Nathan E. Lewis

15 papers Journal 13
YearRankTypeTitle / Venue / Authors
2022 J jnl
An improved algorithm for flux variability analysis.
BMC Bioinform.
Dustin Kenefake, Erick Armingol, Nathan E. Lewis, Efstratios N. Pistikopoulos
2022 J jnl
Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models.
PLoS Comput. Biol.
Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O'Rourke, Nathan E. Lewis
2022 J jnl
Inferring a spatial code of cell-cell interactions across a whole animal body.
PLoS Comput. Biol.
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, Nathan E. Lewis
2022 J jnl
What are housekeeping genes?
PLoS Comput. Biol.
Chintan J. Joshi, Wenfan Ke, Anna Drangowska-Way, Eyleen J. O'Rourke, Nathan E. Lewis
2020 J jnl
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.
PLoS Comput. Biol.
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
2020 J jnl
StanDep: Capturing transcriptomic variability improves context-specific metabolic models.
PLoS Comput. Biol.
Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O'Rourke, Nathan E. Lewis
2019 J jnl
Assessing key decisions for transcriptomic data integration in biochemical networks.
PLoS Comput. Biol.
Anne Richelle, Chintan J. Joshi, Nathan E. Lewis
2019 J jnl
Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions.
PLoS Comput. Biol.
Anne Richelle, Austin W. T. Chiang, Chih-Chung Kuo, Nathan E. Lewis
2018 J jnl
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
PLoS Comput. Biol.
Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi
2016 J jnl
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Nucleic Acids Res.
Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis
2015 J jnl
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
PLoS Comput. Biol.
Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson
2015 J jnl
JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Bioinform.
Nicolas Rodriguez, 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, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger
2012 J jnl
A proof for loop-law constraints in stoichiometric metabolic networks.
BMC Syst. Biol.
Elad Noor, Nathan E. Lewis, Ron Milo
2012 — —
Causation in biology : a biomolecular systems view.
Nathan E. Lewis
2009 — ch.
Metabolic Systems Biology.
Encyclopedia of Complexity and Systems Science
Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson