Nathan Enoch Lewis - Publications

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

106 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
2021 Weiss RJ, Spahn PN, Chiang AWT, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PLSM, Lewis NE, et al. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nature Chemical Biology. PMID 33846619 DOI: 10.1038/s41589-021-00776-9  1
2021 Karottki KJC, Hefzi H, Li S, Pedersen LE, Spahn PN, Joshi C, Ruckerbauer D, Bort JAH, Thomas A, Lee JS, Borth N, Lee GM, Kildegaard HF, Lewis NE. A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metabolic Engineering. PMID 33813034 DOI: 10.1016/j.ymben.2021.03.017  1
2021 Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells. Metabolic Engineering. PMID 33771719 DOI: 10.1016/j.ymben.2021.03.013  0.36
2021 Granados JC, Richelle A, Gutierrez JM, Zhang P, Zhang X, Bhatnagar V, Lewis NE, Nigam SK. \Coordinate regulation of systemic and kidney tryptophan metabolism by the drug transporters OAT1 and OAT3. The Journal of Biological Chemistry. 100575. PMID 33757768 DOI: 10.1016/j.jbc.2021.100575  1
2021 Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures. Biotechnology and Bioengineering. PMID 33580712 DOI: 10.1002/bit.27714  0.36
2021 Hsieh LY, Chiang AWT, Duong LD, Kuo CC, Dong SX, Dohil R, Kurten R, Lewis NE, Aceves SS. A Unique Esophageal Extracellular Matrix Proteome Alters Normal Fibroblast Function in Severe Eosinophilic Esophagitis. The Journal of Allergy and Clinical Immunology. PMID 33556465 DOI: 10.1016/j.jaci.2021.01.023  1
2021 Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. A Systems View of the Heparan Sulfate Interactome. The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society. 69: 105-119. PMID 33494649 DOI: 10.1369/0022155420988661  1
2021 Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. Bmc Genomics. 22: 69. PMID 33478392 DOI: 10.1186/s12864-021-07381-z  1
2020 Chiang AWT, Duong LD, Shoda T, Nhu QM, Ruffner M, Hara T, Aaron B, Joplin E, Manresa M, Abonia JP, Dellon E, Hirano I, Gonsalves N, Gupta S, Furuta G, ... ... Lewis NE, et al. Type 2 Immunity and Age Modify Gene Expression of COVID19 Receptors in Eosinophilic Gastrointestinal Disorders. Journal of Pediatric Gastroenterology and Nutrition. PMID 33394891 DOI: 10.1097/MPG.0000000000003032  1
2020 Lin D, Yalamanchili HB, Zhang X, Lewis NE, Alves CS, Groot J, Arnsdorf J, Bjørn SP, Wulff T, Voldborg BG, Zhou Y, Zhang B. CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. Plos Computational Biology. 16: e1008498. PMID 33351794 DOI: 10.1371/journal.pcbi.1008498  1
2020 Samoudi M, Kuo CC, Robinson CM, Shams-Ud-Doha K, Schinn SM, Kol S, Weiss L, Petersen Bjorn S, Voldborg BG, Rosa Campos A, Lewis NE. In situ detection of protein interactions for recombinant therapeutic enzymes. Biotechnology and Bioengineering. PMID 33169829 DOI: 10.1002/bit.27621  1
2020 Armingol E, Officer A, Harismendy O, Lewis NE. Deciphering cell-cell interactions and communication from gene expression. Nature Reviews. Genetics. PMID 33168968 DOI: 10.1038/s41576-020-00292-x  1
2020 Fouladiha H, Marashi SA, Li S, Li Z, Masson HO, Vaziri B, Lewis NE. Systematically gap-filling the genome-scale metabolic model of CHO cells. Biotechnology Letters. PMID 33040240 DOI: 10.1007/s10529-020-03021-w  1
2020 Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido Benítez RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, ... ... Lewis NE, et al. Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. Biorxiv : the Preprint Server For Biology. PMID 32839779 DOI: 10.1101/2020.08.17.238444  1
2020 Manresa MC, Chiang AWT, Kurten RC, Dohil R, Brickner H, Dohil L, Herro R, Akuthota P, Lewis NE, Croft M, Aceves SS. Increased Production of LIGHT by T Cells in Eosinophilic Esophagitis Promotes Differentiation of Esophageal Fibroblasts Toward an Inflammatory Phenotype. Gastroenterology. PMID 32712105 DOI: 10.1053/J.Gastro.2020.07.035  1
2020 Széliová D, Ruckerbauer DE, Galleguillos SN, Petersen LB, Natter K, Hanscho M, Troyer C, Causon T, Schoeny H, Christensen HB, Lee DY, Lewis NE, Koellensperger G, Hann S, Nielsen LK, et al. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metabolic Engineering. PMID 32619503 DOI: 10.1016/J.Ymben.2020.06.002  1
2020 Ke W, Saba JA, Yao CH, Hilzendeger MA, Drangowska-Way A, Joshi C, Mony VK, Benjamin SB, Zhang S, Locasale J, Patti GJ, Lewis N, O'Rourke EJ. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nature Communications. 11: 2587. PMID 32444616 DOI: 10.1038/S41467-020-16220-W  1
2020 Joshi CJ, Schinn SM, Richelle A, Shamie I, O'Rourke EJ, Lewis NE. StanDep: Capturing transcriptomic variability improves context-specific metabolic models. Plos Computational Biology. 16: e1007764. PMID 32396573 DOI: 10.1371/Journal.Pcbi.1007764  1
2020 Courchesne E, Gazestani VH, Lewis NE. Prenatal Origins of ASD: The When, What, and How of ASD Development. Trends in Neurosciences. 43: 326-342. PMID 32353336 DOI: 10.1016/J.Tins.2020.03.005  1
2020 Kol S, Ley D, Wulff T, Decker M, Arnsdorf J, Schoffelen S, Hansen AH, Jensen TL, Gutierrez JM, Chiang AWT, Masson HO, Palsson BO, Voldborg BG, Pedersen LE, Kildegaard HF, ... ... Lewis NE, et al. Multiplex secretome engineering enhances recombinant protein production and purity. Nature Communications. 11: 1908. PMID 32313013 DOI: 10.1038/S41467-020-15866-W  1
2020 Liang C, Chiang AWT, Hansen AH, Arnsdorf J, Schoffelen S, Sorrentino JT, Kellman BP, Bao B, Voldborg BG, Lewis NE. A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering. Current Research in Biotechnology. 2: 22-36. PMID 32285041 DOI: 10.1016/j.crbiot.2020.01.001  1
2020 Weiss RJ, Spahn PN, Toledo AG, Chiang AWT, Kellman BP, Li J, Benner C, Glass CK, Gordts PLSM, Lewis NE, Esko JD. ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 32277030 DOI: 10.1073/Pnas.1920880117  1
2020 Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Lewis NE, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4  1
2020 Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Lewis NE, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y  1
2020 Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nature Communications. 11: 68. PMID 31896772 DOI: 10.1038/S41467-019-13867-Y  1
2019 Dahodwala H, Kaushik P, Tejwani V, Kuo CC, Menard P, Henry M, Voldborg BG, Lewis NE, Meleady P, Sharfstein ST. Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter. Current Research in Biotechnology. 1: 49-57. PMID 32577618 DOI: 10.1016/j.crbiot.2019.09.001  1
2019 Gazestani VH, Lewis NE. From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology. Current Opinion in Systems Biology. 15: 68-73. PMID 31777764 DOI: 10.1016/J.Coisb.2019.04.001  1
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 Toledo AG, Golden G, Campos AR, Cuello H, Sorrentino J, Lewis N, Varki N, Nizet V, Smith JW, Esko JD. Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis. Nature Communications. 10: 4656. PMID 31604940 DOI: 10.1038/S41467-019-12672-X  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
2019 LaMonte GM, Orjuela-Sanchez P, Calla J, Wang LT, Li S, Swann J, Cowell AN, Zou BY, Abdel-Haleem Mohamed AM, Villa Galarce ZH, Moreno M, Tong Rios C, Vinetz JM, Lewis N, Winzeler EA. Dual RNA-seq identifies human mucosal immunity protein Mucin-13 as a hallmark of Plasmodium exoerythrocytic infection. Nature Communications. 10: 488. PMID 30700707 DOI: 10.1038/S41467-019-08349-0  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
2018 Lewis NE, Chiang AWT, Bao B, Kuo C, Kellman B, Richelle A, Liang A, Arnsdorf J, Sukhova Z, Ménard P, Hansen AH, Yang Z, Joshi H, Clausen H, Voldborg BG. The cellular impact of glycoengineering Glycobiology. 28: 1074-1074. DOI: 10.1093/Glycob/Cwy088  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
2017 Dräger A, King ZA, Yurkovich JT, Blessing C, Khandelwa D, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Visualization and creation of biochemical networks with Escher F1000research. 6. DOI: 10.7490/F1000Research.1114756.1  1
2017 Weiss RJ, Spahn PN, Lewis NE, Esko JD. Abstract 5945: CRISPR-Cas9 dissection of heparan sulfate Cancer Research. 77: 5945-5945. DOI: 10.1158/1538-7445.Am2017-5945  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  0.4
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
2016 Dräger A, King ZA, Lu JS, Ebrahim A, Sonnenschein N, Miller PC, Lerman JA, Palsson BO, Lewis NE. New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher F1000research. 5. DOI: 10.7490/F1000Research.1112788.1  1
2016 Mohamed A, Abuelela A, Merzaban J, Mineta K, Jamshidi N, Lewis N, Gao X, Gojobori T. Systems-biology guided identification of metabolic genes implicated in the activation of T-cells F1000research. 5. DOI: 10.7490/F1000Research.1112667.1  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 DOI: 10.15252/Msb.20156157  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 DOI: 10.15252/Msb.20145508  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  0.64
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
2011 Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A, Zielinski D, Bordbar A, Lewis N, Rahmanian S, Kang J, Palsson B. COBRA Toolbox 2.0 Protocol Exchange. DOI: 10.1038/Protex.2011.234  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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