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
Masson H.*, Tat J.*, Di Giusto P.*, Antonakoudis A., Shamie I., Baghdassarian H., Samoudi M., Robinson C. M., Kuo C.C., Koga N., Singh S., Gezalyan A., Li Z., Movsessian A., Richelle A., Lewis N.E.‡ A reconstruction of the mammalian secretory pathway identifies mechanisms regulating antibody production, bioRxiv (2024). doi: 10.1101/2024.11.14.623668
Kellman B., Sandoval D., Zaytseva O., Brock K., Baboo S., Nachmanson D., Irvine E., Armingol E., Mih N., Zhang Y., Jeffris M., Bartels P., Nguyen T., Tam A., Gasman S., Ilan S., Shamie I., Diedrich J., Wang X., van Woudenbergh E., Altman M., Aylward A., Bao B., Castro A., Sorrentino J., Chiang A., Campbell M., Bartsch Y., Aguilar-Calvo P., Sigurdson C., Alter G., Lauc G., Yates J. III, Marks D., Lisacek F., Lewis N.E. Protein structure, a genetic encoding for glycosylation, bioRxiv (2024).
Kellman B., Mariethoz J., Zhang Y., Shaul S., Jeffris M., Sandoval D., Jeffris M., Armingol E., Bao B., Lisacek F., Bojar D., Lewis N.E. Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network, bioRxiv (2024).
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).
2024
177. Scapin G., Çagdas E., Grav L.M., Lewis N.E., Goletz S., Hafkenscheid L. Implications of glycosylation for the development of selected cytokines and their derivatives for medical use. Biotechnology Advances, in press (2024).
176. 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. JCI Insight, in press (2024).
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
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
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.
151. Zhang Y., Krishnan S., Bao B., Chiang A.W.T., Sorrentino J.T., Schinn S.M., Kellman B.P.‡, Lewis N.E.‡ Preparing glycomics data for robust statistical analysis with GlyCompareCT, STAR Protocols, 4 (2), 102162 (2023). doi: 10.1016/j.xpro.2023.102162
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
2022
144. Sasmal A., Khan N., Khedri Z., Kellman B.P., Srivastava S., Verhagen A., Yu H., Bruntse A.B., Diaz S., Varki N., Beddoe T., Paton A.W., Paton J.C., Chen X., Lewis N.E., Varki A. Simple and practical sialoglycan encoding system reveals vast diversity in nature and identifies a universal sialoglycan-recognizing probe derived from AB5 toxin B subunits. Glycobiology, 32, 1101-1115 (2022). doi: 10.1093/glycob/cwac057
142. Sorrentino JT, Golden GJ, Morris C, Painter C, Nizet V, Campos AR, Smith JW, Karlsson C, Malmström J, Lewis NE, Esko JD, Toledo AG. Vascular proteome responses precede organ dysfunction in a murine model of Staphylococcus aureus bacteremia, mSystems, 7(4) (2022). doi: 10.1128/msystems.00395-22
141. Li H., Chiang A.W.T.‡, Lewis N.E.‡. Artificial Intelligence in the analysis of glycosylation data. Biotechnology Advances, 60, 108008 (2022). doi: 10.1016/j.biotechadv.2022.108008
137. Kellman B.P.*, Richelle A.*, Yang J.Y.E., Chapla D.G., Chiang A.W.T., Najera J., Liang C, Fürst A, Bao B., Koga N., Mohammad M.A., Bruntse A.B., Haymond M.W., Moremen K.W., Bode L., Lewis N.E.. Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration. Nature Communications, 13, 2455 (2022). doi: 10.1038/s41467-022-29867-4
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
134. Stanley P., Moremen K.W., Lewis N.E., Taniguchi N., Aebi M. N-Glycans, in Essentials of Glycobiology, 4th Edition (2022), Cold Spring Harbor Laboratory Press.
2021
129. 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. Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis, mBio,12(5):e0118121 (2021). PMCID: PMC8546592
127. Bao, B.*, Kellman, B.P.*, Chiang, A.W.T., Zhang, Y., Sorrentino, J.T., York, A.K., Mohammad, M.A., Haymond, M.W., Bode, L., Lewis, N.E. Correcting for sparsity and interdependence in glycomic data by accounting for glycan biosynthesis. Nature Communications, 12, 4988 (2021). doi: 10.1038/s41467-021-25183-5, PMCID: PMC8371009
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
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
110. Toledo, A.G., Sorrentino, J., Sandoval, D., Malmström, J., Lewis, N.E., Esko, J.D. A Systems View of the Heparan Sulfate Interactome. Journal of Histochemistry & Cytochemistry, 69(2):105–119 (2021). doi: 10.1369/0022155420988661, PMCID: PMC7841697
104. Kellman, B.P., Lewis, N.E. Big-data glycomics: tools to connect glycan biosynthesis to extracellular communication. Trends in Biochemical Sciences, 46:P284-300, (2021). doi: 10.1016/j.tibs.2020.10.004, PMCID: PMC7954846
2020
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
99. Kellman, B.P.*, Zhang, Y.*, Logomasini, E., Meinhardt, E., Godinez-Macias, K.P., Chiang, A.W.T., Sorrentino, J., Liang, A., Bao, B., Zhou, Y., Akase, S., Sogabe, I, Kuoka, T., Winzeler, E.A., Wilson, I.B.H., Campbell, M.P., Neelamegham, S., Krambeck, F.,J., Aoki-Kinoshita, K.F., Lewis, N.E. A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). Beilstein Journal of Organic Chemistry, 16, 2645–2662 (2020). doi: 10.3762/bjoc.16.215, PMCID: PMC7607430
98. 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. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. Cell Host & Microbe. 28, P586-601.E6 (2020). doi:10.1016/j.chom.2020.08.004, PMCID: PMC7443692
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 purity. Nature 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
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, Phys.org, Genetic Engineering and Biotechnology News, Biopharma Reporter
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
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
2019
83. Toledo, A.G., Golden, G., Campos, A.R., Cuello, H., Sorrentino, J., Lewis, N.E., Varki, N., Nizet, V., Smith, J.W., Esko, J.D. Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis. Nature Communications, 10:4656 (2019). doi: 10.1038/s41467-019-12672-x
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 infection. Nature Communications, 10:488 (2019). doi: 10.1038/s41467-019-08349-0
68. Landig, C.S., Hazel, A., Kellman, B.P., Fong, J.J., Schwarz, F., Agarwal, S., Varki, N., Massari, P., Lewis, N.E., Ram, S., Varki, A. The exclusively human-pathogen Neisseria gonorrhoeae engages 4 immunoregulatory siglecs in a species-specific manner. Evolutionary Applications, 12:337-349 (2019). doi: 10.1111/eva.12744
2018
2017
53. Autran, C.A.*, Kellman, B. *, Asztalos, E., Blood, A., Hamilton Spense, E.C., Patel, A.L., Kim, J.H., Hou, J., Lewis, N.E., Bode, L. Human milk oligosaccharide composition predicts risk of necrotizing enterocolitis in preterm infants. Gut, 67:312819. DOI: 10.1136/gutjnl-2016-312819, Highlighted in Nature Reviews Gastroenterology and Chemical and Engineering News
51. Spahn, P.N., Hansen, A.H., Kol, S., Voldborg, B.G., Lewis, N.E.‡ Predictive glycoengineering of biosimilars using a Markov chain glycosylation model. Biotechnology Journal,12:1600489 (2017). DOI:10.1002/biot.201600489
2016
44. Chiang, A.W.T., Li, S., Spahn, P.N., Richelle, A., Kuo, C.C., Samoudi, M., Lewis, N.E. Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology. Current Opinion in Structural Biology, 10, 104–111 (2016). DOI: 10.1016/j.sbi.2016.08.008
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 glycoengineering. Metabolic Engineering, 33: 52–66 (2016). DOI:10.1016/j.ymben.2015.10.007
2015
2014
29. Spahn, P., Lewis, N.E.‡ Systems glycomics for glycoengineering. Current Opinion in Biotechnology, 30:218–224 (2014). DOI: 10.1016/j.copbio.2014.08.004
2013
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 genome. Nature Biotechnology. 31:759-65 (2013). doi: 10.1038/nbt.2624. * equal contribution
2012
2011
14. Xu, X.*, Nagarajan, H.*, Lewis, N.E.*, Pan, S.*,et al. The Genomic Sequence of the Chinese Hamster Ovary (CHO) K1 cell line. Nature Biotechnology, 29:735-41 (2011). * equal contribution
2010
2009
2004
Patents and applications
13. Kellman, BP, Lewis, NE, Sandoval, D, Nachmenson, D, Chiang, AWT. Glycosylation engineering. Patent pending – provisional.
12. Lewis, N.E., Chiang, W.T., Kellman, B.P., Bao, B., Schinn, M.S. Clinical diagnostics using glycans. Patent WO2023034383A3.
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.
9. Lewis, N.E., Chiang, W.T., Liang, C., Sorrentino, J.T. Method of Measuring Complex Carbohydrates. Patent PCT/US2021/044139.
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.
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.
