Nathan Lewis

Title(s)Associate Professor In Residence, Pediatrics
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research Activities and Funding
    ImmCellFIE: producing high-resolution snapshots of the functions of immune cells
    NIH UH2AI153029Jun 22, 2020 - May 31, 2022
    Role: Principal Investigator
    Developmental Functional Genomics in ASD Toddlers
    NIH R01MH110558Sep 1, 2016 - Jun 30, 2021
    Role: Principal Investigator
    Unraveling the mammalian secretory pathway through systems biology and algorithm development
    NIH R35GM119850Jul 15, 2016 - Jun 30, 2026
    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. 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 are housekeeping genes? PLoS Comput Biol. 2022 07; 18(7):e1010295. Joshi CJ, Ke W, Drangowska-Way A, O'Rourke EJ, Lewis NE. PMID: 35830477; PMCID: PMC9312424.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    2. Non-protective immune imprint underlies failure of Staphylococcus aureus IsdB vaccine. Cell Host Microbe. 2022 08 10; 30(8):1163-1172.e6. Tsai CM, Caldera JR, Hajam IA, Chiang AWT, Tsai CH, Li H, Díez ML, Gonzalez C, Trieu D, Martins GA, Underhill DM, Arditi M, Lewis NE, Liu GY. PMID: 35803276; PMCID: PMC9378590.
      View in: PubMed   Mentions:    Fields:    
    3. Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nat Commun. 2022 06 27; 13(1):3665. Armingol E, Baghdassarian HM, Martino C, Perez-Lopez A, Aamodt C, Knight R, Lewis NE. PMID: 35760817; PMCID: PMC9237099.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Artificial intelligence in the analysis of glycosylation data. Biotechnol Adv. 2022 11; 60:108008. Li H, Chiang AWT, Lewis NE. PMID: 35738510.
      View in: PubMed   Mentions:    Fields:    
    5. Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration. Nat Commun. 2022 05 04; 13(1):2455. Kellman BP, Richelle A, Yang JY, Chapla D, Chiang AWT, Najera JA, Liang C, Fürst A, Bao B, Koga N, Mohammad MA, Bruntse AB, Haymond MW, Moremen KW, Bode L, Lewis NE. PMID: 35508452; PMCID: PMC9068700.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    6. Author Correction: Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol. 2022 May; 18(5):575. 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, Esko JD. PMID: 35354934.
      View in: PubMed   Mentions:    Fields:    
    7. Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins. Metab Eng. 2022 07; 72:171-187. Malm M, Kuo CC, Barzadd MM, Mebrahtu A, Wistbacka N, Razavi R, Volk AL, Lundqvist M, Kotol D, Tegel H, Hober S, Edfors F, Gräslund T, Chotteau V, Field R, Varley PG, Roth RG, Lewis NE, Hatton D, Rockberg J. PMID: 35301123; PMCID: PMC9189052.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    8. Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. Appl Microbiol Biotechnol. 2022 Feb; 106(3):1113-1126. Savizi ISP, Maghsoudi N, Motamedian E, Lewis NE, Shojaosadati SA. PMID: 35044498.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    9. Multiplex genome editing of mammalian cells for producing recombinant heparin. Metab Eng. 2022 03; 70:155-165. Thacker BE, Thorne KJ, Cartwright C, Park J, Glass K, Chea A, Kellman BP, Lewis NE, Wang Z, Di Nardo A, Sharfstein ST, Jeske W, Walenga J, Hogwood J, Gray E, Mulloy B, Esko JD, Glass CA. PMID: 35038554.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    10. Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models. PLoS Comput Biol. 2022 Jan; 18(1):e1009776. Joshi CJ, Schinn SM, Richelle A, Shamie I, O'Rourke EJ, Lewis NE. PMID: 35007280; PMCID: PMC8746765.
      View in: PubMed   Mentions:    Fields:    
    11. Restoration of DNA repair mitigates genome instability and increases productivity of Chinese hamster ovary cells. Biotechnol Bioeng. 2022 03; 119(3):963-982. Spahn PN, Zhang X, Hu Q, Lu H, Hamaker NK, Hefzi H, Li S, Kuo CC, Huang Y, Lee JC, Davis AJ, Ly P, Lee KH, Lewis NE. PMID: 34953085; PMCID: PMC8821244.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    12. Neural responses to affective speech, including motherese, map onto clinical and social eye tracking profiles in toddlers with ASD. Nat Hum Behav. 2022 03; 6(3):443-454. Xiao Y, Wen TH, Kupis L, Eyler LT, Goel D, Vaux K, Lombardo MV, Lewis NE, Pierce K, Courchesne E. PMID: 34980898.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    13. LIGHT controls distinct homeostatic and inflammatory gene expression profiles in esophageal fibroblasts via differential HVEM and LTβR-mediated mechanisms. Mucosal Immunol. 2022 02; 15(2):327-337. Manresa MC, Wu A, Nhu QM, Chiang AWT, Okamoto K, Miki H, Kurten R, Pham E, Duong LD, Lewis NE, Akuthota P, Croft M, Aceves SS. PMID: 34903876; PMCID: PMC8866113.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    14. Erratum: An optimized genome-wide, virus-free CRISPR screen for mammalian cells. Cell Rep Methods. 2021 Nov 22; 1(7):100115. Xiong K, Karottki KJC, Hefzi H, Li S, Grav LM, Li S, Spahn P, Lee JS, Ventina I, Lee GM, Lewis NE, Kildegaard HF, Pedersen LE. PMID: 35475003; PMCID: PMC9017133.
      View in: PubMed   Mentions:
    15. Immune response to intravenous immunoglobulin in patients with Kawasaki disease and MIS-C. J Clin Invest. 2021 10 15; 131(20). Zhu YP, Shamie I, Lee JC, Nowell CJ, Peng W, Angulo S, Le LN, Liu Y, Miao H, Xiong H, Pena CJ, Moreno E, Griffis E, Labou SG, Franco A, Broderick L, Hoffman HM, Shimizu C, Lewis NE, Kanegaye JT, Tremoulet AH, Burns JC, Croker BA, Pediatric Emergency Medicine Kawasaki Disease Research Group Consortium. PMID: 34464357; PMCID: PMC8516453.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    16. Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis. mBio. 2021 10 26; 12(5):e0118121. Golden GJ, Toledo AG, Marki A, Sorrentino JT, Morris C, Riley RJ, Spliid C, Chen Q, Cornax I, Lewis NE, Varki N, Le D, Malmström J, Karlsson C, Ley K, Nizet V, Esko JD. PMID: 34544271; PMCID: PMC8546592.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    17. Atypical genomic cortical patterning in autism with poor early language outcome. Sci Adv. 2021 Sep 03; 7(36):eabh1663. Lombardo MV, Eyler L, Pramparo T, Gazestani VH, Hagler DJ, Chen CH, Dale AM, Seidlitz J, Bethlehem RAI, Bertelsen N, Barnes CC, Lopez L, Campbell K, Lewis NE, Pierce K, Courchesne E. PMID: 34516910; PMCID: PMC8442861.
      View in: PubMed   Mentions: 3     Fields:    
    18. Synergisms of machine learning and constraint-based modeling of metabolism for analysis and optimization of fermentation parameters. Biotechnol J. 2021 Nov; 16(11):e2100212. Khaleghi MK, Savizi ISP, Lewis NE, Shojaosadati SA. PMID: 34390201.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    19. Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis. Nat Commun. 2021 08 17; 12(1):4988. Bao B, Kellman BP, Chiang AWT, Zhang Y, Sorrentino JT, York AK, Mohammad MA, Haymond MW, Bode L, Lewis NE. PMID: 34404781; PMCID: PMC8371009.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    20. An optimized genome-wide, virus-free CRISPR screen for mammalian cells. Cell Rep Methods. 2021 Aug 23; 1(4). Xiong K, Karottki KJC, Hefzi H, Li S, Grav LM, Li S, Spahn P, Lee JS, Ventina I, Lee GM, Lewis NE, Kildegaard HF, Pedersen LE. PMID: 34935002; PMCID: PMC8687118.
      View in: PubMed   Mentions: 1  
    21. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform. 2021 Sep; 3(3):lqab061. Shamie I, Duttke SH, Karottki KJC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. PMID: 34268494; PMCID: PMC8276764.
      View in: PubMed   Mentions: 2  
    22. Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell Rep Methods. 2021 Jul 26; 1(3). Richelle A, Kellman BP, Wenzel AT, Chiang AWT, Reagan T, Gutierrez JM, Joshi C, Li S, Liu JK, Masson H, Lee J, Li Z, Heirendt L, Trefois C, Juarez EF, Bath T, Borland D, Mesirov JP, Robasky K, Lewis NE. PMID: 34761247; PMCID: PMC8577426.
      View in: PubMed   Mentions: 4  
    23. Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation. Cell Syst. 2021 09 22; 12(9):873-884.e4. Kuo CC, Chiang AWT, Baghdassarian HM, Lewis NE. PMID: 34171228; PMCID: PMC8505362.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    24. Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy. J Biomed Sci. 2021 Jun 22; 28(1):50. Chiang AWT, Baghdassarian HM, Kellman BP, Bao B, Sorrentino JT, Liang C, Kuo CC, Masson HO, Lewis NE. PMID: 34158025; PMCID: PMC8218521.
      View in: PubMed   Mentions: 4     Fields:    
    25. Type 2 Immunity and Age Modify Gene Expression of Coronavirus-induced Disease 2019 Receptors in Eosinophilic Gastrointestinal Disorders. J Pediatr Gastroenterol Nutr. 2021 05 01; 72(5):718-722. Chiang AWT, Duong LD, Shoda T, Nhu QM, Ruffner M, Hara T, Aaron B, Joplin E, Manresa MC, Abonia JP, Dellon ES, Hirano I, Gonsalves N, Gupta SK, Furuta GT, Rothenberg ME, Lewis NE, Muir AB, Aceves SS, CEGIR Investigator Group. PMID: 33394891; PMCID: PMC8048378.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    26. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol. 2021 06; 17(6):684-692. 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, Esko JD. PMID: 33846619; PMCID: PMC8159865.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    27. A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metab Eng. 2021 07; 66:114-122. 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. PMID: 33813034; PMCID: PMC8193919.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    28. Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells. Metab Eng. 2021 07; 66:21-30. Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. PMID: 33771719.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    29. Coordinate regulation of systemic and kidney tryptophan metabolism by the drug transporters OAT1 and OAT3. J Biol Chem. 2021 Jan-Jun; 296:100575. Granados JC, Richelle A, Gutierrez JM, Zhang P, Zhang X, Bhatnagar V, Lewis NE, Nigam SK. PMID: 33757768; PMCID: PMC8102410.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    30. The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection. Nat Commun. 2021 02 23; 12(1):1230. Askarian F, Uchiyama S, Masson H, Sørensen HV, Golten O, Bunæs AC, Mekasha S, Røhr ÅK, Kommedal E, Ludviksen JA, Arntzen MØ, Schmidt B, Zurich RH, van Sorge NM, Eijsink VGH, Krengel U, Mollnes TE, Lewis NE, Nizet V, Vaaje-Kolstad G. PMID: 33623002; PMCID: PMC7902821.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    31. A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures. Biotechnol Bioeng. 2021 05; 118(5):2118-2123. Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. PMID: 33580712.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    32. A unique esophageal extracellular matrix proteome alters normal fibroblast function in severe eosinophilic esophagitis. J Allergy Clin Immunol. 2021 08; 148(2):486-494. Hsieh LY, Chiang AWT, Duong LD, Kuo CC, Dong SX, Dohil R, Kurten R, Lewis NE, Aceves SS. PMID: 33556465; PMCID: PMC8342625.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    33. A Systems View of the Heparan Sulfate Interactome. J Histochem Cytochem. 2021 02; 69(2):105-119. Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. PMID: 33494649; PMCID: PMC7841697.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    34. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics. 2021 Jan 21; 22(1):69. 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. PMID: 33478392; PMCID: PMC7818915.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    35. CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PLoS Comput Biol. 2020 12; 16(12):e1008498. Lin D, Yalamanchili HB, Zhang X, Lewis NE, Alves CS, Groot J, Arnsdorf J, Bjørn SP, Wulff T, Voldborg BG, Zhou Y, Zhang B. PMID: 33351794; PMCID: PMC7790544.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    36. Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. Trends Biochem Sci. 2021 04; 46(4):284-300. Kellman BP, Lewis NE. PMID: 33349503; PMCID: PMC7954846.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    37. In situ detection of protein interactions for recombinant therapeutic enzymes. Biotechnol Bioeng. 2021 02; 118(2):890-904. 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. PMID: 33169829; PMCID: PMC7855575.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    38. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet. 2021 02; 22(2):71-88. Armingol E, Officer A, Harismendy O, Lewis NE. PMID: 33168968; PMCID: PMC7649713.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansAnimalsCells
    39. A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). Beilstein J Org Chem. 2020; 16:2645-2662. Kellman BP, Zhang Y, Logomasini E, Meinhardt E, Godinez-Macias KP, Chiang AWT, Sorrentino JT, Liang C, Bao B, Zhou Y, Akase S, Sogabe I, Kouka T, Winzeler EA, Wilson IBH, Campbell MP, Neelamegham S, Krambeck FJ, Aoki-Kinoshita KF, Lewis NE. PMID: 33178355; PMCID: PMC7607430.
      View in: PubMed   Mentions: 5  
    40. Systematically gap-filling the genome-scale metabolic model of CHO cells. Biotechnol Lett. 2021 Jan; 43(1):73-87. Fouladiha H, Marashi SA, Li S, Li Z, Masson HO, Vaziri B, Lewis NE. PMID: 33040240.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    41. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. Cell Host Microbe. 2020 10 07; 28(4):586-601.e6. Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L. PMID: 32841605; PMCID: PMC7443692.
      View in: PubMed   Mentions: 140     Fields:    Translation:HumansCellsPHPublic Health
    42. Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. bioRxiv. 2020 Aug 18. 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, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R. PMID: 32839779; PMCID: PMC7444296.
      View in: PubMed   Mentions:
    43. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. bioRxiv. 2020 Jul 24. Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L. PMID: 32743578; PMCID: PMC7386495.
      View in: PubMed   Mentions:
    44. Increased Production of LIGHT by T Cells in Eosinophilic Esophagitis Promotes Differentiation of Esophageal Fibroblasts Toward an Inflammatory Phenotype. Gastroenterology. 2020 11; 159(5):1778-1792.e13. Manresa MC, Chiang AWT, Kurten RC, Dohil R, Brickner H, Dohil L, Herro R, Akuthota P, Lewis NE, Croft M, Aceves SS. PMID: 32712105; PMCID: PMC7726704.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    45. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metab Eng. 2020 09; 61:288-300. 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: 10     Fields:    Translation:AnimalsCells
    46. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nat Commun. 2020 05 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; PMCID: PMC7244588.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    47. StanDep: Capturing transcriptomic variability improves context-specific metabolic models. PLoS Comput Biol. 2020 05; 16(5):e1007764. Joshi CJ, Schinn SM, Richelle A, Shamie I, O'Rourke EJ, Lewis NE. PMID: 32396573; PMCID: PMC7244210.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    48. Multiplex secretome engineering enhances recombinant protein production and purity. Nat Commun. 2020 04 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; PMCID: PMC7170862.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    49. Prenatal Origins of ASD: The When, What, and How of ASD Development. Trends Neurosci. 2020 05; 43(5):326-342. Courchesne E, Gazestani VH, Lewis NE. PMID: 32353336; PMCID: PMC7373219.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    50. ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis. Proc Natl Acad Sci U S A. 2020 04 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; PMCID: PMC7196839.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    51. 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; PMCID: PMC7138757.
      View in: PubMed   Mentions: 2     Fields:    
    52. 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: 8     Fields:    Translation:AnimalsCells
    53. 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; PMCID: PMC7082222.
      View in: PubMed   Mentions: 91     Fields:    
    54. 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; PMCID: PMC7153765.
      View in: PubMed   Mentions: 8  
    55. 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; PMCID: PMC6940358.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    56. 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; PMCID: PMC6923591.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    57. 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; PMCID: PMC7261405.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    58. 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; PMCID: PMC6789120.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    59. 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; PMCID: PMC7311070.
      View in: PubMed   Mentions: 1  
    60. A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-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; PMCID: PMC6764590.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    61. 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; PMCID: PMC6668847.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    62. 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; PMCID: PMC6586939.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    63. 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; PMCID: PMC6571120.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    64. 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; PMCID: PMC6483243.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    65. 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; PMCID: PMC6711371.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
    66. 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; PMCID: PMC6880750.
      View in: PubMed   Mentions: 9  
    67. 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; PMCID: PMC6545153.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    68. 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: 9     Fields:    Translation:AnimalsCells
    69. 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: 2     Fields:    Translation:AnimalsCells
    70. 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; PMCID: PMC6635304.
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    71. 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; PMCID: PMC6353872.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    72. 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; PMCID: PMC6346652.
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    73. 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; PMCID: PMC6445349.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    74. 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; PMCID: PMC6246695.
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    75. 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; PMCID: PMC6535434.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    76. 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; PMCID: PMC6205427.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    77. 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: 12     Fields:    Translation:AnimalsCells
    78. 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; PMCID: PMC6129399.
      View in: PubMed   Mentions: 105     Fields:    Translation:HumansCells
    79. 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; PMCID: PMC6309606.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimals
    80. 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; PMCID: PMC6045439.
      View in: PubMed   Mentions: 27     Fields:    Translation:Animals
    81. 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; PMCID: PMC5771636.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    82. 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; PMCID: PMC5988649.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    83. 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; PMCID: PMC5696473.
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    84. 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; PMCID: PMC5660072.
      View in: PubMed   Mentions: 21     Fields:    
    85. Hierarchical cortical transcriptome disorganization in autism. Mol Autism. 2017; 8:29. Lombardo MV, Courchesne E, Lewis NE, Pramparo T. PMID: 28649314; PMCID: PMC5480153.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    86. 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; PMCID: PMC5663301.
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    87. 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: 76     Fields:    Translation:HumansCTClinical Trials
    88. 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; PMCID: PMC5449203.
      View in: PubMed   Mentions: 138     Fields:    Translation:HumansCells
    89. 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; PMCID: PMC5526624.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimals
    90. 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; PMCID: PMC5238448.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    91. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 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; PMCID: PMC5225314.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    92. 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; PMCID: PMC5293603.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    93. 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; PMCID: PMC5132346.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    94. 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; PMCID: PMC5161599.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    95. 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; PMCID: PMC4896983.
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    96. Characterizing the effect of multiple Fc glycan attributes on the effector functions and FcγRIIIa 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: 9     Fields:    Translation:HumansAnimalsCells
    97. 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; PMCID: PMC4818393.
      View in: PubMed   Mentions: 59     Fields:    Translation:Humans
    98. 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: 12     Fields:    Translation:AnimalsCells
    99. 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; PMCID: PMC4704485.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    100. 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; PMCID: PMC5031499.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    101. 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; PMCID: PMC4702785.
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    102. 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; PMCID: PMC4631202.
      View in: PubMed   Mentions: 25     Fields:    
    103. 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; PMCID: PMC4721571.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    104. 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; PMCID: PMC4552468.
      View in: PubMed   Mentions: 104     Fields:    Translation:Cells
    105. 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; PMCID: PMC4679367.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    106. Differential binding of heavy chain variable domain 3 antigen binding fragments to protein A chromatography resins. J Chromatogr A. 2015 Aug 28; 1409:60-9. Bach J, Lewis N, Maggiora K, Gillespie AJ, Connell-Crowley L. PMID: 26189670.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    107. 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: 9     Fields:    Translation:HumansAnimalsCells
    108. 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; PMCID: PMC4595895.
      View in: PubMed   Mentions: 15     Fields:    
    109. 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: 22     Fields:    Translation:HumansAnimalsCells
    110. 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; PMCID: PMC4299601.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansCells
    111. Systems glycobiology for glycoengineering. Curr Opin Biotechnol. 2014 Dec; 30:218-24. Spahn PN, Lewis NE. PMID: 25202878.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    112. 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; PMCID: PMC4100879.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    113. 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; PMCID: PMC4299494.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    114. 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; PMCID: PMC4103745.
      View in: PubMed   Mentions: 123     Fields:    Translation:Humans
    115. The evolution of genome-scale models of cancer metabolism. Front Physiol. 2013 Sep 03; 4:237. Lewis NE, Abdel-Haleem AM. PMID: 24027532; PMCID: PMC3759783.
      View in: PubMed   Mentions: 37  
    116. 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: 86     Fields:    Translation:HumansAnimalsCells
    117. 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: 40     Fields:    Translation:HumansAnimalsCells
    118. 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; PMCID: PMC3594511.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimals
    119. 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; PMCID: PMC3560238.
      View in: PubMed   Mentions: 7     Fields:    
    120. 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; PMCID: PMC3772721.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    121. 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; PMCID: PMC3536066.
      View in: PubMed   Mentions: 105     Fields:    Translation:Cells
    122. 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; PMCID: PMC3827721.
      View in: PubMed   Mentions: 106     Fields:    Translation:Cells
    123. 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; PMCID: PMC3536058.
      View in: PubMed   Mentions: 302     Fields:    Translation:Cells
    124. 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; PMCID: PMC3319681.
      View in: PubMed   Mentions: 553     Fields:    
    125. 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; PMCID: PMC3164356.
      View in: PubMed   Mentions: 205     Fields:    Translation:AnimalsCells
    126. 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; PMCID: PMC3159978.
      View in: PubMed   Mentions: 122     Fields:    Translation:Cells
    127. 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; PMCID: PMC3173765.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    128. 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; PMCID: PMC3030201.
      View in: PubMed   Mentions: 84     Fields:    Translation:Cells
    129. 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; PMCID: PMC3140076.
      View in: PubMed   Mentions: 116     Fields:    Translation:Humans
    130. 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; PMCID: PMC2996682.
      View in: PubMed   Mentions: 97     Fields:    Translation:Cells
    131. 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; PMCID: PMC2990636.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansCells
    132. 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; PMCID: PMC2950451.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    133. 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; PMCID: PMC2925526.
      View in: PubMed   Mentions: 246     Fields:    Translation:Cells
    134. 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; PMCID: PMC2889323.
      View in: PubMed   Mentions: 120     Fields:    Translation:Cells
    135. 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; PMCID: PMC2681886.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    136. 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; PMCID: PMC2291707.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
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