Metabolic Systems Biology. - Nathan E. Lewis; Neema Jamshidi; Ines Thiele; Bernhard O. Palsson (Encyclopedia of Complexity and Systems Science, 2009)

A proof for loop-law constraints in stoichiometric metabolic networks. - Elad Noor; Nathan E. Lewis; Ron Milo (BMC Syst. Biol., 2012)

Causation in biology : a biomolecular systems view. - Nathan E. Lewis (2012)

JSBML 1.0: providing a smorgasbord of options to encode systems biology models. - Nicolas Rodriguez 001; Alex Thomas; Leandro H. Watanabe; Ibrahim Y. Vazirabad; Victor Kofia; Harold F. Gómez; Florian Mittag; Jakob Matthes; Jan Rudolph; Finja Wrzodek; Eugen Netz; Alexander Diamantikos; et al. (Bioinform., 2015)

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. - Zachary A. King; Andreas Dräger; Ali Ebrahim; Nikolaus Sonnenschein; Nathan E. Lewis; Bernhard O. Palsson (PLoS Comput. Biol., 2015)

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. - Zachary A. King; Justin Lu; Andreas Dräger; Philip Miller; Stephen Federowicz; Joshua A. Lerman; Ali Ebrahim; Bernhard O. Palsson; Nathan E. Lewis (Nucleic Acids Res., 2016)

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. - Alyaa M. Abdel-Haleem; Hooman Hefzi; Katsuhiko Mineta; Xin Gao 001; Takashi Gojobori; Bernhard O. Palsson; Nathan E. Lewis; Neema Jamshidi (PLoS Comput. Biol., 2018)

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions. - Anne Richelle; Austin W. T. Chiang; Chih-Chung Kuo; Nathan E. Lewis (PLoS Comput. Biol., 2019)

Assessing key decisions for transcriptomic data integration in biochemical networks. - Anne Richelle; Chintan J. Joshi; Nathan E. Lewis (PLoS Comput. Biol., 2019)

StanDep: Capturing transcriptomic variability improves context-specific metabolic models. - Chintan J. Joshi; Song-Min Schinn; Anne Richelle; Isaac Shamie; Eyleen J. O'Rourke; Nathan E. Lewis (PLoS Comput. Biol., 2020)

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. - Dongdong Lin; Hima B. Yalamanchili; Xinmin Zhang; Nathan E. Lewis; Christina S. Alves; Joost Groot; Johnny Arnsdorf; Sara P. Bjørn; Tune Wulff; Bjørn G. Voldborg; Yizhou Zhou; Baohong Zhang (PLoS Comput. Biol., 2020)

What are housekeeping genes? - Chintan J. Joshi; Wenfan Ke; Anna Drangowska-Way; Eyleen J. O'Rourke; Nathan E. Lewis (PLoS Comput. Biol., 2022)

Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models. - Chintan J. Joshi; Song-Min Schinn; Anne Richelle; Isaac Shamie; Eyleen J. O'Rourke; Nathan E. Lewis (PLoS Comput. Biol., 2022)

Inferring a spatial code of cell-cell interactions across a whole animal body. - Erick Armingol; Abbas Ghaddar; Chintan J. Joshi; Hratch Baghdassarian; Isaac Shamie; Jason Chan; Hsuan-Lin Her; Samuel Berhanu; Anushka Dar; Fabiola Rodriguez-Armstrong; Olivia Yang; Eyleen J. O'Rourke; et al. (PLoS Comput. Biol., 2022)

An improved algorithm for flux variability analysis. - Dustin Kenefake; Erick Armingol; Nathan E. Lewis; Efstratios N. Pistikopoulos (BMC Bioinform., 2022)