Nathan E. Lewis

According to our database, Nathan E. Lewis authored at least 15 papers between 2009 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

An improved algorithm for flux variability analysis.

Dustin Kenefake, Erick Armingol, Nathan E. Lewis, Efstratios N. Pistikopoulos

BMC Bioinform., December, 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, Nathan E. Lewis

PLoS Comput. Biol., November, 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

What are housekeeping genes?

Chintan J. Joshi, Wenfan Ke, Anna Drangowska-Way, Eyleen J. O'Rourke, Nathan E. Lewis

PLoS Comput. Biol., 2022

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

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

2019

Assessing key decisions for transcriptomic data integration in biochemical networks.

Anne Richelle, Chintan J. Joshi, Nathan E. Lewis

PLoS Comput. Biol., 2019

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

2018

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, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi

PLoS Comput. Biol., 2018

2016

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

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

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.

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

Bioinform., 2015

2012

Causation in biology : a biomolecular systems view.

Nathan E. Lewis

PhD thesis, 2012

A proof for loop-law constraints in stoichiometric metabolic networks.

Elad Noor, Nathan E. Lewis, Ron Milo

BMC Syst. Biol., 2012

2009

Metabolic Systems Biology.

Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson

Proceedings of the Encyclopedia of Complexity and Systems Science, 2009