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    Nathan Lewis

    TitleAssistant Adjunct Professor
    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0760
    CA La Jolla 92093
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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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      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.
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      1. Lombardo MV, Courchesne E, Lewis N, Pramparo T. Hierarchical cortical transcriptome disorganization in autism. Mol Autism. 2017; 8:29. PMID: 28649314.
        View in: PubMed
      2. Autran CA, Kellman BP, Kim JH, Asztalos E, Blood AB, Spence EC, Patel AL, Hou J, Lewis N, Bode L. Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants. Gut. 2017 Apr 05. PMID: 28381523.
        View in: PubMed
      3. 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 N, 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.
        View in: PubMed
      4. Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis N. 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
      5. Kallehauge TB, Li S, Pedersen LE, Ha TK, Ley D, Andersen MR, Kildegaard HF, Lee GM, Lewis N. Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Sci Rep. 2017 Jan 16; 7:40388. PMID: 28091612.
        View in: PubMed
      6. Spahn PN, Hansen AH, Kol S, Voldborg BG, Lewis N. Predictive glycoengineering of biosimilars using a Markov chain glycosylation model. Biotechnol J. 2017 Feb; 12(2). PMID: 27860290.
        View in: PubMed
      7. 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 N. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 Nov 23; 3(5):434-443.e8. PMID: 27883890.
        View in: PubMed
      8. Chiang AW, Li S, Spahn PN, Richelle A, Kuo CC, Samoudi M, Lewis N. Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology. Curr Opin Struct Biol. 2016 Oct; 40:104-111. PMID: 27639240.
        View in: PubMed
      9. 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 N, Mendes P. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics. 2016; 12:109. PMID: 27358602.
        View in: PubMed
      10. Stadler JG, Donlon K, Siewert JD, Franken T, Lewis N. Improving the Efficiency and Ease of Healthcare Analysis Through Use of Data Visualization Dashboards. Big Data. 2016 Jun; 4(2):129-35. PMID: 27441717.
        View in: PubMed
      11. Huang S, Chong N, Lewis N, 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.
      12. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis N. 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.
        View in: PubMed
      13. 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.
      14. Spahn PN, Hansen AH, Hansen HG, Arnsdorf J, Kildegaard HF, Lewis N. 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.
        View in: PubMed
      15. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis N. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 04; 44(D1):D515-22. PMID: 26476456; PMCID: PMC4702785.
      16. 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 N, 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.
      17. Kumar A, Baycin-Hizal D, Wolozny D, Pedersen LE, Lewis N, 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; PMCID: PMC4721571.
      18. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis N, 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; PMCID: PMC4552468.
      19. Swann J, Jamshidi N, Lewis N, Winzeler EA. Systems analysis of host-parasite interactions. Wiley Interdiscip Rev Syst Biol Med. 2015 Nov-Dec; 7(6):381-400. PMID: 26306749.
        View in: PubMed
      20. Gutierrez JM, Lewis N. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling. Biotechnol J. 2015 Jul; 10(7):939-49. PMID: 26099571.
        View in: PubMed
      21. 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 N, 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; PMCID: PMC4595895.
      22. Lee JS, Grav LM, Lewis N, 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.
        View in: PubMed
      23. Busskamp V, Lewis N, 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.
      24. Spahn PN, Lewis N. Systems glycobiology for glycoengineering. Curr Opin Biotechnol. 2014 Dec; 30:218-24. PMID: 25202878.
        View in: PubMed
      25. Kumar A, Harrelson T, Lewis N, 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.
      26. Bordbar A, Nagarajan H, Lewis N, 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.
      27. Robasky K, Lewis N, 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.
      28. Lewis N, Abdel-Haleem AM. The evolution of genome-scale models of cancer metabolism. Front Physiol. 2013 Sep 03; 4:237. PMID: 24027532; PMCID: PMC3759783.
      29. Lewis N, 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.
        View in: PubMed
      30. Kildegaard HF, Baycin-Hizal D, Lewis N, 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.
        View in: PubMed
      31. Hyduke DR, Lewis N, 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.
      32. Noor E, Lewis N, Milo R. A proof for loop-law constraints in stoichiometric metabolic networks. BMC Syst Biol. 2012 Nov 12; 6:140. PMID: 23146116; PMCID: PMC3560238.
      33. Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis N, 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.
      34. Nam H, Lewis N, 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.
      35. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis N, 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.
      36. Lewis N, 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.
      37. Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis N, 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.
      38. Xu X, Nagarajan H, Lewis N, 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.
      39. Conrad TM, Lewis N, Palsson BØ. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol. 2011 Jul 05; 7:509. PMID: 21734648; PMCID: PMC3159978.
      40. Nam H, Conrad TM, Lewis N. 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.
      41. Schellenberger J, Lewis N, Palsson BØ. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J. 2011 Feb 02; 100(3):544-53. PMID: 21281568; PMCID: PMC3030201.
      42. Lewis N, 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; PMCID: PMC3140076.
      43. Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis N, 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.
      44. 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.
      45. Bordbar A, Lewis N, 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; PMCID: PMC2990636.
      46. Portnoy VA, Scott DA, Lewis N, 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; PMCID: PMC2950451.
      47. Lewis N, 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.
      48. Bar-Even A, Noor E, Lewis N, 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.
      49. Lewis N, 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.
      50. Merrell K, Southwick K, Graves SW, Esplin MS, Lewis N, 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.
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