Nathan Lewis

Assistant Professor

DTU BIOSUSTAIN
Novo Nordisk Foundation Center for Biosustainability

Technical University of Denmark

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2016
 

A Markov chain model for N-linked protein glycosylation – towards a low-parameter tool for model-driven glycoengineering

Spahn, Philipp N. ; Hansen, Anders Holmgaard ; Hansen, Henning Gram ; Arnsdorf, Johnny ; Kildegaard, Helene Faustrup ; Lewis, Nathan
in journal: Metabolic Engineering (ISSN: 1096-7176) (DOI: http://dx.doi.org/10.1016/j.ymben.2015.10.007), vol: 33, pages: 52-66, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1016/j.ymben.2015.10.007

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Zachary A. ; Lu, Justin ; Dräger, Andreas ; Miller, Philip ; Federowicz, Stephen ; Lerman, Joshua A. ; Ebrahim, Ali ; Palsson, Bernhard ; Lewis, Nathan
in journal: Nucleic Acids Research (ISSN: 0305-1048) (DOI: http://dx.doi.org/10.1093/nar/gkv1049), vol: 44, pages: D515-D522, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1093/nar/gkv1049

 

Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow

Golabgir, Aydin ; Gutierrez, Jahir M. ; Hefzi, Hooman ; Li, Shangzhong ; Palsson, Bernhard ; Herwig, Christoph ; Lewis, Nathan
in journal: Biotechnology Advances (ISSN: 0734-9750) (DOI: http://dx.doi.org/10.1016/j.biotechadv.2016.02.011), vol: 34, issue: 5, pages: 621-633, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1016/j.biotechadv.2016.02.011

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Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis

Huang, Sijia ; Chong, Nicole ; Lewis, Nathan ; Jia, Wei ; Xie, Guoxiang ; Garmire, Lana X.
in journal: Genome Medicine (ISSN: 1756-994X) (DOI: http://dx.doi.org/10.1186/s13073-016-0289-9), vol: 8, issue: 1, 2016

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1186/s13073-016-0289-9

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Recon 2.2

Swainston, Neil ; Smallbone, Kieran ; Hefzi, Hooman ; Dobson, Paul D. ; Brewer, Judy ; Hanscho, Michael ; Zielinski, Daniel C. ; Ang, Kok Siong ; Gardiner, Natalie J. ; Gutierrez, Jahir M. ; Kyriakopoulos, Sarantos ; Lakshmanan, Meiyappan ; Li, Shangzhong ; Liu, Joanne K. ; Martínez, Veronica S. ; Orellana, Camila A. ; Quek, Lake Ee ; Thomas, Alex ; Zanghellini, Juergen ; Borth, Nicole ; Lee, Dong Yup ; Nielsen, Lars K. ; Kell, Douglas B. ; Lewis, Nathan ; Mendes, Pedro
in journal: Metabolomics (ISSN: 1573-3882) (DOI: http://dx.doi.org/10.1007/s11306-016-1051-4), vol: 12, 2016

Type: Journal article

Status: Published     |    Year: 2016     |    DOI: http://dx.doi.org/10.1007/s11306-016-1051-4

2015
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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

King, Zachary A. ; Draeger, Andreas ; Ebrahim, Ali ; Sonnenschein, Nikolaus ; Lewis, Nathan ; Palsson, Bernhard O.
in journal: PLoS Computational Biology (ISSN: 1553-7358) (DOI: http://dx.doi.org/10.1371/journal.pcbi.1004321), vol: 11, issue: 8, 2015

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: http://dx.doi.org/10.1371/journal.pcbi.1004321

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Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A. ; Almaas, E. ; Bauer, E. ; Bordbar, A. ; Burgard, A. P. ; Chang, R. L. ; Drager, A. ; Famili, I. ; Feist, A. M. ; Fleming, R. M. ; Fong, S. S. ; Hatzimanikatis, V. ; Herrgard, Markus ; Holder, A. ; Hucka, M. ; Hyduke, D. ; Jamshidi, N. ; Lee, Sang Yup ; Le Novere, N. ; Lerman, J. A. ; Lewis, Nathan ; Ma, D. ; Mahadevan, R. ; Maranas, C. ; Nagarajan, H. ; Navid, A. ; Nielsen, Jens ; Nielsen, L. K. ; Nogales, J. ; Noronha, A. ; Pal, C. ; Palsson, Bernhard ; Papin, J. A. ; Patil, Kiran R. ; Price, N. D. ; Reed, J. L. ; Saunders, M. ; Senger, R. S. ; Sonnenschein, Nikolaus ; Sun, Yuekai ; Thiele, I.
in journal: Molecular Systems Biology (ISSN: 1744-4292) (DOI: http://dx.doi.org/10.15252/msb.20156157), vol: 11, issue: 10, 2015

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: http://dx.doi.org/10.15252/msb.20156157

 

Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling

Gutierrez, Jahir M. ; Lewis, Nathan
in journal: Biotechnology Journal (ISSN: 1860-6768) (DOI: http://dx.doi.org/10.1002/biot.201400647), vol: 10, issue: 7, pages: 939-949, 2015

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: http://dx.doi.org/10.1002/biot.201400647

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

Rodriguez, Nicolas ; Thomas, Alex ; Watanabe, Leandro ; Vazirabad, Ibrahim Y. ; Kofia, Victor ; Gómez, Harold F. ; Mittag, Florian ; Matthes, Jakob ; Rudolph, Jan ; Wrzodek, Finja ; Netz, Eugen ; Diamantikos, Alexander ; Eichner, Johannes ; Keller, Roland ; Wrzodek, Clemens ; Fröhlich, Sebastian ; Lewis, Nathan ; Myers, Chris J. ; Le Novère, Nicolas ; Palsson, Bernhard ; Hucka, Michael ; Dräger, Andreas
in journal: Bioinformatics (ISSN: 1367-4803) (DOI: http://dx.doi.org/10.1093/bioinformatics/btv341), vol: 31, issue: 20, pages: 3383-6, 2015

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: http://dx.doi.org/10.1093/bioinformatics/btv341

 

Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics

Kumar, Amit ; Baycin-Hizal, Deniz ; Wolozny, Daniel ; Pedersen, Lasse Ebdrup ; Lewis, Nathan ; Heffner, Kelley ; Chaerkady, Raghothama ; Cole, Robert N. ; Shiloach, Joseph ; Zhang, Hui ; Bowen, Michael A. ; Betenbaugh, Michael J.
in journal: Journal of Proteome Research (ISSN: 1535-3893) (DOI: http://dx.doi.org/10.1021/acs.jproteome.5b00588), vol: 14, issue: 11, pages: 4687-4703, 2015

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: http://dx.doi.org/10.1021/acs.jproteome.5b00588