin-Hizal, D., Latif, H., Forster, J., Betenbaugh, M.J., Famili, I., Xu, X., Wang, J., Palsson, B.O. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotechnology. 31:759-65 (2013). doi: 10.1038/nbt.2624.
* equal contribution

22. Kildegaard, H.F., Baycin-Hizal, D., Lewis, N.E., Betenbaugh, M.J The Emerging CHO Systems Biology Era: Harnessing the ‘Omics Revolution for Biotechnology. Current Opinion in Biotechnology. S0958-1669(13):00021-9 (2013). doi: 10.1016/j.copbio.2013.02.007

21. Hyduke, D.R., Lewis, N.E., Palsson, B.Ø. Analysis of omics data with genome-scale models of metabolism. Molecular BioSystems, 9:167 (2013). doi: 10.1039/c2mb25453k



20. Nam, H.J.*, Lewis, N.E.‡*, Lerman, J.A., Lee, D.H., Chang, R.L., Kim, D., Palsson, B.Ø.‡ Network context and selection in the evolution to enzyme specificity. Science. 337:1101-1104 (2012).
corresponding author, * equal contribution

19. Noor, E.‡, Lewis, N.E.‡, Milo, R. A proof for loop-law constraints in stoichiometric metabolic networks. BMC Systems Biology. 6:140 (2012). Highly Accessed.
corresponding author

18. Baycin-Hizal, D., Tabb, D.L., Chaerkady, R., Chen, L., Lewis, N.E., Nagarajan, H., Sarkaria, V., Kumar, A., Wolozny, D., Colao, J., Jacobson, E., Tian, Y., O’Malley, R.N., Krag, S., Cole, R.N., Palsson, B.O., Zhang, H., Betenbaugh, M.J. Proteomic analysis of Chinese hamster ovary cells. Journal of Proteome Research. 11:5265-76 (2012).

17. Hefzi, H., Palsson, B.Ø., Lewis, N.E.‡. Reconstruction of genome-scale metabolic networks. In Handbook of Systems Biology. 229 (2013). doi:10.1016/B978-0-12-385944-0.00012-5
corresponding author

16. Lerman, J.A., Hyduke, D.R., Latif, H., Portnoy, V.A., Lewis, N.E., Orth, J.D., Schrimpe-Rutledge, A.C., Smith, R.D., Adkins, J.N., Zengler, K.A., Palsson, B.Ø. In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications. 3:929 (2012).

15. Lewis, N.E., Nagarajan, H., Palsson, B.Ø. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews Microbiology. 10:291-305 (2012). Click here for accompanying website with a catalog of constraint-based methods.



14. Xu, X.*, Nagarajan, H.*, Lewis, N.E.*, Pan, S.*,et al. The Genomic Sequence of the Chinese Hamster Ovary (CHO) K1 cell line. Nature Biotechnology, 29:735-41 (2011).
* equal contribution

13. Schellenberger, J., Que, R., Fleming, R.T., Thiele, I., Orth, J., Feist, A.M., Zielinski , D.C., Bordbar, A., Lewis, N.E., Rahmanian, S., Kang, J., Hyduke, D., Palsson, B.Ø. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols, 6:1290-307 (2011).

12. Nam, H.J.*, Conrad, T.M., Lewis, N.E.*‡. The role of cellular objectives and selective pressures in metabolic pathway evolution. Current Opinion in Biotechnology, 22:595-600 (2011).
* equal contribution, corresponding author

11. Conrad, T.M., Lewis, N.E., Palsson, B.Ø. Microbial Laboratory Evolution in the Era of Genome-Scale Science. Molecular Systems Biology, 7:509 (2011).

10. Schellenberger, J., Lewis, N.E., Palsson, B.Ø. Elimination of thermodynamically infeasible loops in steady state metabolic models. Biophysical Journal, 100:544-53 (2011).



9. Lewis, N.E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M.P., Cheng, J.K., Patel, N., Yee, A., Lewis, R.A., Eils, R., König, R., Palsson, B.Ø. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology, 28:1279–1285 (2010). Paper highlighted by Nature Methods (January 2011).

8. Conrad, T.M., Frazier, M., Joyce, A.R., Cho, B. K., Knight, E. M., Lewis, N.E., Landick, R., Palsson, B.Ø. RNA polymerase mutants found through adaptive evolution re-program Escherichia coli K-12 MG1655 for optimal growth in minimal media. Proc. Nat. Acad. Sci. USA, 107:20500-5 (2010).

7. Bordbar, A., Lewis, N.E., Schellenberger, J., Palsson, B.Ø., Jamshidi, N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems Biology, 6:422 (2010).

6. Portnoy, V.A., Scott, D.A., Lewis, N.E., Tarasova, Y., Osterman, A.L., Palsson, B.Ø. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl. Environ. Microbiol., 76:6529-40 (2010).

5. Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez-Ferrer, D., Weitz, K.K., Eils, R., König, R., Smith, R.D., Palsson, B.Ø. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Molecular Systems Biology, 6:390 (2010).

4. Bar-Even, A., Noor, E., Lewis, N.E., Milo, R. Design and analysis of synthetic carbon fixation pathways. Proc. Natl. Acad. Sci. USA., 107:8889-8894 (2010).



3. Lewis, N.E., Cho, B.K., Knight, E.M. Palsson, B. Ø. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J. Bacteriol., 191:3437-44 (2009).

2. Lewis, N.E., Jamshidi, N., Thiele, I. & Palsson, B.Ø. Metabolic systems biology: a constraint-based approach. In Encyclopedia of Complexity and Systems Science 5535 (Springer, New York, 2009).


1. Merrell, K., Southwick, K., Graves, S.W., Esplin, M.S., Lewis, N.E., Thulin, C.D. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J. Biomol. Tech., 15:238-48 (2004).


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