Assessing key decisions for transcriptomic data integration in biochemical networks.

by Anne Richelle, Chintan Joshi, Nathan E Lewis
Published 2019-07-01

The evolution of genome-scale models of cancer metabolism

by Nathan E Lewis, Alyaa M Abdel-Haleem
Published 2013-09-01

The Emerging Facets of Non-Cancerous Warburg Effect

by Alyaa M. Abdel-Haleem, Alyaa M. Abdel-Haleem, Nathan E. Lewis, Nathan E. Lewis, Nathan E. Lewis, Neema Jamshidi, Neema Jamshidi, Katsuhiko Mineta, Katsuhiko Mineta, Xin Gao, Xin Gao, Takashi Gojobori, Takashi Gojobori
Published 2017-10-01

Hierarchical cortical transcriptome disorganization in autism

by Michael V. Lombardo, Eric Courchesne, Nathan E. Lewis, Tiziano Pramparo
Published 2017-06-01

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions.

by Anne Richelle, Austin W T Chiang, Chih-Chung Kuo, Nathan E Lewis
Published 2019-04-01

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

by Zachary A King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E Lewis, Bernhard O Palsson
Published 2015-08-01

StanDep: Capturing transcriptomic variability improves context-specific metabolic models.

by Chintan J Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J O'Rourke, Nathan E Lewis
Published 2020-05-01

Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice.

by Amit Kumar, Thomas Harrelson, Nathan E Lewis, Emily J Gallagher, Derek LeRoith, Joseph Shiloach, Michael J Betenbaugh
Published 2014-01-01

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

by Alyaa M Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O Palsson, Nathan E Lewis, Neema Jamshidi
Published 2018-01-01

Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter

by Hussain Dahodwala, Prashant Kaushik, Vijay Tejwani, Chih-Chung Kuo, Patrice Menard, Michael Henry, Bjorn G. Voldborg, Nathan E. Lewis, Paula Meleady, Susan T. Sharfstein
Published 2019-11-01

Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy

by Austin W. T. Chiang, Hratch M. Baghdassarian, Benjamin P. Kellman, Bokan Bao, James T. Sorrentino, Chenguang Liang, Chih-Chung Kuo, Helen O. Masson, Nathan E. Lewis
Published 2021-06-01

Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

by Michael Witting, Michael Witting, Janna Hastings, Nicolas Rodriguez, Chintan J. Joshi, Jake P. N. Hattwell, Paul R. Ebert, Michel van Weeghel, Arwen W. Gao, Michael J. O. Wakelam, Riekelt H. Houtkooper, Abraham Mains, Nicolas Le Novère, Sean Sadykoff, Frank Schroeder, Nathan E. Lewis, Nathan E. Lewis, Horst-Joachim Schirra, Christoph Kaleta, Olivia Casanueva
Published 2018-11-01

A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering

by Chenguang Liang, Austin W.T. Chiang, Anders H. Hansen, Johnny Arnsdorf, Sanne Schoffelen, James T. Sorrentino, Benjamin P. Kellman, Bokan Bao, Bjørn G. Voldborg, Nathan E. Lewis
Published 2020-11-01

Evolution of the exclusively human pathogen Neisseria gonorrhoeae: Human‐specific engagement of immunoregulatory Siglecs

by Corinna S. Landig, Ashley Hazel, Benjamin P. Kellman, Jerry J. Fong, Flavio Schwarz, Sarika Agarwal, Nissi Varki, Paola Massari, Nathan E. Lewis, Sanjay Ram, Ajit Varki
Published 2019-02-01

Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis

by Bokan Bao, Benjamin P. Kellman, Austin W. T. Chiang, Yujie Zhang, James T. Sorrentino, Austin K. York, Mahmoud A. Mohammad, Morey W. Haymond, Lars Bode, Nathan E. Lewis
Published 2021-08-01

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines.

by 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
Published 2020-12-01

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

by Benjamin P. Kellman, Hratch M. Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid Gazestani, Arjana Begzati, Shangzhong Li, Srinivasa Nalabolu, Sarah Murray, Linda Lopez, Karen Pierce, Eric Courchesne, Nathan E. Lewis
Published 2021-01-01

An optimized genome-wide, virus-free CRISPR screen for mammalian cells

by Kai Xiong, Karen Julie la Cour Karottki, Hooman Hefzi, Songyuan Li, Lise Marie Grav, Shangzhong Li, Philipp Spahn, Jae Seong Lee, Ildze Ventina, Gyun Min Lee, Nathan E. Lewis, Lasse Ebdrup Pedersen
Published 2021-08-01

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

by Jahir M. Gutierrez, Amir Feizi, Shangzhong Li, Thomas B. Kallehauge, Hooman Hefzi, Lise M. Grav, Daniel Ley, Deniz Baycin Hizal, Michael J. Betenbaugh, Bjorn Voldborg, Helene Faustrup Kildegaard, Gyun Min Lee, Bernhard O. Palsson, Jens Nielsen, Nathan E. Lewis
Published 2020-01-01

Multiplex secretome engineering enhances recombinant protein production and purity

by Stefan Kol, Daniel Ley, Tune Wulff, Marianne Decker, Johnny Arnsdorf, Sanne Schoffelen, Anders Holmgaard Hansen, Tanja Lyholm Jensen, Jahir M. Gutierrez, Austin W. T. Chiang, Helen O. Masson, Bernhard O. Palsson, Bjørn G. Voldborg, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Gyun Min Lee, Nathan E. Lewis
Published 2020-04-01