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See below for our recent publications in peer-reviewed journals, books, and patents. Also, icons to the right filter publications by major topics. Public presentations and lectures can also be downloaded from here.

corresponding/senior author, * equal contribution
For a current list, click here.

Preprints under peer review

Rocamora F., Schoffelen S., Arnsdorf J., Toth E.A., Abdul Y., Cleveland T.E., Bjorn S.P., Wu Y.M., McElvaney N.G., Voldborg B.G.R., Fuerst T.R., Lewis N.E.Glycoengineered recombinant alpha1-antitrypsin results in comparable in vitro and in vivo activities to human plasma-derived protein, bioRxiv (2024).

Li H*Peralta A.G.*, Schoffelen S., Hansen A.H., Arnsdorf J., Schinn S., Skidmore J., Choudhury B., Paulchakrabarti M., Voldborg B.G., Chiang A.W.T.Lewis N.E.LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling, bioRxiv (2024).

Gopalakrishnan S., Johnson W., Valderrama-Gomez M.A., Icten E., Tat J., Lay F., Diep J., Gomez N., Stevens J., Schlegel F., Rolandi P., Kontoravdi C., Lewis N.E.Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks. bioRxiv (2023).

Masson H.O., Kuo C.C., Malm M., Lundqvist M., Sievertsson Å, Berling A., Tegel H., Hober S., Uhlén M., Grassi L., Hatton D., Rockberg J.‡, Lewis N.E.Deciphering the determinants of recombinant protein yield across the human secretome, bioRxiv (2022).


173. Yom A., Chiang A.W.T., Lewis N.E.‡. A Boltzmann model predicts glycan structures from lectin binding. Analytical Chemistry, 96:8332–8341 (2024). doi: 10.1021/acs.analchem.3c04992

172. Park S., Choi D., Song J., Lakshmanan M., Richelle A., Yoon S., Kontoravdi C., Lewis N.E., Lee D. Driving towards digital biomanufacturing by CHO genome-scale models. Trends in Biotechnology, accepted (2024)

171. Gopalakrishnan S., Johnson W., Valderrama-Gomez M.A., Icten E., Tat J., Ingram M., Shek C.F., Chan P.K., Schlegel F., Rolandi P., Kontoravdi C., Lewis N.E. COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling. Metabolic Engineering, 82:183-192 (2024).

167. Armingol E.‡, Baghdassarian H., Lewis N.E. The diversification of methods for studying cell–cell interactions and communication. Nature Reviews Genetics, in press (2024).

166. Pong A., Mah C.K., Yeo G.W., Lewis N.E. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment. Current Opinion in Biotechnology, 85:103048 (2024).

165. Masson H.O., Samoudi M., Robinson C.M., Kuo C.C., Weiss L., Shams-Ud-Doha K., Campos A.R., Tejwani V., Dahodwala H., Menard P., Voldborg B.G., Sharfstein S.T., Lewis N.E. Inferring secretory and metabolic pathway activity from omic data with secCellFie. Metabolic Engineering, 81, 273-285 (2024). bioRxiv preprint

163. Baghdassarian H., Lewis N.E. Resource Allocation in Mammalian Systems. Biotechnology Advances, 71, 108305 (2024). Preprint


160. Kim S.H., Shin S.H., Baek M, Xiong K., Karottki K.J.L.C.Hefzi H., Grav L.M., Pedersen L.E., Kildegaard H.F., Lewis N.E., Lee J.S., Lee G.M. Identification of hyperosmotic stress-responsive genes in Chinese hamster ovary cells via genome-wide virus-free CRISPR/Cas9 screening. Metabolic Engineering, 80:66-77 (2023). doi:10.1016/j.ymben.2023.09.006

159. Aamodt CM, Lewis, NE. Single-cell A/B testing for cell-cell communication, Cell Systems, 14, 428-429 (2023).

158. Rocamora F., Peralta A.G., Shin S., Sorrentino J., Wu M., Toth E.A., Fuerst T.A., Lewis N.E. Glycosylation Shapes the Efficacy and Safety of Diverse Protein, Gene and Cell Therapies, Biotechnology Advances, 67, 108206 (2023). preprint

153. Liang C., Chiang A.W.T.‡, Lewis N.E.‡ GlycoMME, a Markov modeling platform for studying N-glycosylation biosynthesis from glycomics data, STAR Protocols, 4, 102244 (2023). doi: 10.1016/j.xpro.2023.102244.

152. Masson H.O., Karottki K.J.L.C., Tat J., Hefzi H.‡, Lewis N.E.From Observational to Actionable: rethinking Omics in Biologics Production, Trends in Biotechnology, 41(9), 1127-1138 (2023). preprint doi: 10.1016/j.tibtech.2023.03.009

149. Ha TK*, Òdena A*, Karottki KJLC, Kim CL, Hefzi H, Lee GM, Kildegaard HF, Nielsen LK, Grav LM, Lewis NE. Enhancing CHO cell productivity through a dual selection system in glutamine free medium. Biotechnology & Bioengineering, 120 (4), 1159-1166. (2023). doi: 10.1002/bit.28318, Preprint

147. Kotidis P., Donini R., Arnsdorf J., Hansen A.H., Voldborg B.G.R., Chiang A.W.T., Haslam S., Betenbaugh M., Jimenez del Val I., Lewis N.E., Krambeck F, Kontoravdi C. CHOGlycoNET: Comprehensive Glycosylation Reaction Network for CHO cells, Metabolic Engineering, 76, 87-96 (2023). doi: 10.1016/j.ymben.2022.12.009


136. Malm M.*, Kuo C.C.*, Barzadd M.M., Mebrahtu A., Wistbacka N., Razavi R., Volk A.L., Lundqvist M., Kotol D., Edfors F., Gräslund T., Chotteau V., Field R., Varley P.G., Roth R.G., Lewis N.E.‡, Hatton D., Rockberg J.‡ Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins. Metabolic Engineering, 72, 171-187 (2022). bioRxiv doi: 10.1101/2021.08.16.455786, DOI: 10.1016/j.ymben.2022.03.009, PMCID: PMC9189052

135. Thacker B.E., Thorne K.J., Cartwright C., Park J., Glass K., Chea A., Kellman B.P., Lewis N.E., Wang Z., Di Nardo A., Sharfstein S.T., Jeske W., Walenga J., Hogwood J., Gray E., Mulloy B., Esko J.D., Glass C.A. Multiplex genome editing of mammalian cells for producing recombinant heparin. Metabolic Engineering, 70, 155-165 (2022). doi: 10.1016/j.ymben.2022.01.002

133. Spahn, P.N.*, Zhang, X.*, Hu, Q., Hamaker, N., Hefzi, H., Li, S., Kuo, C.C., Huang, Y., Lee, J.C., Ly, P. , Lee, K.H.,‡ Lewis, N.E.‡ Restoration of deficient DNA Repair Genes Mitigates Genome Instability and Increases Productivity of Chinese Hamster Ovary Cells. Biotechnology & Bioengineering, 119, 963-982 (2022). doi: 10.1002/bit.28016, bioRxiv doi: 10.1101/2021.01.07.425558

131. Savizi I.S.P., Maghsoudi N., Motamedian E., Lewis N.E., Shojaosadati S.A. Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. Applied Microbiology and Biotechnology, 106, 1113–1126 (2022). doi:10.1007/s00253-021-11755-4, Authorea preprint


126. Khaleghi M.K., Savizi I.S.P., Lewis N.E., Shojaosadati S.A. Synergisms of machine learning and constraint-based modeling of metabolism for analysis and optimization of fermentation parameters. Biotechnology Journal, 16:2100212. (2021). doi: 10.22541/au.162083622.21592768/v1

123. Xiong, K., Karottki, K.J.L.C., Hefzi, H., Li, S., Grav, L.M., Li, S., Spahn, P., Lee, J.S., Lee, G.M., Lewis, N.E., Kildegaard, H.F.,Pedersen, L.E. An optimized genome-wide, virus-free CRISPR screen for mammalian cells. Cell Reports Methods, 1:100062 (2021). bioRxiv doi: 10.1101/2020.05.19.103648

122. Shamie I.*, Duttke S.H.*, Karottki K.J.L.C., Han C.Z., Hansen A.H., Hefzi H., Xiong K., Li S., Roth S., Tao J., Lee G.M., Glass C.K., Kildegaard H.F., Benner C., Lewis N.E. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genomics and Bioinformatics, 3: lqab061 (2021). doi: 10.1093/nargab/lqab061

119. Samoudi M, Masson H, Kuo CC, Robinson C, Lewis NE. From omics to cellular mechanisms in mammalian cell factory development, Curr Opin in Chem Eng, 32: 100688 (2021). doi: 10.1016/j.coche.2021.100688

118. Chiang A.W.T.‡, Baghdassarian H.M., Kellman B.P., Bao B., Sorrentino J.T., Liang C., Kuo C.C., Masson H.O., Lewis N.E. Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy. Journal of Biomedical Science, 28:50 (2021). doi: 10.1186/s12929-021-00746-2, PMCID: PMC8218521

117. Savizi I.S.P., Motamedian E., Maghsoudi N., Lewis N.E., Jimenez del Val I., Shojaosadati S.A. An integrated modular framework for modeling the effect of ammonium on the sialylation process of monoclonal antibodies produced by CHO cells. Biotechnology Journal, 16:2100019 (2021). doi: 10.1002/biot.202100019

116. 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‡. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nature Chemical Biology, 17: 684–692 (2021). PMCID: PMC8218521

115. Karottki, K.J.L.C., Hefzi, H., Li, S., Pedersen, L.E., Spahn, P., Ruckerbauer, D., Bort, J.H., Thomas, A., Lee, J.S., Borth, N., Lee, G.M., Kildegaard, H.F.‡, Lewis, N.E.A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metabolic Engineering, 66:114-122 (2021). doi: 10.1016/j.ymben.2021.03.017. bioRxiv doi: 10.1101/2020.05.07.081604, PMCID: PMC8193919

114. Schinn S-M, Morrison C, Wei W, Zhang L, Lewis NE. Systematic evaluation of parameterization for genome-scale metabolic models of cultured mammalian cells. Metabolic Engineering, 66:21-30 (2021). bioRxiv doi:10.1101/2020.06.24.169938.

112. Schinn S.M., Morrison C., Wei W., Zhang L., Lewis N.E. A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures. Biotechnology & Bioengineering, 118:2118-2123 (2021). doi: 10.1002/bit.27714 bioRxiv doi: 10.1101/2020.09.02.279687

105. Samoudi, M.*, Kuo, C.C.*, Robinson, C.M.*, Shams-Ud-Doha, K., Schinn, S.M., Kol, S., Weiss, L., Bjorn, S.P., Voldborg, B.G., Campos, A.R., Lewis, N.E. In situ detection of protein interactions for recombinant therapeutic enzymes. Biotechnology & Bioengineering, 118 (2):890-904 (2021). doi: 10.1002/bit.27621, PMCID: PMC7855575

103. Fouladiha, H., Marashi, S.A., Li, S., Li, Z., Masson, H.O., Vaziri, B., Lewis, N.E. Systematically gap-filling the genome-scale model of CHO cells. Biotechnology Letters, 43:73–87 (2021). doi: 10.1007/s10529-020-03021-w, bioRxiv: 10.1101/2020.01.27.921296


102. Martino, C.*, Kellman, B.P.*, Sandoval, D.R.*, Clausen, T.M., Marotz, C., Song, S.J., Wandro, S., Zaramela, L., Benítez, R.A.S., Zhu, Q., Armingol, E., Vázquez-Baeza, Y., McDonald, D., Sorrentino, J., Taylor, B., Belda-Ferre, P., Liang, C., Zhang, Y., Schifanella, L., Klatt, N.R., Havulinna, A.S., Jousilahti, P., Huang, S., Haiminen, N., Parida, L., Kim, H.C., Swafford, A.D., Zengler, K., Cheng, S., Inouye, M., Niiranen, T., Jain, M., Salomaa, V., Esko, J.D., Lewis, N.E.‡, Knight, R.‡ Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. bioRxiv, (2020). DOI: 10.1101/2020.08.17.238444. News Coverage: Medical News

101. Lin, D., Yalamanchili, H., Zhang, X., Lewis, N.E., Alves, C.L., Groot, J., Arnsdorf, J., Bjørn, S.P., Wulff, T., Voldborg, B.G., Zhou, Y., Zhang, B. CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell linesPLoS Computational Biology, 16: e1008498 (2020). doi: 10.1371/journal.pcbi.1008498

96. Kol, S., Ley, D., Wulff, T., Decker, M., Arnsdorf, J., Schoffelen, S., Hansen, A.H., Gutierrez, J.M., Chiang, A.W.T., Masson, H.O., Palsson, B.O., Voldborg, B.G., Pedersen, L.E., Kildegaard, H.F., Lee, G.M., Lewis, N.E. Multiplex secretome engineering enhances recombinant protein production and purityNature Communications, 11:1908 (2020). doi: 10.1038/s41467-020-15866-w. News coverage: Nature Bioengineering, UCSD Jacobs,, Genetic Engineering and Biotechnology News,

94. Szeliova, D., Ruckerbauer, D.E., Galleguillos, S.N., Petersen, L.B., Natter, K., Hanscho, M., Troyer, C. Causon, T., Schoeny, H., Christensen, H.B., Lee, D.Y., Lewis, N.E., Koellensperger, G., Hann, S., Nielsen, L., Borth, N., Zanghellini, J. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metabolic Engineering, 61:288-300 (2020). doi: 10.1016/j.ymben.2020.06.002

93. Weiss, R.J.*, Spahn, P.N.*, Chiang, A.W.T., Li, J., Kellman, B.P., Benner, C., Glass, C.K., Gordts, P.L.S.M., Lewis, N.E.‡, Esko, J.D.‡ ZNF263 is a novel transcriptional regulator of heparin and heparan sulfate biosynthesis, Proc. Nat. Acad. Sci. USA, 117:9311-9317 (2020). doi: 10.1073/pnas.1920880117 News coverage: UCSD Jacobs,, Genetic Engineering and Biotechnology News, Biopharma Reporter

90. Fouladiha, H., Marashi, S.A., Torkashvand, F., Mahboudi, F., Lewis, N.E., Vaziri, B. A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody productionBioprocess and Biosystems Engineering, 43, 1381–1389 (2020). doi: 10.1007/s00449-020-02332-6

89. Liang, C.*, Chiang,. A.W.T.*, Hansen, A.H., Arnsdorf, J., Schoffelen, S., Sorrentino, J.T., Kellman, B.P., Bao, B., Voldborg, B.G., Lewis, N.E. A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering. Current Research in Biotechnology, 2:22-36 (2020). doi: 10.1016/j.crbiot.2020.01.001 News coverage: Bioanalysis Zone

88.  Gutierrez, J.M.*, Feizi, A.*, Li, S., Kallehauge, T.B., Grav, L.M., Hefzi, H., Ley, D., Baycin Hizal, D., Betenbaugh, M.J., Voldborg, B., Kildegaard, H.F., Lee, G.M., Palsson, B.O., Nielsen, J., Lewis, N.E. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretionNature Communications, 11:68 (2020). doi: 10.1038/s41467-019-13867-y News coverage:

86. Karottki, K.J.L.C., Hefzi, H., Xiong, K., Shamie, I., Hansen, A.H., Li, S., Li, S., Lee, J.S., Lee, G.M., Kildegaard, H.F.‡, Lewis, N.E.‡ Awakening dormant glycosyltransferases in CHO cells with CRISPRa. Biotechnology & Bioengineering, 117, 593-598 (2020). doi: 10.1002/bit.27199


82. Dahodwala, H., Kaushik, P., Tejwani, V., Kuo, C.C., Menard, P., Henry, M., Voldborg, B.G., Lewis, N.E., Meleady, P., Sharfstein, S.T. Increased mAb titers from amplification are associated with increased interaction of CREB1 with transgene promoter. Current Research in Biotechnology, 1:49-57 (2019). doi: 10.1016/j.crbiot.2019.09.001

81. Li, S.*, Richelle, A.*, Lewis, N.E. Enhancing product and bioprocess attributes using genome-scale models of CHO metabolismCell Culture Engineering: Recombinant Protein Production , p.73 (2019). ISBN: 978-3-527-34334-8

80. Cyrielle, C., Joshi, C., Lewis, N.E., Laetitia, M., Andersen, M.R.Adaption of Generic Metabolic Models to Specific Cell Lines for Improved Modeling of Biopharmaceutical Production and Prediction of ProcessesCell Culture Engineering: Recombinant Protein Production , p.127 (2019). ISBN: 978-3-527-34334-8

78. Chiang, A.W.T., Li, S., Kellman, B.P., Chattopadhyay, G., Zhang, Y., Kuo, C.C., Gutierrez, J.M., Ghazi, F., Schmeisser, H., Menard, P., Bjorn, S.P., Voldborg, B.G., Rosenberg, A.S., Puig, M.‡, Lewis, N.E.‡ Combating viral contaminants in CHO cells by engineering innate immunityScientific Reports, 9:8827 (2019). doi: 10.1038/s41598-019-45126-x

77. Li, S., Cha, S.W., Heffner, K., Baycin-Hizal, D., Bowen, M., Chaerkady, R., Cole, R., Tejwani, V., Kaushik, P., Henry, M., Meleady, P., Sharfstein, S., Betenbaugh, M.J., Bafna, V., Lewis, N.E. Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elementsJournal of Proteome Research, 18:2433-2445 (2019). bioRxiv: 10.1101/468181 , Download genome and annotation here

75. Xiong, K.*, Marquart, K.F.*, Karottki, K.J.L.C.*, Li, S.Shamie, I., Lee, J.S., Signe Gerling, S., Yeo, N.C., Chavez, A., Lee, G.M., Lewis, N.E.‡, Kildegaard, H.F.Reduced Apoptosis in Chinese Hamster Ovary Cells via Optimized CRISPR InterferenceBiotechnology & Bioengineering, 116:1813-1819 (2019). doi: 10.1002/bit.26969

73. Pristovsek, N., Nallapareddy, S., Grav, L.M., Hefzi, H.Lewis, N.E., Rugbjerg, P., Hansen, H.G., Lee, G.M., Andersen, M.R., Kildegaard, H.F. Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell EngineeringACS Synthetic Biology, 8:758–774 (2019). doi: 10.1021/acssynbio.8b00453

72. Lytle, N., Ferguson, L.P., Rajbhandari, N., Gilroy, K., Fox, R.G., Robertson, N., Deshpande, A., Schürch, C., Hamilton, M., Robertson, N., Lin, W., Noel, P., Wartenberg, M, Zlobec, I., Eichmann, M., Galván, J.A., Karamitopoulou, E., Gilderman, T., Esparza, L.A., Shima, Y., Spahn, P., French, R., Lewis, N.E., Fisch, K.M., Sasik, R., Rosenthal, S.B., Kritzik, M., Von Hoff, D., Han, H., Ideker, T., Deshpande, A., Lowy, A.M., Adams, P., Reya, T. A multiscale map of the stem cell state in pancreatic adenocarcinomaCell, 177:572-586 (2019).

71. Lee, J.S., Kildegaard, H.F., Lewis, N.E., Lee, G.M. Deciphering Clonal Variation in Recombinant Mammalian Cell LinesTrends in Biotechnology, 37, 931-942 (2019). doi: 10.1016/j.tibtech.2019.02.007


66. Lee, J.S., Park, J.H., Ha, T.K., Samoudi, M., Lewis, N.E., Palsson, B.O., Kildegaard, H.F., Lee, G.M. Revealing key determinants of clonal variation in transgene expression in recombinant CHO cells using targeted genome editingACS Synthetic Biology, 7 (12):2867-2878 (2018). doi: 10.1021/acssynbio.8b00290

65. Brunk, E.*, Chang, R.L., Xia, J., Hefzi, H., Yurkovich, J., Kim, D., Buckmiller, E., Wang, H.H., Yang, C., Palsson, B.Ø., Church, G.M.Lewis, N.E.*‡ Characterizing post-translational modifications in prokaryotic metabolism using a multi-scale workflowProc. Nat. Acad. Sci. USA, 115 (43): 11096-11101 (2018). bioRxiv doi: 10.1101/180646

64. Grav, L.M., Sergeeva, D., Lee, J.S., Marin de Mas, I., Lewis, N.E., Andersen, M.R., Nielsen, L.K., Lee, G.M., Kildegaard, H.F. Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generationACS Synthetic Biology, 7 (9):2148–2159. doi:10.1021/acssynbio.8b00140

63. Yeo, N.C., Chavez, A., Lance-Byrne, A., Chan, Y., Menn, D., Milanova, D., Kuo, C.C., Guo, X., Sharma, S., Tung, A., Cecchi, R.J., Tuttle, M., Pradhan, S., Lim, E.T., Davidsohn, N., Ebrahimkhani, M.R., Collins, J.J., Lewis, N.E., Kiani, S., Church, G.M.  An enhanced CRISPR repressor for targeted mammalian gene regulationNature Methods, 15:611-616 (2018) . doi:10.1038/s41592-018-0048-5

61. Rupp, O.*, MacDonald, M.L.*, Li, S.*, Dhiman, H.*, Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., Samoudi, M., Hou, H., Kingham, B., Goesmann, A., Betenbaugh, M.J. ‡, Lewis, N.E.‡, Borth, N.‡, Lee, K.‡ A reference genome of the Chinese hamster based on a hybrid assembly strategyBiotechnology & Bioengineering, 115:2087-2100 (2018). doi: 10.1002/bit.26722

59.  Kuo, C.C., Chiang, A.W.T., Shamie, I., Samoudi, M., Gutierrez, J.M.Lewis, N.E.‡ The emerging role of systems biology for engineering protein production in CHO cellsCurrent Opinion in Biotechnology, 51:64–69 (2018). doi: 10.1016/j.copbio.2017.11.015

57. Uhlen, M, Tegel, H, Sivertsson, Å, Kuo, C C, Gutierrez, J M, Lewis, N E, Forsström, B, Dannemeyer, M, Fagerberg, L, Rockberg, J, Malm, M, Vunk, H, Edfors, F, Hober, A, Sjöstedt, E, Mulder, J, Mardinoglu, A, Schwenk, J, Nilsson, P, Zwahlen, M, von Feilitzen, K, Lindskog, C, Ponten, F, Nielsen, J, Voldborg, B G, Palsson, B O, Volk, A L R, Lundqvist, M, Berling, A, Svensson, A S, Kanje, A, Enstedt, H, Afshari, D, Ekblad, S, Scheffel, J, Xu, L L, Mihai, R, Bremer, L, Westin, M, Muse, M, Mayr, L, Knight, S, Göpel, S, Davies, R, Varley, P, Hatton, D, Takanen, J O, Schiavone, L H, Hober, S. The human secretome – the proteins secreted from human cellsbioRxiv (2018). doi: 10.1101/465815


56.  Spahn, P.N., Bath, T., Weiss, R.J., Kim, J., Esko, J.D., Lewis, N.E.‡, Harismendy, O.‡. PinAPL-Py: a web-service for the analysis of CRISPR-Cas9 ScreensScientific Reports, 15854 (2017). DOI: 10.1038/s41598-017-16193-9

54.  Richelle, A., Lewis, N.E.Improvements in protein production in mammalian cells from targeted metabolic engineeringCurrent Opinion in Systems Biology, 6:1-6 (2017). DOI: 10.1016/j.coisb.2017.05.019

52. Opdam, S.*, Richelle, A.*, Kellman, B., Li, S., Zielinski, D.C., Lewis, N.E.‡ A systematic evaluation of methods for tailoring genome-scale metabolic modelsCell Systems, 4:1-12 (2017). DOI:10.1016/j.cels.2017.01.010

51. Spahn, P.N., Hansen, A.H., Kol, S., Voldborg, B.G., Lewis, N.E.‡  Predictive glycoengineering of biosimilars using a Markov chain glycosylation modelBiotechnology Journal,12:1600489 (2017). DOI:10.1002/biot.201600489

50. Kallehauge, T.B., Li, S., Pedersen, L.E., Ha, T.K., Ley, D., Andersen, M.R., Kildegaard, H.F., Lee, G.M.‡, Lewis, N.E.‡  Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretionScientific Reports,  7:40388 (2017). DOI:10.1038/srep40388

49. Shen, J.P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A.N., Sanchez, K.S., Thomas, A.Kuo, C.C., Du, D., Roguev, A., Lewis, N.E., Chang, A.N., Kreisberg, J.F., Krogan, N., Qi, L., Ideker, T., Mali, P.M.  Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactionsNature Methods,  14:573-576 (2017). DOI:10.1038/nmeth.4225

48. van Wijk, X.M., Döhrmann, S., Hallström, B.M., Li, S., Voldborg, B.G., Meng, B.X., McKee, K.K., van Kuppevelt, T.H., Yurchenco, P.D., Palsson, B.O., Lewis, N.E., Nizet, V., Esko, J.D.Whole Genome Sequencing of Invasion-Resistant Cells Identifies Laminin a2 as a Host Factor For Bacterial InvasionmBio, 8:e02128-16 (2017). DOI:10.1128/mBio.02128-16


45. Hefzi, H.*, Ang, K.S.*, Hanscho, M.*, Bordbar, A., Ruckerbauer, D., Lakshmanan, M., Orellana, C.A., Baycin-Hizal, D., Huang, H., Ley, D., Martínez, V.S., Kyriakopoulos, S., Jiménez, N.E., Zielinski, D.C., Quek, L.E., Wulff, T., Arnsdorf, J., Li, S., Lee, J.S., Paglia, G., Loira, N., Spahn, P.N., Pedersen, L.E., Gutierrez, J.M., King, Z.A., Lund, A.M., Nagarajan, H., Thomas, A., Abdel-Haleem, A.M., Zanghellini, J., Kildegaard, H.F., Voldborg, B.G., Gerdtzen, Z.P., Betenbaugh, M.J., Palsson, B.O., Andersen, M.R., Nielsen, L.K., Borth, N.‡, Lee, D.Y.‡, Lewis, N.E.‡ A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolismCell Systems, 3, 434-443 (2016). DOI:10.1016/j.cels.2016.10.020, News coverage: phys.orgUCSD Health Sciences, Nordic Life Science News, Novo Nordisk Fonden

44. Chiang, A.W.T., Li, S., Spahn, P.N., Richelle, A., Kuo, C.C., Samoudi, M.,  Lewis, N.EModulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiologyCurrent Opinion in Structural Biology, 10, 104–111 (2016). DOI: 10.1016/

41. Golabgir, A.*, Gutierrez, J.M.*, Hefzi, H., Li, S., Palsson, B.O., Herwig, C.‡, Lewis, N.E.‡ Quantitative feature extraction from the Chinese Hamster Ovary bioprocess bibliome using a novel meta-analysis workflow Biotechnology Advances, 34(5):621–633 (2016). DOI:10.1016/j.biotechadv.2016.02.011 * equal contribution, listed alphabetically The CHO Bibliome website

39. Spahn, P.N., Hansen, A.H., Hansen, H.G., Arnsdorf, J., Kildegaard, H.F., Lewis, N.E.‡  A Markov chain model for N-linked protein glycosylation – towards a low-parameter tool for model-driven glycoengineeringMetabolic Engineering,  33: 52–66 (2016). DOI:10.1016/j.ymben.2015.10.007


36. Kumar, A., Baycin-Hizal, D., Wolozny, D., Pedersen, L.E., Lewis, N.E., Heffner, K., Chaerkady, R., Cole, R.N., Shiloach, J., Zhang, H., Bowen, M.A., Betenbaugh, M.J. Elucidation of the CHO Super-Ome (CHO-SO) by ProteoInfomatics.  Journal of Proteome Research, 14 (11), pp 4687–4703 (2015). DOI: 10.1021/acs.jproteome.5b00588

33. Gutierrez, J.M., Lewis, N.E.‡ Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modelingBiotechnology Journal, 10:939–949 (2015). DOI: 10.1002/biot.201400647

31. Lee, J.S., Grav, L.M., Lewis, N.E., Kildegaard, H.F. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnology Journal, 10:979–994 (2015). DOI: 10.1002/biot.201500082.


30. Busskamp, V.*, Lewis, N.E.*, Guye, P.*, Ng, A.H.M., Shipman, S.L., Byrne, S.M., Sanjana, N.E., Murn, J., Li, Y., Li, S., Stadler, M., Weiss, R., Church, G.M. Rapid neurogenesis through transcriptional activation in human stem cellsMolecular Systems Biology, 10:760 (2014). DOI: 10.15252/msb.20145508. * equal contribution

29. Spahn, P., Lewis, N.E.‡ Systems glycomics for glycoengineeringCurrent Opinion in Biotechnology, 30:218–224 (2014). DOI: 10.1016/j.copbio.2014.08.004

28. Hefzi, H., Lewis, N.E.‡ From random mutagenesis to systems biology in metabolic engineering of mammalian cellsPharmaceutical Bioprocessing, 2:355-358 (2014). DOI: 10.4155/pbp.14.36


23. Lewis, N.E.*, Liu, X.*, Li, Y.*, Nagarajan, H.*, Yerganian, G., O’Brien, E., Bordbar, A., Roth, A.M., Rosenbloom, J., Bian, C., Xie, M., Chen, W., Li, N., Baycin-Hizal, D., Latif, H., Forster, J., Betenbaugh, M.J., Famili, I., Xu, X., Wang, J., Palsson, B.O. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genomeNature Biotechnology. 31:759-65 (2013). doi: 10.1038/nbt.2624. * equal contribution

22. Kildegaard, H.F., Baycin-Hizal, D., Lewis, N.E., Betenbaugh, M.J. The Emerging CHO Systems Biology Era: Harnessing the ‘Omics Revolution for BiotechnologyCurrent Opinion in Biotechnology. S0958-1669(13):00021-9 (2013). doi: 10.1016/j.copbio.2013.02.007


18. Baycin-Hizal, D., Tabb, D.L., Chaerkady, R., Chen, L., Lewis, N.E., Nagarajan, H., Sarkaria, V., Kumar, A., Wolozny, D., Colao, J., Jacobson, E., Tian, Y., O’Malley, R.N., Krag, S., Cole, R.N., Palsson, B.O., Zhang, H., Betenbaugh, M.J. Proteomic analysis of Chinese hamster ovary cellsJournal of Proteome Research. 11:5265-76 (2012).


cho graphic

14. Xu, X.*, Nagarajan, H.*, Lewis, N.E.*, Pan, S.*,et al. The Genomic Sequence of the Chinese Hamster Ovary (CHO) K1 cell lineNature Biotechnology, 29:735-41 (2011). * equal contribution


4. Bar-Even, A., Noor, E., Lewis, N.E., Milo, R. Design and analysis of synthetic carbon fixation pathwaysProc. Natl. Acad. Sci. USA., 107:8889-8894 (2010).


coli graphic


Patents and applications

11. Hefzi, H., Lewis, N.E., Karottki, K.J.L.C., Kildegaard, H. Asparaginase Based Selection System for Heterologous Protein Expression in Mammalian Cells. Patent pending.

10. Fuerst, T.R., Toth, E.A., Lewis, N.E., Voldborg, B.G., Chiang, W.T. Compositions and methods for producing glyco-modified viral antigens. Patent PCT/US2022/014338.

8. Martino, C., Kellman, B., Lewis, N.E., Knight, R., Sandoval, D., Esko, J., Mandel-Clausen, T. Application of microbial glycosidase as a therapeutic or anti-viral. Patent PCT/US2021/046144.

7. Lewis, N.E., Liang, C., Chiang, W.T. Methods of Designing Carbohydrates. Patent PCT/EP2020/082713.

6. Lewis, N.E., Spahn, P., Li, S., Hefzi, H., Shamie, I. Methods to Stabilize Mammalian Cells. Patent PCT/EP2020/078435.

5. Lewis, N.E., Chiang, W.T., Puig, M., Zhang, Y., Rosenberg, A.  Method to Suppress Viral Infection of Mammalian Cells. Patent PCT/US2019/048361.

3. Hefzi, H., Lewis, N.E. Mammalian cells devoid of lactate dehydrogenase activity Patent US11242510B2.

2. Spahn, P., Lewis, N.E. Systems and methods for predicting glycosylation on proteins. WO Patent 2016187341 A1.

1. Herrgard, M. J., Pedersen, L.E., Lewis, N.E.Bruntse, A.B. Methods for modeling Chinese hamster ovary (CHO) cell metabolism. WO Patent WO2015010088-A1.