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Nathan Lewis

Title(s)Associate Professor In Residence, Pediatrics
SchoolHealth Sciences
Address9500 Gilman Drive #0760
La Jolla CA 92093
Phone858-997-5844
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    Collapse Research 
    Collapse Research Activities and Funding
    ImmCellFIE: producing high-resolution snapshots of the functions of immune cells
    NIH/NIAID UH2AI153029Jun 22, 2020 - May 31, 2022
    Role: Principal Investigator
    Developmental Functional Genomics in ASD Toddlers
    NIH/NIMH R01MH110558Sep 1, 2016 - Jun 30, 2021
    Role: Principal Investigator
    Unraveling the mammalian secretory pathway through systems biology and algorithm development
    NIH/NIGMS R35GM119850Jul 15, 2016 - Jun 30, 2021
    Role: Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metab Eng. 2020 Jun 30. 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, Borth N, Zanghellini J. PMID: 32619503.
      View in: PubMed   Mentions:    Fields:    
    2. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nat Commun. 2020 May 22; 11(1):2587. 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. PMID: 32444616.
      View in: PubMed   Mentions:    Fields:    
    3. StanDep: Capturing transcriptomic variability improves context-specific metabolic models. PLoS Comput Biol. 2020 May; 16(5):e1007764. Joshi CJ, Schinn SM, Richelle A, Shamie I, O'Rourke EJ, Lewis NE. PMID: 32396573.
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    4. Multiplex secretome engineering enhances recombinant protein production and purity. Nat Commun. 2020 Apr 20; 11(1):1908. 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, Lee GM, Lewis NE. PMID: 32313013.
      View in: PubMed   Mentions:    Fields:    
    5. Prenatal Origins of ASD: The When, What, and How of ASD Development. Trends Neurosci. 2020 May; 43(5):326-342. Courchesne E, Gazestani VH, Lewis NE. PMID: 32353336.
      View in: PubMed   Mentions:    Fields:    
    6. ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis. Proc Natl Acad Sci U S A. 2020 Apr 28; 117(17):9311-9317. Weiss RJ, Spahn PN, Toledo AG, Chiang AWT, Kellman BP, Li J, Benner C, Glass CK, Gordts PLSM, Lewis NE, Esko JD. PMID: 32277030.
      View in: PubMed   Mentions:    Fields:    
    7. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 Apr; 38(4):504. 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, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32265554.
      View in: PubMed   Mentions:    Fields:    
    8. A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production. Bioprocess Biosyst Eng. 2020 Aug; 43(8):1381-1389. Fouladiha H, Marashi SA, Torkashvand F, Mahboudi F, Lewis NE, Vaziri B. PMID: 32211960.
      View in: PubMed   Mentions: 1     Fields:    
    9. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 03; 38(3):272-276. 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, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32123384.
      View in: PubMed   Mentions: 2     Fields:    
    10. A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering. Curr Res Biotechnol. 2020 Nov; 2:22-36. Liang C, Chiang AWT, Hansen AH, Arnsdorf J, Schoffelen S, Sorrentino JT, Kellman BP, Bao B, Voldborg BG, Lewis NE. PMID: 32285041.
      View in: PubMed   Mentions:
    11. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nat Commun. 2020 01 02; 11(1):68. 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. PMID: 31896772.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    12. Ptpn6 inhibits caspase-8- and Ripk3/Mlkl-dependent inflammation. Nat Immunol. 2020 01; 21(1):54-64. Speir M, Nowell CJ, Chen AA, O'Donnell JA, Shamie IS, Lakin PR, D'Cruz AA, Braun RO, Babon JJ, Lewis RS, Bliss-Moreau M, Shlomovitz I, Wang S, Cengia LH, Stoica AI, Hakem R, Kelliher MA, O'Reilly LA, Patsiouras H, Lawlor KE, Weller E, Lewis NE, Roberts AW, Gerlic M, Croker BA. PMID: 31819256.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    13. Awakening dormant glycosyltransferases in CHO cells with CRISPRa. Biotechnol Bioeng. 2020 02; 117(2):593-598. Karottki KJC, Hefzi H, Xiong K, Shamie I, Hansen AH, Li S, Pedersen LE, Li S, Lee JS, Lee GM, Kildegaard HF, Lewis NE. PMID: 31631317.
      View in: PubMed   Mentions: 1     Fields:    
    14. Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis. Nat Commun. 2019 10 11; 10(1):4656. Toledo AG, Golden G, Campos AR, Cuello H, Sorrentino J, Lewis N, Varki N, Nizet V, Smith JW, Esko JD. PMID: 31604940.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    15. Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter. Curr Res Biotechnol. 2019 Nov; 1:49-57. Dahodwala H, Kaushik P, Tejwani V, Kuo CC, Menard P, Henry M, Voldborg BG, Lewis NE, Meleady P, Sharfstein ST. PMID: 32577618.
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    16. A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-ß-catenin pathways in leukocytes is linked to ASD genetics and symptom severity. Nat Neurosci. 2019 10; 22(10):1624-1634. Gazestani VH, Pramparo T, Nalabolu S, Kellman BP, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. PMID: 31551593.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    17. Assessing key decisions for transcriptomic data integration in biochemical networks. PLoS Comput Biol. 2019 07; 15(7):e1007185. Richelle A, Joshi C, Lewis NE. PMID: 31323017.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    18. Combating viral contaminants in CHO cells by engineering innate immunity. Sci Rep. 2019 06 20; 9(1):8827. 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. PMID: 31222165.
      View in: PubMed   Mentions: 3     Fields:    
    19. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res. 2019 06 07; 18(6):2433-2445. Li S, Cha SW, Heffner 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. PMID: 31020842.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    20. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions. PLoS Comput Biol. 2019 04; 15(4):e1006867. Richelle A, Chiang AWT, Kuo CC, Lewis NE. PMID: 30986217.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    21. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 04 18; 177(3):572-586.e22. Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. PMID: 30955884.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    22. From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology. Curr Opin Syst Biol. 2019 Jun; 15:68-73. Gazestani VH, Lewis NE. PMID: 31777764.
      View in: PubMed   Mentions:
    23. Reduced apoptosis in Chinese hamster ovary cells via optimized CRISPR interference. Biotechnol Bioeng. 2019 07; 116(7):1813-1819. Xiong K, Marquart KF, la Cour Karottki KJ, Li S, Shamie I, Lee JS, Gerling S, Yeo NC, Chavez A, Lee GM, Lewis NE, Kildegaard HF. PMID: 30883679.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    24. Mitigating Clonal Variation in Recombinant Mammalian Cell Lines. Trends Biotechnol. 2019 09; 37(9):931-942. Lee JS, Kildegaard HF, Lewis NE, Lee GM. PMID: 30898338.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    25. Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering. ACS Synth Biol. 2019 04 19; 8(4):758-774. Pristovšek N, Nallapareddy S, Grav LM, Hefzi H, Lewis NE, Rugbjerg P, Hansen HG, Lee GM, Andersen MR, Kildegaard HF. PMID: 30807689.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    26. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc. 2019 03; 14(3):639-702. 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, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT. PMID: 30787451.
      View in: PubMed   Mentions: 22     Fields:    
    27. Dual RNA-seq identifies human mucosal immunity protein Mucin-13 as a hallmark of Plasmodium exoerythrocytic infection. Nat Commun. 2019 01 30; 10(1):488. 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. PMID: 30700707.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    28. Evolution of the exclusively human pathogen Neisseria gonorrhoeae: Human-specific engagement of immunoregulatory Siglecs. Evol Appl. 2019 Feb; 12(2):337-349. Landig CS, Hazel A, Kellman BP, Fong JJ, Schwarz F, Agarwal S, Varki N, Massari P, Lewis NE, Ram S, Varki A. PMID: 30697344.
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    29. Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypes. Nat Neurosci. 2018 12; 21(12):1680-1688. Lombardo MV, Pramparo T, Gazestani V, Warrier V, Bethlehem RAI, Carter Barnes C, Lopez L, Lewis NE, Eyler L, Pierce K, Courchesne E. PMID: 30482947.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    30. Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. Front Mol Biosci. 2018; 5:96. Witting M, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis NE, Schirra HJ, Kaleta C, Casanueva O. PMID: 30488036.
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    31. Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing. ACS Synth Biol. 2018 12 21; 7(12):2867-2878. Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM. PMID: 30388888.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    32. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11096-11101. 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. PMID: 30301795.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    33. Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation. ACS Synth Biol. 2018 09 21; 7(9):2148-2159. Grav LM, Sergeeva D, Lee JS, Marin de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF. PMID: 30060646.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    34. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 08; 15(8):611-616. 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, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM. PMID: 30013045.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    35. The ASD Living Biology: from cell proliferation to clinical phenotype. Mol Psychiatry. 2019 01; 24(1):88-107. Courchesne E, Pramparo T, Gazestani VH, Lombardo MV, Pierce K, Lewis NE. PMID: 29934544.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    36. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng. 2018 08; 115(8):2087-2100. 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, Borth N, Lee KH. PMID: 29704459.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    37. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput Biol. 2018 01; 14(1):e1005895. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. PMID: 29300748.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    38. The emerging role of systems biology for engineering protein production in CHO cells. Curr Opin Biotechnol. 2018 06; 51:64-69. Kuo CC, Chiang AW, Shamie I, Samoudi M, Gutierrez JM, Lewis NE. PMID: 29223005.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    39. PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep. 2017 Nov 20; 7(1):15854. Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O. PMID: 29158538.
      View in: PubMed   Mentions: 2     Fields:    
    40. The Emerging Facets of Non-Cancerous Warburg Effect. Front Endocrinol (Lausanne). 2017; 8:279. Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T. PMID: 29109698.
      View in: PubMed   Mentions:
    41. Hierarchical cortical transcriptome disorganization in autism. Mol Autism. 2017; 8:29. Lombardo MV, Courchesne E, Lewis NE, Pramparo T. PMID: 28649314.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    42. Improvements in protein production in mammalian cells from targeted metabolic engineering. Curr Opin Syst Biol. 2017 Dec; 6:1-6. Richelle A, Lewis NE. PMID: 29104947.
      View in: PubMed   Mentions:
    43. Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants. Gut. 2018 06; 67(6):1064-1070. Autran CA, Kellman BP, Kim JH, Asztalos E, Blood AB, Spence ECH, Patel AL, Hou J, Lewis NE, Bode L. PMID: 28381523.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCTClinical Trials
    44. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. 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, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. PMID: 28319113.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    45. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Syst. 2017 03 22; 4(3):318-329.e6. Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. PMID: 28215528.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    46. Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Sci Rep. 2017 01 16; 7:40388. Kallehauge TB, Li S, Pedersen LE, Ha TK, Ley D, Andersen MR, Kildegaard HF, Lee GM, Lewis NE. PMID: 28091612.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    47. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin a2 as a Host Factor for Bacterial Invasion. mBio. 2017 01 10; 8(1). 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. PMID: 28074024.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    48. Predictive glycoengineering of biosimilars using a Markov chain glycosylation model. Biotechnol J. 2017 Feb; 12(2). Spahn PN, Hansen AH, Kol S, Voldborg BG, Lewis NE. PMID: 27860290.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    49. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 11 23; 3(5):434-443.e8. 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, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. PMID: 27883890.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    50. Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology. Curr Opin Struct Biol. 2016 10; 40:104-111. Chiang AW, Li S, Spahn PN, Richelle A, Kuo CC, Samoudi M, Lewis NE. PMID: 27639240.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    51. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics. 2016; 12:109. 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, Orellana CA, Quek LE, Thomas A, Zanghellini J, Borth N, Lee DY, Nielsen LK, Kell DB, Lewis NE, Mendes P. PMID: 27358602.
      View in: PubMed   Mentions: 34     Fields:    
    52. Characterizing the effect of multiple Fc glycan attributes on the effector functions and Fc?RIIIa receptor binding activity of an IgG1 antibody. Biotechnol Prog. 2016 09; 32(5):1181-1192. Pace D, Lewis N, Wu T, Gillespie R, Leiske D, Velayudhan J, Rohrbach A, Connell-Crowley L. PMID: 27160519.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    53. Improving the Efficiency and Ease of Healthcare Analysis Through Use of Data Visualization Dashboards. Big Data. 2016 06; 4(2):129-35. Stadler JG, Donlon K, Siewert JD, Franken T, Lewis NE. PMID: 27441717.
      View in: PubMed   Mentions: 4     Fields:    
    54. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. Genome Med. 2016 Mar 31; 8(1):34. Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX. PMID: 27036109.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    55. Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow. Biotechnol Adv. 2016 Sep-Oct; 34(5):621-633. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE. PMID: 26948029.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    56. Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. Mol Syst Biol. 2015 Dec 14; 11(12):841. 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. PMID: 26668231.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    57. A Markov chain model for N-linked protein glycosylation--towards a low-parameter tool for model-driven glycoengineering. Metab Eng. 2016 Jan; 33:52-66. Spahn PN, Hansen AH, Hansen HG, Arnsdorf J, Kildegaard HF, Lewis NE. PMID: 26537759.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    58. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 04; 44(D1):D515-22. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE. PMID: 26476456.
      View in: PubMed   Mentions: 89     Fields:    
    59. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015 Oct 14; 11(10):831. 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, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. PMID: 26467284.
      View in: PubMed   Mentions: 10     Fields:    
    60. Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. J Proteome Res. 2015 Nov 06; 14(11):4687-703. 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. PMID: 26418914.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    61. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol. 2015 Aug; 11(8):e1004321. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. PMID: 26313928.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    62. Systems analysis of host-parasite interactions. Wiley Interdiscip Rev Syst Biol Med. 2015 Nov-Dec; 7(6):381-400. Swann J, Jamshidi N, Lewis NE, Winzeler EA. PMID: 26306749.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    63. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling. Biotechnol J. 2015 Jul; 10(7):939-49. Gutierrez JM, Lewis NE. PMID: 26099571.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    64. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics. 2015 Oct 15; 31(20):3383-6. 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, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A. PMID: 26079347.
      View in: PubMed   Mentions: 4     Fields:    
    65. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnol J. 2015 Jul; 10(7):979-94. Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H. PMID: 26058577.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    66. Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol. 2014 Nov 17; 10:760. 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. PMID: 25403753.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    67. Systems glycobiology for glycoengineering. Curr Opin Biotechnol. 2014 Dec; 30:218-24. Spahn PN, Lewis NE. PMID: 25202878.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    68. Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PLoS One. 2014; 9(7):e102319. Kumar A, Harrelson T, Lewis NE, Gallagher EJ, LeRoith D, Shiloach J, Betenbaugh MJ. PMID: 25029527.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    69. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014 Jul 01; 10:737. Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. PMID: 24987116.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    70. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet. 2014 01; 15(1):56-62. Robasky K, Lewis NE, Church GM. PMID: 24322726.
      View in: PubMed   Mentions: 75     Fields:    Translation:Humans
    71. The evolution of genome-scale models of cancer metabolism. Front Physiol. 2013 Sep 03; 4:237. Lewis NE, Abdel-Haleem AM. PMID: 24027532.
      View in: PubMed   Mentions:
    72. Hydroxocobalamin association during cell culture results in pink therapeutic proteins. MAbs. 2013 Nov-Dec; 5(6):974-81. Prentice KM, Gillespie R, Lewis N, Fujimori K, McCoy R, Bach J, Connell-Crowley L, Eakin CM. PMID: 23924851.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    73. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug; 31(8):759-65. 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, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO. PMID: 23873082.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansAnimalsCells
    74. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. Curr Opin Biotechnol. 2013 Dec; 24(6):1102-7. Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ. PMID: 23523260.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    75. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst. 2013 Feb 02; 9(2):167-74. Hyduke DR, Lewis NE, Palsson BØ. PMID: 23247105.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimals
    76. A proof for loop-law constraints in stoichiometric metabolic networks. BMC Syst Biol. 2012 Nov 12; 6:140. Noor E, Lewis NE, Milo R. PMID: 23146116.
      View in: PubMed   Mentions: 7     Fields:    
    77. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012 Nov 02; 11(11):5265-76. 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, Palsson BO, Zhang H, Betenbaugh M. PMID: 22971049.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    78. Network context and selection in the evolution to enzyme specificity. Science. 2012 Aug 31; 337(6098):1101-4. Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. PMID: 22936779.
      View in: PubMed   Mentions: 75     Fields:    Translation:Cells
    79. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. PMID: 22760628.
      View in: PubMed   Mentions: 70     Fields:    Translation:Cells
    80. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 Feb 27; 10(4):291-305. Lewis NE, Nagarajan H, Palsson BO. PMID: 22367118.
      View in: PubMed   Mentions: 219     Fields:    Translation:Cells
    81. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011 Aug 04; 6(9):1290-307. 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. PMID: 21886097.
      View in: PubMed   Mentions: 405     Fields:    
    82. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol. 2011 Jul 31; 29(8):735-41. 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, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J. PMID: 21804562.
      View in: PubMed   Mentions: 139     Fields:    Translation:AnimalsCells
    83. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol. 2011 Jul 05; 7:509. Conrad TM, Lewis NE, Palsson BØ. PMID: 21734648.
      View in: PubMed   Mentions: 98     Fields:    Translation:Cells
    84. The role of cellular objectives and selective pressures in metabolic pathway evolution. Curr Opin Biotechnol. 2011 Aug; 22(4):595-600. Nam H, Conrad TM, Lewis NE. PMID: 21481583.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    85. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J. 2011 Feb 02; 100(3):544-553. Schellenberger J, Lewis NE, Palsson BØ. PMID: 21281568.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    86. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol. 2010 Dec; 28(12):1279-85. Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ. PMID: 21102456.
      View in: PubMed   Mentions: 89     Fields:    Translation:Humans
    87. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci U S A. 2010 Nov 23; 107(47):20500-5. Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BØ. PMID: 21057108.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    88. Photochemical degradation of citrate buffers leads to covalent acetonation of recombinant protein therapeutics. Protein Sci. 2010 Nov; 19(11):2152-63. Valliere-Douglass JF, Connell-Crowley L, Jensen R, Schnier PD, Trilisky E, Leith M, Follstad BD, Kerr J, Lewis N, Vunnum S, Treuheit MJ, Balland A, Wallace A. PMID: 20836085.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    89. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol. 2010 Oct 19; 6:422. Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. PMID: 20959820.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansCells
    90. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl Environ Microbiol. 2010 Oct; 76(19):6529-40. Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ. PMID: 20709841.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    91. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol. 2010 Jul; 6:390. 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. PMID: 20664636.
      View in: PubMed   Mentions: 138     Fields:    Translation:Cells
    92. Design and analysis of synthetic carbon fixation pathways. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8889-94. Bar-Even A, Noor E, Lewis NE, Milo R. PMID: 20410460.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    93. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol. 2009 Jun; 191(11):3437-44. Lewis NE, Cho BK, Knight EM, Palsson BO. PMID: 19363119.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    94. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J Biomol Tech. 2004 Dec; 15(4):238-48. Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD. PMID: 15585820.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
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