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Nathan E Lewis
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0
J Schellenberger, R Que, RMT Fleming, I Thiele, JD Orth, AM Feist, ...
Nature protocols 6 (9), 1290-1307, 2011
15532011
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
X Xu*, H Nagarajan*, NE Lewis*, S Pan*, Z Cai*, X Liu, W Chen, M Xie, ...
Nature biotechnology 29 (8), 735, 2011
8472011
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
NE Lewis, H Nagarajan, BO Palsson
Nature Reviews Microbiology 10 (4), 291-305, 2012
8422012
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3. 0
L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ...
Nature Protocols 14, 639–702, 2019
6912019
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
ZA King, J Lu, A Dräger, P Miller, S Federowicz, JA Lerman, A Ebrahim, ...
Nucleic acids research 44 (D1), D515-D522, 2016
6742016
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
NE Lewis, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, ...
Molecular systems biology 6 (1), 390, 2010
6352010
Design and analysis of synthetic carbon fixation pathways
A Bar-Even, E Noor, NE Lewis, R Milo
Proceedings of the National Academy of Sciences 107 (19), 8889-8894, 2010
4832010
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome
NE Lewis*, X Liu*, Y Li*, H Nagarajan*, G Yerganian, E O'brien, ...
Nature biotechnology 31 (8), 759, 2013
4012013
Microbial laboratory evolution in the era of genome‐scale science
TM Conrad, NE Lewis, BØ Palsson
Molecular systems biology 7 (1), 509, 2011
3242011
In silico method for modelling metabolism and gene product expression at genome scale
JA Lerman, DR Hyduke, H Latif, VA Portnoy, NE Lewis, JD Orth, ...
Nature communications 3 (1), 1-10, 2012
2992012
The role of replicates for error mitigation in next-generation sequencing
K Robasky*, NE Lewis*, GM Church
Nature Reviews Genetics 15 (1), 56, 2014
2972014
Deciphering cell–cell interactions and communication from gene expression
E Armingol, A Officer, O Harismendy, NE Lewis
Nature Reviews Genetics 22 (2), 71-88, 2021
2952021
Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions
JP Shen, D Zhao, R Sasik, J Luebeck, A Birmingham, ...
Nature methods 14 (6), 573-576, 2017
2952017
Virus-receptor interactions of glycosylated SARS-CoV-2 spike and human ACE2 receptor
P Zhao, JL Praissman, OC Grant, Y Cai, T Xiao, KE Rosenbalm, K Aoki, ...
Cell host & microbe 28 (4), 586-601. e6, 2020
2942020
An enhanced CRISPR repressor for targeted mammalian gene regulation
NC Yeo, A Chavez, A Lance-Byrne, Y Chan, D Menn, D Milanova, ...
Nature methods 15 (8), 611-616, 2018
2882018
Large-scale in silico modeling of metabolic interactions between cell types in the human brain
NE Lewis, G Schramm, A Bordbar, J Schellenberger, MP Andersen, ...
Nature biotechnology 28 (12), 1279-1285, 2010
2862010
Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
ZA King, A Dräger, A Ebrahim, N Sonnenschein, NE Lewis, BO Palsson
PLoS computational biology 11 (8), e1004321, 2015
2842015
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
A Bordbar, NE Lewis, J Schellenberger, BØ Palsson, N Jamshidi
Molecular systems biology 6 (1), 422, 2010
2832010
Network context and selection in the evolution to enzyme specificity
H Nam*, NE Lewis*, JA Lerman, DH Lee, RL Chang, D Kim, BO Palsson
Science 337 (6098), 1101-1104, 2012
2822012
Recon 2.2: from reconstruction to model of human metabolism
N Swainston, K Smallbone, H Hefzi, PD Dobson, J Brewer, M Hanscho, ...
Metabolomics 12 (7), 1-7, 2016
2702016
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