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

154. 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, bioRxiv (2022).

153. 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)

151. Ha TK, Òdena A, la Cour Karottki KJ, 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. Authorea, (2022).

148. 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

2022

143. 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)

136. 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)

134. 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

133. 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

131. 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

126. 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

121. Xiong, K., la Cour Karottki, K.J., 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

119. 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

117. 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

116. 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

115. 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

105. 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

103. 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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2010

2009

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2004

Patents and applications

10. Fuerst, T.R., Toth, E.A., Lewis, N.E., Voldborg, B.G., Chiang, W.T. Glycoengineered Vaccines and Methods of Making the Same. 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.