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Nathan Lewis

Title(s)Associate Professor In Residence, Pediatrics
SchoolHealth Sciences
Phone858-997-5844
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    Collapse Research 
    Collapse Research Activities and Funding
    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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    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.
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    1. Richelle A, Joshi C, Lewis NE. Assessing key decisions for transcriptomic data integration in biochemical networks. PLoS Comput Biol. 2019 Jul; 15(7):e1007185. PMID: 31323017.
      View in: PubMed
    2. 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. Sci Rep. 2019 Jun 20; 9(1):8827. PMID: 31222165.
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    3. 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. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res. 2019 Jun 07; 18(6):2433-2445. PMID: 31020842.
      View in: PubMed
    4. Richelle A, Chiang AWT, Kuo CC, Lewis NE. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions. PLoS Comput Biol. 2019 04; 15(4):e1006867. PMID: 30986217.
      View in: PubMed
    5. 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. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 Apr 18; 177(3):572-586.e22. PMID: 30955884.
      View in: PubMed
    6. 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. Reduced apoptosis in Chinese hamster ovary cells via optimized CRISPR interference. Biotechnol Bioeng. 2019 Jul; 116(7):1813-1819. PMID: 30883679.
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    7. Lee JS, Kildegaard HF, Lewis NE, Lee GM. Mitigating Clonal Variation in Recombinant Mammalian Cell Lines. Trends Biotechnol. 2019 Mar 18. PMID: 30898338.
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    8. Pristovšek N, Nallapareddy 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 Synth Biol. 2019 Apr 19; 8(4):758-774. PMID: 30807689.
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    9. 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. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc. 2019 03; 14(3):639-702. PMID: 30787451.
      View in: PubMed
    10. 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. Nat Commun. 2019 01 30; 10(1):488. PMID: 30700707.
      View in: PubMed
    11. Landig CS, Hazel A, Kellman BP, Fong JJ, Schwarz F, Agarwal S, Varki N, Massari P, Lewis NE, Ram S, Varki A. Evolution of the exclusively human pathogen Neisseria gonorrhoeae: Human-specific engagement of immunoregulatory Siglecs. Evol Appl. 2019 Feb; 12(2):337-349. PMID: 30697344.
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    12. 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. Nat Neurosci. 2018 Dec; 21(12):1680-1688. PMID: 30482947.
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    13. 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. Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. Front Mol Biosci. 2018; 5:96. PMID: 30488036.
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    14. Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM. Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing. ACS Synth Biol. 2018 Nov 14. PMID: 30388888.
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    15. 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. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11096-11101. PMID: 30301795.
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    16. Grav LM, Sergeeva D, Lee JS, Marin 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 Synth Biol. 2018 Sep 21; 7(9):2148-2159. PMID: 30060646.
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    17. 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. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Aug; 15(8):611-616. PMID: 30013045.
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    18. Courchesne E, Pramparo T, Gazestani VH, Lombardo MV, Pierce K, Lewis NE. The ASD Living Biology: from cell proliferation to clinical phenotype. Mol Psychiatry. 2019 Jan; 24(1):88-107. PMID: 29934544.
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    19. 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. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng. 2018 08; 115(8):2087-2100. PMID: 29704459.
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    20. 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 Comput Biol. 2018 01; 14(1):e1005895. PMID: 29300748.
      View in: PubMed
    21. 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. Curr Opin Biotechnol. 2018 06; 51:64-69. PMID: 29223005.
      View in: PubMed
    22. 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. Sci Rep. 2017 Nov 20; 7(1):15854. PMID: 29158538.
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    23. Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T. The Emerging Facets of Non-Cancerous Warburg Effect. Front Endocrinol (Lausanne). 2017; 8:279. PMID: 29109698.
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    24. Lombardo MV, Courchesne E, Lewis NE, Pramparo T. Hierarchical cortical transcriptome disorganization in autism. Mol Autism. 2017; 8:29. PMID: 28649314.
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    25. Richelle A, Lewis NE. Improvements in protein production in mammalian cells from targeted metabolic engineering. Curr Opin Syst Biol. 2017 Dec; 6:1-6. PMID: 29104947.
      View in: PubMed
    26. Autran CA, Kellman BP, Kim JH, Asztalos E, Blood AB, Spence ECH, Patel AL, Hou J, Lewis NE, Bode L. Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants. Gut. 2018 06; 67(6):1064-1070. PMID: 28381523.
      View in: PubMed
    27. 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. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. PMID: 28319113.
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    28. Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Syst. 2017 Mar 22; 4(3):318-329.e6. PMID: 28215528.
      View in: PubMed
    29. 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. Sci Rep. 2017 01 16; 7:40388. PMID: 28091612.
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    30. 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 a2 as a Host Factor for Bacterial Invasion. MBio. 2017 01 10; 8(1). PMID: 28074024.
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    31. Spahn PN, Hansen AH, Kol S, Voldborg BG, Lewis NE. Predictive glycoengineering of biosimilars using a Markov chain glycosylation model. Biotechnol J. 2017 Feb; 12(2). PMID: 27860290.
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    32. 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. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 11 23; 3(5):434-443.e8. PMID: 27883890.
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    33. 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. Curr Opin Struct Biol. 2016 10; 40:104-111. PMID: 27639240.
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    34. 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. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics. 2016; 12:109. PMID: 27358602.
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    35. Pace D, Lewis N, Wu T, Gillespie R, Leiske D, Velayudhan J, Rohrbach A, Connell-Crowley L. 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. PMID: 27160519.
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    36. Stadler JG, Donlon K, Siewert JD, Franken T, Lewis NE. Improving the Efficiency and Ease of Healthcare Analysis Through Use of Data Visualization Dashboards. Big Data. 2016 06; 4(2):129-35. PMID: 27441717.
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    37. 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 Med. 2016 Mar 31; 8(1):34. PMID: 27036109; PMCID: PMC4818393.
    38. 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. Biotechnol Adv. 2016 Sep-Oct; 34(5):621-633. PMID: 26948029.
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    39. 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. Mol Syst Biol. 2015 Dec 14; 11(12):841. PMID: 26668231; PMCID: PMC4704485.
    40. 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. Metab Eng. 2016 Jan; 33:52-66. PMID: 26537759.
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    41. 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 Res. 2016 Jan 04; 44(D1):D515-22. PMID: 26476456.
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    42. 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. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015 Oct 14; 11(10):831. PMID: 26467284; PMCID: PMC4631202.
    43. 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 Proteoinformatics. J Proteome Res. 2015 Nov 06; 14(11):4687-703. PMID: 26418914.
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    44. 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 Comput Biol. 2015 Aug; 11(8):e1004321. PMID: 26313928.
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    45. Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. Wiley Interdiscip Rev Syst Biol Med. 2015 Nov-Dec; 7(6):381-400. PMID: 26306749.
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    46. Gutierrez JM, Lewis NE. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling. Biotechnol J. 2015 Jul; 10(7):939-49. PMID: 26099571.
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    47. 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. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics. 2015 Oct 15; 31(20):3383-6. PMID: 26079347.
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    48. Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnol J. 2015 Jul; 10(7):979-94. PMID: 26058577.
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    49. 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. Mol Syst Biol. 2014 Nov 17; 10:760. PMID: 25403753; PMCID: PMC4299601.
    50. Spahn PN, Lewis NE. Systems glycobiology for glycoengineering. Curr Opin Biotechnol. 2014 Dec; 30:218-24. PMID: 25202878.
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    51. 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. 2014; 9(7):e102319. PMID: 25029527; PMCID: PMC4100879.
    52. 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. Mol Syst Biol. 2014 Jul 01; 10:737. PMID: 24987116; PMCID: PMC4299494.
    53. Robasky K, Lewis NE, Church GM. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet. 2014 01; 15(1):56-62. PMID: 24322726; PMCID: PMC4103745.
    54. Lewis NE, Abdel-Haleem AM. The evolution of genome-scale models of cancer metabolism. Front Physiol. 2013 Sep 03; 4:237. PMID: 24027532; PMCID: PMC3759783.
    55. 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. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug; 31(8):759-65. PMID: 23873082.
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    56. Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. Curr Opin Biotechnol. 2013 Dec; 24(6):1102-7. PMID: 23523260.
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    57. Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst. 2013 Feb 02; 9(2):167-74. PMID: 23247105; PMCID: PMC3594511.
    58. Noor E, Lewis NE, Milo R. A proof for loop-law constraints in stoichiometric metabolic networks. BMC Syst Biol. 2012 Nov 12; 6:140. PMID: 23146116; PMCID: PMC3560238.
    59. 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. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012 Nov 02; 11(11):5265-76. PMID: 22971049; PMCID: PMC3772721.
    60. 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. 2012 Aug 31; 337(6098):1101-4. PMID: 22936779; PMCID: PMC3536066.
    61. 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. Nat Commun. 2012 Jul 03; 3:929. PMID: 22760628; PMCID: PMC3827721.
    62. Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 Feb 27; 10(4):291-305. PMID: 22367118; PMCID: PMC3536058.
    63. 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. Nat Protoc. 2011 Aug 04; 6(9):1290-307. PMID: 21886097; PMCID: PMC3319681.
    64. 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. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol. 2011 Jul 31; 29(8):735-41. PMID: 21804562; PMCID: PMC3164356.
    65. Conrad TM, Lewis NE, Palsson BØ. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol. 2011 Jul 05; 7:509. PMID: 21734648; PMCID: PMC3159978.
    66. Nam H, Conrad TM, Lewis NE. The role of cellular objectives and selective pressures in metabolic pathway evolution. Curr Opin Biotechnol. 2011 Aug; 22(4):595-600. PMID: 21481583; PMCID: PMC3173765.
    67. Schellenberger J, Lewis NE, Palsson BØ. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J. 2011 Feb 02; 100(3):544-553. PMID: 21281568.
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    68. 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. Nat Biotechnol. 2010 Dec; 28(12):1279-85. PMID: 21102456.
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    69. 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. Proc Natl Acad Sci U S A. 2010 Nov 23; 107(47):20500-5. PMID: 21057108; PMCID: PMC2996682.
    70. 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. Photochemical degradation of citrate buffers leads to covalent acetonation of recombinant protein therapeutics. Protein Sci. 2010 Nov; 19(11):2152-63. PMID: 20836085; PMCID: PMC3005786.
    71. Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol. 2010 Oct 19; 6:422. PMID: 20959820.
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    72. 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. Appl Environ Microbiol. 2010 Oct; 76(19):6529-40. PMID: 20709841.
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    73. 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. Mol Syst Biol. 2010 Jul; 6:390. PMID: 20664636; PMCID: PMC2925526.
    74. Bar-Even A, Noor E, Lewis NE, Milo R. Design and analysis of synthetic carbon fixation pathways. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8889-94. PMID: 20410460; PMCID: PMC2889323.
    75. 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. J Bacteriol. 2009 Jun; 191(11):3437-44. PMID: 19363119; PMCID: PMC2681886.
    76. Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J Biomol Tech. 2004 Dec; 15(4):238-48. PMID: 15585820; PMCID: PMC2291707.