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

146. 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 sepsis, bioRxiv (2021). doi: 10.1101/2021.12.07.471579

140. 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. Sialoglycan microarray encoding reveals differential sialoglycan binding of phylogenetically-related bacterial AB5 toxin B subunits. bioRxiv (2021). doi: 10.1101/2021.05.28.446191

139. 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

136. Kellman B.P., Richelle A., Yang J.Y.E., Chapla D.G., Chiang A.W.T., Najera J., 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. bioRxiv, (2020). DOI: 10.1101/2020.09.02.278663

135. 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

2022

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, in press (2022). DOI: 10.1016/j.ymben.2022.01.002

132. 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, in press.

2021

127. 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

125. 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 biosynthesisNature Communications, 12, 4988 (2021). DOI: 10.1038/s41467-021-25183-5, PMCID: PMC8371009

121. Shamie I.*, Duttke S.H.*, la Cour Karottki K.J., 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

115. 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

109. 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

103. 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

100. 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

99. 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

97. 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

94. 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

90. 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

87. la Cour Karottki, K.J., 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

84. 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

70. 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

69. 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 mannerEvolutionary 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 infantsGut, 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 modelBiotechnology 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.EModulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiologyCurrent 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 glycoengineeringMetabolic Engineering,  33: 52–66 (2016). DOI:10.1016/j.ymben.2015.10.007

2015

2014

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

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 genomeNature Biotechnology. 31:759-65 (2013). doi: 10.1038/nbt.2624. * equal contribution

2012

2011

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

2010

2009

coli graphic

2004

Patents and applications

12. Lewis, N.E., Chiang, W.T., Kellman, B.P., Bao, B., Schinn, M.S., Clinical diagnostics using glycans. Patent pending – provisional.

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 pending – provisional.

9. Lewis, N.E., Chiang, W.T., Liang, C., Sorrentino, J.T. Method of Measuring Complex Carbohydrates at the Nano-Scale. Patent PCT .

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.

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 WO Patent WO2017192437A1.

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.