Publications

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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

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).

Armingol E., Larsen R.O., Cequeira M, Baghdassarian H., Lewis N.E. Unraveling the coordinated dynamics of protein- and metabolite-mediated cell-cell communication. bioRxiv (2022)

Pessentheiner A.R., Spann N.J., Autran C.A., Ramms B., Chiang A.W.T., Grunddal K.V., Wang Y., Quach A., Booshehri L.M., Hammond A., Tognaccini C., Latasiewicz J., Witztum J.L., Hoffman H.M., Lewis N.E., Glass C.K., Bode L., Gordts P.L.S.M. The Human Milk Oligosaccharide 3-Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice. bioRxiv, (2021). doi: 10.1101/2021.03.19.433472

2024

172. 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, accepted (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

2023

161. Toledo A.G., Bratanis E., Velásquez E., Chowdhury S., Sorrentino J.T., Karlsson C., Lewis N.E., Esko J.D., Collin M., Shannon O., Malmström J. Pathogen-driven degradation of endogenous and therapeutic antibodies in vivo during streptococcal infections. Nature Communications, 14(1):6693 (2023). doi:10.1038/s41467-023-42572-0

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

156. Ghaddar A., Armingol E., Huynh C., Gevirtzman L., Lewis N.E., Waterston R., O’Rourke E. Whole-body gene expression atlas of an adult metazoan, Science Advances, 9:eadg0506. (2023).

154. Azadiana S., Doustmohammadi A., Naseri M., Khodarahmi M., Arab S.S., Yazdanifar M., Zahiri J.*, Lewis N.E.* Reconstructing the Cell-Cell Interaction Network Among Mouse Immune Cells. Biotechnology & Bioengineering, 120(9), 2756-2764 (2023). doi: 10.1002/bit.28431

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

2022

146. Armingol E., Ghaddar A., Joshi C.J., Baghdassarian H.M., Shamie I., Chan J., Her H.L., Berhanu S., Dar A., Rodriguez-Armstrong F., Yang O., O’Rourke E.J.‡, Lewis N.E.‡ Inferring the spatial code of cell-cell interactions across a whole animal body. PLoS Computational Biology, 18(11): e1010715 (2022). DOI: 10.1371/journal.pcbi.1010715 (see https://lewislab.ucsd.edu/cell2cell/ for cell2cell code)

138. Armingol E.*, Baghdassarian H.*, Martino C., Perez-Lopez A., Aamodt C., Knight R., Lewis N.E. Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nature Communications, 13, 3665 (2022). doi: 10.1038/s41467-022-31369-2 , Nature Portfolio Bioengineering (see https://lewislab.ucsd.edu/cell2cell/ for more info)

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

2021

128. Zhu, Y.P., Shamie, I., Lee, J.C., Nowell, C.J., Peng, W., Angulo, S., Le, L.N.N., Liu, Y., Miao, H., Xiong, H., Pena, C.J., Moreno, E., Griffis, E., Labou, S.G., Franco, A., Broderick, L., Hoffman, H.M. Shimizu, C. Lewis, N.E. Kanegaye, J.T., Tremoulet, A.H., Burns, J.C., Croker, B.A. Immune response to intravenous immunoglobulin in patients with Kawasaki disease and MIS-C. Journal of Clinical Investigation, 131(20):e147076 (2021). PMCID: PMC8516453

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

121. Kuo, C.C., Chiang, A.W.T., Baghdassarian H.M., Lewis, N.E. Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation. Cell Systems, 12: P873-884.E4, (2021). doi: 10.1016/j.cels.2021.06.001 bioRxiv doi: 10.1101/2020.08.10.243634, PMCID: PMC8505362. Highlighted by ScienceNews.dk

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

107. Armingol, E.*, Officer, A.*, Harismendy, O.‡, Lewis, N.E.Deciphering cell-cell interactions and communication from gene expression. Nature Reviews Genetics, 22:71–88 (2021). doi: 10.1038/s41576-020-00292-x

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

2020

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, Phys.org, Genetic Engineering and Biotechnology News, ScienceNews.dk

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

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: ScienceNews.dk

2019

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

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

69. LaMonte, G., Orjuela-Sanchez, P., Wang, L., Li, S., Swann, J., Cowell, A., Zou, B.Y., Abdel-Haleem, A.M., Villa-Galarce, Z., Moreno, M., Tong-Rios, C., Vinetz, J., Lewis, N.E., Winzeler, E.A. Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infectionNature Communications, 10:488 (2019). doi: 10.1038/s41467-019-08349-0

2018

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

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

2017

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

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

2016

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

2015

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

2014

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2004

Patents and applications

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.

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

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