Nathan Enoch Lewis - Publications

Affiliations: 
2012 Bioengineering University of California, San Diego, La Jolla, CA 
Website:
http://lewislab.ucsd.edu

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Julie la Cour Karottki K, Hefzi H, Xiong K, Shamie I, Hansen AH, Li S, Pedersen LE, Li S, Lee JS, Lee GM, Kildegaard HF, Lewis NE. Awakening dormant glycosyltransferases in CHO cells with CRISPRa. Biotechnology and Bioengineering. PMID 31631317 DOI: 10.1002/bit.27199  1
2019 Gazestani VH, Pramparo T, Nalabolu S, Kellman BP, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity. Nature Neuroscience. 22: 1624-1634. PMID 31551593 DOI: 10.1038/s41593-019-0489-x  1
2019 Richelle A, Joshi C, Lewis NE. Assessing key decisions for transcriptomic data integration in biochemical networks. Plos Computational Biology. 15: e1007185. PMID 31323017 DOI: 10.1371/journal.pcbi.1007185  1
2019 Chiang AWT, Li S, Kellman BP, Chattopadhyay G, Zhang Y, Kuo CC, Gutierrez JM, Ghazi F, Schmeisser H, Ménard P, Bjørn SP, Voldborg BG, Rosenberg AS, Puig M, Lewis NE. Combating viral contaminants in CHO cells by engineering innate immunity. Scientific Reports. 9: 8827. PMID 31222165 DOI: 10.1038/s41598-019-45126-x  1
2019 Li S, Cha SW, Hefner K, Hizal DB, Bowen MA, Chaerkady R, Cole RN, Tejwani V, Kaushik P, Henry M, Meleady P, Sharfstein ST, Betenbaugh MJ, Bafna V, Lewis NE. Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements. Journal of Proteome Research. PMID 31020842 DOI: 10.1021/acs.jproteome.8b00935  1
2019 Richelle A, Chiang AWT, Kuo CC, Lewis NE. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions. Plos Computational Biology. 15: e1006867. PMID 30986217 DOI: 10.1371/journal.pcbi.1006867  1
2019 Lee JS, Kildegaard HF, Lewis NE, Lee GM. Mitigating Clonal Variation in Recombinant Mammalian Cell Lines. Trends in Biotechnology. PMID 30898338 DOI: 10.1016/j.tibtech.2019.02.007  1
2019 Xiong K, Marquart KF, Karottki KJC, Li S, Shamie I, Lee JS, Gerling S, Yeo NC, Chavez A, Lee GM, Lewis NE, Kildegaard HF. Reduced Apoptosis in Chinese Hamster Ovary Cells via Optimized CRISPR Interference. Biotechnology and Bioengineering. PMID 30883679 DOI: 10.1002/bit.26969  1
2019 Pristovsek N, Nallapereddy S, Grav LM, Hefzi H, Lewis NE, Rugbjerg P, Hansen HG, Lee GM, Andersen MR, Kildegaard HF. Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering. Acs Synthetic Biology. PMID 30807689 DOI: 10.1021/acssynbio.8b00453  1
2019 Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, ... ... Lewis NE, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/s41596-018-0098-2  1
2018 Lombardo MV, Pramparo T, Gazestani V, Warrier V, Bethlehem RAI, Carter Barnes C, Lopez L, Lewis NE, Eyler L, Pierce K, Courchesne E. Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypes. Nature Neuroscience. 21: 1680-1688. PMID 30482947 DOI: 10.1038/s41593-018-0281-3  1
2018 Lee JS, Park JH, Ha TK, Samoudi M, Lewis N, Palsson BØ, Kildegaard HF, Lee GM. Revealing key determinants of clonal variation in transgene expression in recombinant CHO cells using targeted genome editing. Acs Synthetic Biology. PMID 30388888 DOI: 10.1021/acssynbio.8b00290  1
2018 Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences of the United States of America. PMID 30301795 DOI: 10.1073/pnas.1811971115  1
2018 Grav LM, Sergeeva D, Lee JS, Marín de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF. Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generation. Acs Synthetic Biology. PMID 30060646 DOI: 10.1021/acssynbio.8b00140  1
2018 Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, ... ... Lewis NE, et al. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nature Methods. PMID 30013045 DOI: 10.1038/s41592-018-0048-5  1
2018 Courchesne E, Pramparo T, Gazestani VH, Lombardo MV, Pierce K, Lewis NE. The ASD Living Biology: from cell proliferation to clinical phenotype. Molecular Psychiatry. PMID 29934544 DOI: 10.1038/s41380-018-0056-y  1
2018 Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, ... Lewis NE, et al. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnology and Bioengineering. PMID 29704459 DOI: 10.1002/bit.26722  1
2018 Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. Plos Computational Biology. 14: e1005895. PMID 29300748 DOI: 10.1371/journal.pcbi.1005895  1
2017 Kuo CC, Chiang AW, Shamie I, Samoudi M, Gutierrez JM, Lewis NE. The emerging role of systems biology for engineering protein production in CHO cells. Current Opinion in Biotechnology. 51: 64-69. PMID 29223005 DOI: 10.1016/j.copbio.2017.11.015  1
2017 Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O. PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Scientific Reports. 7: 15854. PMID 29158538 DOI: 10.1038/s41598-017-16193-9  1
2017 Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T. The Emerging Facets of Non-Cancerous Warburg Effect. Frontiers in Endocrinology. 8: 279. PMID 29109698 DOI: 10.3389/fendo.2017.00279  1
2017 Richelle A, Lewis NE. Improvements in protein production in mammalian cells from targeted metabolic engineering. Current Opinion in Systems Biology. 6: 1-6. PMID 29104947 DOI: 10.1016/j.coisb.2017.05.019  1
2017 Lombardo MV, Courchesne E, Lewis NE, Pramparo T. Hierarchical cortical transcriptome disorganization in autism. Molecular Autism. 8: 29. PMID 28649314 DOI: 10.1186/s13229-017-0147-7  1
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, ... Lewis NE, et al. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature Methods. PMID 28319113 DOI: 10.1038/nmeth.4225  1
2017 Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Systems. PMID 28215528 DOI: 10.1016/j.cels.2017.01.010  1
2017 Kallehauge TB, Li S, Pedersen LE, Ha TK, Ley D, Andersen MR, Kildegaard HF, Lee GM, Lewis NE. Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Scientific Reports. 7: 40388. PMID 28091612 DOI: 10.1038/srep40388  1
2017 van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO, Lewis NE, Nizet V, Esko JD. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion. Mbio. 8. PMID 28074024 DOI: 10.1128/mBio.02128-16  1
2016 Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, ... ... Lewis NE, et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Systems. 3: 434-443.e8. PMID 27883890 DOI: 10.1016/j.cels.2016.10.020  1
2016 Spahn PN, Hansen AH, Kol S, Voldborg BG, Lewis NE. Predictive glycoengineering of biosimilars using a Markov chain glycosylation model. Biotechnology Journal. PMID 27860290 DOI: 10.1002/biot.201600489  1
2016 Chiang AW, Li S, Spahn PN, Richelle A, Kuo CC, Samoudi M, Lewis NE. Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology. Current Opinion in Structural Biology. 40: 104-111. PMID 27639240 DOI: 10.1016/j.sbi.2016.08.008  1
2016 Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, ... ... Lewis NE, et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics : Official Journal of the Metabolomic Society. 12: 109. PMID 27358602 DOI: 10.1007/s11306-016-1051-4  1
2016 Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. Genome Medicine. 8: 34. PMID 27036109 DOI: 10.1186/s13073-016-0289-9  0.36
2016 Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE. Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow. Biotechnology Advances. PMID 26948029 DOI: 10.1016/j.biotechadv.2016.02.011  1
2015 Pramparo T, Lombardo MV, Campbell K, Barnes CC, Marinero S, Solso S, Young J, Mayo M, Dale A, Ahrens-Barbeau C, Murray SS, Lopez L, Lewis N, Pierce K, Courchesne E. Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. Molecular Systems Biology. 11: 841. PMID 26668231 DOI: 10.15252/msb.20156108  1
2015 Spahn PN, Hansen AH, Hansen HG, Arnsdorf J, Kildegaard HF, Lewis NE. A Markov chain model for N-linked protein glycosylation - towards a low-parameter tool for model-driven glycoengineering. Metabolic Engineering. PMID 26537759 DOI: 10.1016/j.ymben.2015.10.007  1
2015 King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research. PMID 26476456 DOI: 10.1093/nar/gkv1049  1
2015 Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, ... ... Lewis NE, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284  1
2015 Kumar A, Baycin-Hizal D, Wolozny D, Pedersen LE, Lewis NE, Heffner K, Chaerkady R, Cole RN, Shiloach J, Zhang H, Bowen MA, Betenbaugh MJ. Elucidation of the CHO Super-Ome (CHO-SO) by ProteoInfomatics. Journal of Proteome Research. PMID 26418914 DOI: 10.1021/acs.jproteome.5b00588  1
2015 King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. Plos Computational Biology. 11: e1004321. PMID 26313928 DOI: 10.1371/journal.pcbi.1004321  1
2015 Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 26306749 DOI: 10.1002/wsbm.1311  1
2015 Gutierrez JM, Lewis NE. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling. Biotechnology Journal. PMID 26099571 DOI: 10.1002/biot.201400647  1
2015 Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, ... ... Lewis NE, et al. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (Oxford, England). PMID 26079347 DOI: 10.1093/bioinformatics/btv341  1
2015 Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnology Journal. 10: 979-94. PMID 26058577 DOI: 10.1002/biot.201500082  1
2014 Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. Rapid neurogenesis through transcriptional activation in human stem cells. Molecular Systems Biology. 10: 760. PMID 25403753  1
2014 Spahn PN, Lewis NE. Systems glycobiology for glycoengineering. Current Opinion in Biotechnology. 30: 218-24. PMID 25202878 DOI: 10.1016/j.copbio.2014.08.004  1
2014 Kumar A, Harrelson T, Lewis NE, Gallagher EJ, LeRoith D, Shiloach J, Betenbaugh MJ. Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. Plos One. 9: e102319. PMID 25029527 DOI: 10.1371/journal.pone.0102319  1
2014 Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Molecular Systems Biology. 10: 737. PMID 24987116 DOI: 10.15252/msb.20145243  1
2014 Robasky K, Lewis NE, Church GM. The role of replicates for error mitigation in next-generation sequencing. Nature Reviews. Genetics. 15: 56-62. PMID 24322726 DOI: 10.1038/nrg3655  0.72
2013 Lewis NE, Abdel-Haleem AM. The evolution of genome-scale models of cancer metabolism. Frontiers in Physiology. 4: 237. PMID 24027532 DOI: 10.3389/fphys.2013.00237  1
2013 Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotechnology. 31: 759-65. PMID 23873082 DOI: 10.1038/nbt.2624  1
2013 Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. Current Opinion in Biotechnology. 24: 1102-7. PMID 23523260 DOI: 10.1016/j.copbio.2013.02.007  1
2013 Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Molecular Biosystems. 9: 167-74. PMID 23247105 DOI: 10.1039/c2mb25453k  1
2013 Hefzi H, Palsson BO, Lewis NE. Reconstruction of Genome-Scale Metabolic Networks Handbook of Systems Biology. 229-250. DOI: 10.1016/B978-0-12-385944-0.00012-5  1
2012 Noor E, Lewis NE, Milo R. A proof for loop-law constraints in stoichiometric metabolic networks. Bmc Systems Biology. 6: 140. PMID 23146116 DOI: 10.1186/1752-0509-6-140  1
2012 Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, et al. Proteomic analysis of Chinese hamster ovary cells. Journal of Proteome Research. 11: 5265-76. PMID 22971049 DOI: 10.1021/pr300476w  1
2012 Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. Network context and selection in the evolution to enzyme specificity. Science (New York, N.Y.). 337: 1101-4. PMID 22936779 DOI: 10.1126/science.1216861  1
2012 Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications. 3: 929. PMID 22760628 DOI: 10.1038/ncomms1928  1
2012 Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews. Microbiology. 10: 291-305. PMID 22367118 DOI: 10.1038/nrmicro2737  1
2011 Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols. 6: 1290-307. PMID 21886097 DOI: 10.1038/nprot.2011.308  1
2011 Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology. 29: 735-41. PMID 21804562 DOI: 10.1038/nbt.1932  1
2011 Conrad TM, Lewis NE, Palsson BØ. Microbial laboratory evolution in the era of genome-scale science. Molecular Systems Biology. 7: 509. PMID 21734648 DOI: 10.1038/msb.2011.42  1
2011 Nam H, Conrad TM, Lewis NE. The role of cellular objectives and selective pressures in metabolic pathway evolution. Current Opinion in Biotechnology. 22: 595-600. PMID 21481583 DOI: 10.1016/j.copbio.2011.03.006  1
2011 Schellenberger J, Lewis NE, Palsson BØ. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophysical Journal. 100: 544-53. PMID 21281568 DOI: 10.1016/j.bpj.2010.12.3707  1
2010 Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology. 28: 1279-85. PMID 21102456 DOI: 10.1038/nbt.1711  1
2010 Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BØ. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proceedings of the National Academy of Sciences of the United States of America. 107: 20500-5. PMID 21057108 DOI: 10.1073/pnas.0911253107  1
2010 Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems Biology. 6: 422. PMID 20959820 DOI: 10.1038/msb.2010.68  1
2010 Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Applied and Environmental Microbiology. 76: 6529-40. PMID 20709841 DOI: 10.1128/AEM.01178-10  1
2010 Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Molecular Systems Biology. 6: 390. PMID 20664636 DOI: 10.1038/msb.2010.47  1
2010 Bar-Even A, Noor E, Lewis NE, Milo R. Design and analysis of synthetic carbon fixation pathways. Proceedings of the National Academy of Sciences of the United States of America. 107: 8889-94. PMID 20410460 DOI: 10.1073/pnas.0907176107  1
2009 Lewis NE, Cho BK, Knight EM, Palsson BO. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. Journal of Bacteriology. 191: 3437-44. PMID 19363119 DOI: 10.1128/JB.00034-09  1
2004 Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. Journal of Biomolecular Techniques : Jbt. 15: 238-48. PMID 15585820  1
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