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

145. Armingol E.*, Baghdassarian H.*, Martino C., Perez-Lopez A., Knight R., Lewis N.E. Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. bioRxiv (2021). doi: 10.1101/2021.09.20.461129

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

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

2021

128. Manresa M.C., Wu A., Nhu Q., Chiang A.W.T., Okamoto K., Miki H., Kurten R., Pham E., Duong L.D., Lewis N.E., Akuthota P., Croft M. Aceves S.S. LIGHT controls distinct homeostatic and inflammatory gene expression profiles in esophageal fibroblasts via differential HVEM and LTβR-mediated mechanisms. Mucosal Immunology, accepted (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

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

110. Askarian, F., Uchiyama, S.*, Masson, H.*, Bunæs, A.C., Golten, O., Mekasha, S., Røhr, Å.K., Kommedal, E., Ludvigsen, J.A., Sørensen, H.V., Arntzen, M.Ø., Schmidt, B., van Sorge, N.M., Eijsink, V.G.H, Krengel, U., Mollnes, T.E., Lewis, N.E., Nizet, V., Vaaje-Kolstad, G. The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection. Nature Communications, 12: 1230 (2021). DOI: 10.1038/s41467-021-21473-0, PMCID: PMC7902821

108. Hsieh LY, Chiang AWT, Duong LD, Kuo CC, Dong S, Dohil R, Kurten R, Lewis NE, Aceves SS. A Unique Esophageal Extracellular Matrix Proteome Alters Normal Fibroblast Function in Severe Eosinophilic Esophagitis. Journal of Allergy and Clinical Immunology, in press (2021). DOI: 10.1016/j.jaci.2021.01.023, PMCID: PMC8342625

106. 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. Chiang AWT, Duong LD, Shoda T, Nhu QM, Ruffner M, Hara T, Aaron B, Joplin E, Manresa M, Abonia JP, Dellon E, Hirano I, Gonsalves N, Gupta S, Furuta G, Rothenberg ME, Lewis NE, Muir AB, Aceves SS, CEGIR Investigator Group. Type 2 Immunity and Age Modify Gene Expression of COVID19 Receptors in Eosinophilic Gastrointestinal Disorders. J Pediatr Gastroenterol Nutr, 72:718-722 (2021). DOI: 10.1097/MPG.0000000000003032.

2020

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

98. Manresa MC, Chiang AWT, Kurten RC, Dohil R, Brickner H, Dohil L, Herro R, Akuthota P, Lewis NE, Croft M, Aceves SS. Increased Production of LIGHT by T Cells in Eosinophilic Esophagitis Promotes Differentiation of Esophageal Fibroblasts Toward an Inflammatory Phenotype. Gastroenterology. S0016-5085(20)34997-0 (2020). DOI: 10.1053/j.gastro.2020.07.035. PMCID: PMC7726704

88. Speir, M., Nowell, C.J., Chen, A.A., O’Donnell, J.A., Shamie, I., Lakin, P.R., D’Cruz, A.A., Braun, R.O., Babon, J.J., Lewis, R.S., Bliss-Moreau, M., Shlomovitz, I., Wang, S., Cengia, L.H., Stoica, A.I., Hakem, R., Kelliher, M.A., O’Reilly, L.A., Patsiouras, H., Lawlor, K.E., Weller, E., Lewis. N.E., Roberts, A.W., Gerlic, M., Croker, B.A. PTPN6 inhibits caspase-8- and RIPK3/MLKL-dependent inflammation. Nature Immunology, 21:54–64 (2020). DOI:10.1038/s41590-019-0550-7

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

79. 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

73. 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).

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

58.  Abdel-Haleem, A.M., Hefzi, H., Mineta, K., Gao, X., Gojobori, T., Palsson, B.O., Lewis, N.E.Jamshidi, N. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targetingPLoS Computational Biology, 14(1): e1005895 (2018). DOI: 10.1371/journal.pcbi.1005895

2017

55. Abdel-Haleem, A.M., Lewis, N.E., Jamshidi, N., Mineta, K., Gao, X., Gojobori, T. The emerging facets of noncancerous Warburg effectFrontiers in Endocrinology, 8:297 (2017). DOI: 10.3389/fendo.2017.00279

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

2016

2015

2014

2013

2012

2011

2010

7. Bordbar, A., Lewis, N.E., Schellenberger, J., Palsson, B.Ø., Jamshidi, N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructionsMolecular Systems Biology, 6:422 (2010).

2009

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2004

Patents and applications

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.