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. Bao B.*, Gazestani V.H.*, Xiao Y., Kim R., Chiang A.W.T., Nalabolu S., Pierce K., Robasky K., Lewis N.E.‡, Courchesne, E.‡. A Highly Accurate Ensemble Classifier for the Molecular Diagnosis of ASD at Ages 1 to 4 Years. medRxiv (2021). doi: 10.1101/2021.07.08.21260225

144. Chiang A.W.T., Gazestani V.H., Altieri M.G., Courchesne E., Lewis N.E. Optimal balancing of clinical factors in large scale clinical RNA-Seq studies. bioRxiv (2021). doi: 10.1101/2021.06.30.450639

143. Robasky K., Kim R., Yi H., Xu H., Bao B., Chiang A.W.T., Courchesne E., Lewis N.E. Transfer learning improves outcome predictions for ASD from gene expression in blood. bioRxiv (2021). doi: 10.1101/2021.06.26.449864

142. 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

141. 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

140. Joshi C.J., Ke W., Drangowska-Way A., O’Rourke E.J., Lewis N.E. What are housekeeping genes? bioRxiv, (2021)

139. Armingol E., Ghaddar A., Joshi C.J., Baghdassarian H.M., Shamie I., Chan J., Her H.L., O’Rourke E.J.‡, Lewis N.E.‡ Inferring the spatial code of cell-cell interactions across a whole animal body. bioRxiv, (2020). DOI: 10.1101/2020.11.22.392217 (see https://lewislab.ucsd.edu/cell2cell/ for more info)

138. 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

137. Gazestani, V., Chiang, A.W.T., Courchesne, E.‡, Lewis, N.E. Autism genetics perturb prenatal neurodevelopment through a hierarchy of broadly-expressed and brain-specific genes. bioRxiv (2020). DOI: 10.1101/2020.05.24.112623

136. Choi YM, Choi DH, Lee YQ, Koduru L, Lewis, N E,  Lakshmanan M, Lee, D.Y. Mitigating biomass composition uncertainties in flux balance analysis using ensemble representationsbioRxiv (2022). DOI: 10.1101/652040

2022

135. 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, accepted (2022). bioRxiv doi: 10.1101/2021.09.20.461129 (see https://lewislab.ucsd.edu/cell2cell/ for more info)

134. 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

133. 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

132. 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. 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.

130. 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

129. Xiao Y, Wen TH, Kupis L, Eyler L, Goel D, Vaux K, Lombardo MV, Lewis NE, Pierce K, Courchesne E. Neural responses to affective speech, including motherese, map onto clinical and social eye tracking profiles in ASD toddlers. Nature Human Behavior, 6, 443–454 (2022).

128. Savizi I.S.P., Maghsoudi N., Motamedian E., Lewis N.E., Shojaosadati S.A. Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. Applied Microbiology and Biotechnology, 106, 1113–1126 (2022). DOI:10.1007/s00253-021-11755-4, Authorea preprint

127. 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, 15, 327–337 (2022).

2021

126. 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. 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

124. 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

123. Khaleghi M.K., Savizi I.S.P., Lewis N.E., Shojaosadati S.A. Synergisms of machine learning and constraint-based modeling of metabolism for analysis and optimization of fermentation parameters. Biotechnology Journal, 16:2100212. (2021). doi: 10.22541/au.162083622.21592768/v1

122. Lombardo MV, Eyler L, Pramparo T, Gazestani VH, Hagler Jr. DJ, Chen CH, Dale AM, Seidlitz J, Bethlehem RAI, Bertelsen N, Barnes CC, Lopez L, Campbell K, Lewis NE, Pierce K, Courchesne E. Atypical genomic patterning of the cerebral cortex in autism with poor early language outcome, Science Advances, 7: eabh1663 (2021). DOI:10.1126/sciadv.abh1663

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

120. 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

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

118. Richelle, A., Kellman, B.P., Wenzel, A.T., Chiang, A.W.T., Reagan, T., Gutierrez, J.M., Joshi, C., Li, S., Liu, J.K., Masson, H., Lee, J., Li, Z., Heirendt, L., Trefois, C., Juarez, E.F., Bath, T., Borland, D., Mesirov, J.P., Robasky, K., Lewis, N.E. Model-based assessment of mammalian cells metabolic functionalities from omics data. Cell Reports Methods, 1:100040 (2021). DOI: 10.1016/j.crmeth.2021.100040

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

114. 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

113. la Cour Karottki, K.J., Hefzi, H., Li, S., Pedersen, L.E., Spahn, P., Ruckerbauer, D., Bort, J.H., Thomas, A., Lee, J.S., Borth, N., Lee, G.M., Kildegaard, H.F.‡, Lewis, N.E.A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metabolic Engineering, 66:114-122 (2021). DOI: 10.1016/j.ymben.2021.03.017. bioRxiv DOI: 10.1101/2020.05.07.081604, PMCID: PMC8193919

112. Schinn S-M, Morrison C, Wei W, Zhang L, Lewis NE. Systematic evaluation of parameterization for genome-scale metabolic models of cultured mammalian cells. Metabolic Engineering, 66:21-30 (2021). bioRxiv DOI:10.1101/2020.06.24.169938.

111. Granados, J.C., Richelle, A., Gutierrez, J.M., Zhang, P., Bhatnagar, V., Lewis, N.E., Nigam, S.K. Coordinate regulation of systemic and kidney tryptophan metabolism by the drug transporters OAT1 and OAT3. Journal of Biological Chemistry. 296:100575 (2021). DOI: 10.1016/j.jbc.2021.100575, PMCID: PMC8102410

110. Schinn S.M., Morrison C., Wei W., Zhang L., Lewis N.E. A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures. Biotechnology & Bioengineering, 118:2118-2123 (2021). DOI: 10.1002/bit.27714 bioRxiv DOI: 10.1101/2020.09.02.279687

109. 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. 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

107. 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. Kellman, B.P.*, Baghdassarian, H.M.*,Pramparo, T., Shamie, I., Gazestani, V.H., Begzati, A., Li, S., Nalabolu, S., Murray, S., Lopez, L., Pierce, K., Courchesne, E., Lewis, N.E. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics, 22, 69 (2021). DOI: 10.1186/s12864-021-07381-z, PMCID: PMC7818915

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

104. 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.

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

102. 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

101. Fouladiha, H., Marashi, S.A., Li, S., Li, Z., Masson, H.O., Vaziri, B., Lewis, N.E. Systematically gap-filling the genome-scale model of CHO cells. Biotechnology Letters, 43:73–87 (2021). DOI: 10.1007/s10529-020-03021-w, bioRxiv: 10.1101/2020.01.27.921296

2020

100. Lin, D., Yalamanchili, H., Zhang, X., Lewis, N.E., Alves, C.L., Groot, J., Arnsdorf, J., Bjørn, S.P., Wulff, T., Voldborg, B.G., Zhou, Y., Zhang, B. CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell linesPLoS Computational Biology, 16: e1008498 (2020). DOI: 10.1371/journal.pcbi.1008498

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

97. 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

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

95. Saba*, J. A. , Ke*, W. , Yao, C. , Drangowska-Way, A. , Joshi, C., Mony, V.K., Hilzendeger, M., Liu, X., Liu, J., Benjamin, S., Locasale, J., Patti, G., Lewis, N.E.‡, O’Rourke, E.J.‡ Dietary serine enhances chemotherapeutic toxicity in C. elegans through promoting thymidine deficiency in the microbiota. Nature Communications, 11:2587 (2020). DOI: 10.1038/s41467-020-16220-w News coverage: UVAToday

94. Szeliova, D., Ruckerbauer, D.E., Galleguillos, S.N., Petersen, L.B., Natter, K., Hanscho, M., Troyer, C. Causon, T., Schoeny, H., Christensen, H.B., Lee, D.Y., Lewis, N.E., Koellensperger, G., Hann, S., Nielsen, L., Borth, N., Zanghellini, J. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metabolic Engineering, 61:288-300 (2020). DOI: 10.1016/j.ymben.2020.06.002

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

92. Joshi, C., Schinn, S., Richelle, A.Shamie, I., O’Rourke, E., Lewis, N.E. StanDep: capturing transcriptomic variability improves context-specific metabolic modelsPLoS Computational Biology, 16(5): e1007764. (2020). DOI: 10.1371/journal.pcbi.1007764

91. Courchesne, E.*, Gazestani, V.H.*, Lewis, N.E.* Prenatal origins of ASD: The when, what and how of ASD development. Trends in Neurosciences, 43:326 (2020).

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

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

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

87. 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

86. 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

85.  Lieven, C., Beber, M.E.,  Olivier, B.G., Bergmann, F.T., Babaei, P., Bartell, J.A., Blank,  L.M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert,  B.E., Edirisinghe, J.N., Fleming, R.M.T., Garcia-Jimenez, B., van Helvoirt, W., Henry, C., Hermjakob, H., Herrgard, M.J., Kim, H.U., King, Z., Koehorst, J.J., Klamt, S., Klipp, E., Lakshmanan, M., Le Novere, N., Lee, D.Y., Lee, S.Y., Lee, S., Lewis, N.E., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G.L., Monk, J., Nielsen, J., Nielsen, L.K., Nogales, J., Nookaew, I., Resendis, O., Palsson, B.O., Papin, J.A.,  Patil, K.R., Price, N.D., Richelle, A., Rocha, I., Schaap, P., Sheriff, R.S.M., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaca, P., Vik, J.O., Wodke, J.A., Xavier, J.C., Yuan, Q., Zakhartsev, M., Zhang, C. Memote: A community driven effort towards a standardized genome-scale metabolic model test suiteNature Biotechnology, 38:272–276 (2020). DOI: 10.1038/s41587-020-0446-y

2019

84. Gazestani, V.H., Pramparo, T., Nalabolu, S., Kellman, B.P., Murray, S., Lopez, L., Pierce, K., Courchesne, E., Lewis, N.E. A perturbed gene network containing PI3K/AKT, RAS/ERK, WNT/β-catenin pathways in leukocytes is linked to ASD genetics and symptom severityNature Neuroscience, 22, 1624–1634 (2019). DOI: 10.1038/s41593-019-0489-x, bioRxiv: 10.1101/435917, News coverage: Spectrum News, Genomeweb, Medical News, Technology Networks, Neuroscience News

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

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

81. Li, S.*, Richelle, A.*, Lewis, N.E. Enhancing product and bioprocess attributes using genome-scale models of CHO metabolismCell Culture Engineering: Recombinant Protein Production , p.73 (2019). ISBN: 978-3-527-34334-8

80. Cyrielle, C., Joshi, C., Lewis, N.E., Laetitia, M., Andersen, M.R.Adaption of Generic Metabolic Models to Specific Cell Lines for Improved Modeling of Biopharmaceutical Production and Prediction of ProcessesCell Culture Engineering: Recombinant Protein Production , p.127 (2019). ISBN: 978-3-527-34334-8

79. Richelle, A.Joshi, C.Lewis, N.E. Assessing key decisions for transcriptomic data integration in biochemical networksPLoS Computational Biology, 15(7): e1007185 (2019). DOI: 10.1371/journal.pcbi.1007185

78. 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

77. Li, S., Cha, S.W., Heffner, K., Baycin-Hizal, D., Bowen, M., Chaerkady, R., Cole, R., Tejwani, V., Kaushik, P., Henry, M., Meleady, P., Sharfstein, S., Betenbaugh, M.J., Bafna, V., Lewis, N.E. Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elementsJournal of Proteome Research, 18:2433-2445 (2019). bioRxiv: 10.1101/468181 , Download genome and annotation here

76. Gazestani, V.H., Lewis, N.E. From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems BiologyCurrent Opinion in Systems Biology, 15:68-73 (2019). DOI: 10.1016/j.coisb.2019.04.001

75. Xiong, K.*, Marquart, K.F.*, la Cour Karottki, K.J.*, Li, S.Shamie, I., Lee, J.S., Signe Gerling, S., Yeo, N.C., Chavez, A., Lee, G.M., Lewis, N.E.‡, Kildegaard, H.F.Reduced Apoptosis in Chinese Hamster Ovary Cells via Optimized CRISPR InterferenceBiotechnology & Bioengineering, 116:1813-1819 (2019). DOI: 10.1002/bit.26969

74. Richelle, A.Chiang, A.W.T.Kuo, C.C.Lewis, N.E. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functionsPLoS Computational Biology, 15: e1006867 (2019). DOI: 10.1371/journal.pcbi.1006867

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

72. 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).

71. Lee, J.S., Kildegaard, H.F., Lewis, N.E., Lee, G.M. Deciphering Clonal Variation in Recombinant Mammalian Cell LinesTrends in Biotechnologyin press (2019). DOI: 10.1016/j.tibtech.2019.02.007

70. Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S.N., Richelle, A., Heinken, A., Haraldsdottir, H.S., Keating, S.M., Vlasov, V., Wachowiak, J., Magnusdottir, S., Ng, C.Y., Preciat, G., Zagare, A., Chan, S.H.J., Aurich, M.K., Clancy, C.M., Modamio, J., Sauls, J.T., Noronha, A., Bordbar, A., Cousins, B., El Assal, D.C., Ghaderi, S., Ahookhosh, M., Ben Guebila, M., Apaolaza, I., Kostromins, A., Le, H.M., Ma, D., Sun, Y., Valcarcel, L.V., Wang, L., Yurkovich, J.T., Vuong, P.T., El Assal, L.P., Hinton, S., Bryant, W.A., Aragon Artacho, F.J., Planes, F.J., Stalidzans, E., Maass, A.,  Santosh Vempala, Hucka, M., Saunders, M.A., Maranas, C.D., Lewis, N.E., Sauter, T., Palsson, B.Ø., Thiele, I., Fleming, R.M.T. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0Nature Protocols, 14:639-702 (2019). DOI: 10.1038/s41596-018-0098-2 ArXiv: 1710.04038

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

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 mannerEvolutionary Applications, 12:337-349 (2019). DOI: 10.1111/eva.12744

2018

67. Lombardo, M.V., Pramparo, T., Gazestani, V., Warrier, V.,  Bethlehem, R.AI., Barnes, C.C., Lopez, L., Lewis, N.E., Eyler, L., Pierce, K., Courchesne, E. Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypesNature Neuroscience, 21, 1680–1688 (2018). DOI: 10.1038/s41593-018-0281-3 News Coverage: ScienceNews.dk

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

65. Brunk, E.*, Chang, R.L., Xia, J., Hefzi, H., Yurkovich, J., Kim, D., Buckmiller, E., Wang, H.H., Yang, C., Palsson, B.Ø., Church, G.M.Lewis, N.E.*‡ Characterizing post-translational modifications in prokaryotic metabolism using a multi-scale workflowProc. Nat. Acad. Sci. USA, 115 (43): 11096-11101 (2018). bioRxiv DOI: 10.1101/180646

64. Grav, L.M., Sergeeva, D., Lee, J.S., Marin de Mas, I., Lewis, N.E., Andersen, M.R., Nielsen, L.K., Lee, G.M., Kildegaard, H.F. Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generationACS Synthetic Biology, 7 (9):2148–2159. DOI:10.1021/acssynbio.8b00140

63. Yeo, N.C., Chavez, A., Lance-Byrne, A., Chan, Y., Menn, D., Milanova, D., Kuo, C.C., Guo, X., Sharma, S., Tung, A., Cecchi, R.J., Tuttle, M., Pradhan, S., Lim, E.T., Davidsohn, N., Ebrahimkhani, M.R., Collins, J.J., Lewis, N.E., Kiani, S., Church, G.M.  An enhanced CRISPR repressor for targeted mammalian gene regulationNature Methods, 15:611-616 (2018) . DOI:10.1038/s41592-018-0048-5

62. Witting, M.A., Hastings, J., Rodriguez, N., Joshi, C.J., Hattwell, J.P., Ebert, P.R., van Weeghel, M., Wakelam, M., Houtkooper, R., Mains, A., Le Novère, N., Sadykoff, S., Schroeder, F.,Lewis, N.E., Schirra, H.J., Kaleta, C., Casanueva, O. Modeling meets Metabolomics – The WormJam Consensus Model as basis for Metabolic Studies in the model organism Caenorhabditis elegansFrontiers in Molecular Biosciences, 5:96 (2018) . DOI:10.3389/fmolb.2018.00096

61. Rupp, O.*, MacDonald, M.L.*, Li, S.*, Dhiman, H.*, Polson, S., Griep, S., Heffner, K., Hernandez, I., Brinkrolf, K., Jadhav, V., Samoudi, M., Hou, H., Kingham, B., Goesmann, A., Betenbaugh, M.J. ‡, Lewis, N.E.‡, Borth, N.‡, Lee, K.‡ A reference genome of the Chinese hamster based on a hybrid assembly strategyBiotechnology & Bioengineering, 115:2087-2100 (2018). DOI: 10.1002/bit.26722

60. Courchesne, E., Pramparo, T., Gazestani, V.H., Lombardo, M.V., Pierce, K., Lewis, N.E. (2018) The ASD living biology: From cell proliferation to clinical phenotypeMolecular Psychiatry, 24:88-107. DOI: 10.1038/s41380-018-0056-y 

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

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

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

56.  Spahn, P.N., Bath, T., Weiss, R.J., Kim, J., Esko, J.D., Lewis, N.E.‡, Harismendy, O.‡. PinAPL-Py: a web-service for the analysis of CRISPR-Cas9 ScreensScientific Reports, 15854 (2017). DOI: 10.1038/s41598-017-16193-9

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

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

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

52. Opdam, S.*, Richelle, A.*, Kellman, B., Li, S., Zielinski, D.C., Lewis, N.E.‡ A systematic evaluation of methods for tailoring genome-scale metabolic modelsCell Systems, 4:1-12 (2017). DOI:10.1016/j.cels.2017.01.010

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

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

49. Shen, J.P., Zhao, D., Sasik, R., Luebeck, J., Birmingham, A., Bojorquez-Gomez, A., Licon, K., Klepper, K., Pekin, D., Beckett, A.N., Sanchez, K.S., Thomas, A.Kuo, C.C., Du, D., Roguev, A., Lewis, N.E., Chang, A.N., Kreisberg, J.F., Krogan, N., Qi, L., Ideker, T., Mali, P.M.  Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactionsNature Methods,  14:573-576 (2017). DOI:10.1038/nmeth.4225

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

47. Lombardo, M.V., Courchesne, E., Lewis, N.E., Pramparo, T. Hierarchical cortical transcriptome disorganization in autismMolecular Autism, 8:29 (2017). DOI: 10.1186/s13229-017-0147-7

46. Hastings, J., et al. WormJam: Consensus C. elegans metabolic reconstruction and metabolomics communityWorm, 6:e1373939 (2017). DOI:10.1080/21624054.2017.1373939

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

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

43. Swainston, N., Smallbone, K., Hefzi, H., Dobson, P.D., Brewer, J., Hanscho, M., Zielinski, D.C., Ang, K.S., Gardiner, N.J., Gutierrez, J.M., Kyriakopoulos, S., Lakshmanan, M., Li, S., Liu, J.K., Martínez, V.S., Orellana, C.A., Quek, L.E., Thomas, A., Zanghellini, J., Borth, N., Lee, D.Y., Nielsen, L.K., Kell, D.B., Lewis, N.E., Mendes, P.  Recon 2.2: from reconstruction to model of human metabolismMetabolomics, 12:109 (2016). DOI: 10.1007/s11306-016-1051-4

42. Huang, S., Chong, N., Lewis, N.E., Jia, W., Xie, G., Garmire, L.X. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosisGenome Medicine, 8(1):1 (2016). DOI: 10.1186/s13073-016-0289-9

41. Golabgir, A.*, Gutierrez, J.M.*, Hefzi, H., Li, S., Palsson, B.O., Herwig, C.‡, Lewis, N.E.‡ Quantitative feature extraction from the Chinese Hamster Ovary bioprocess bibliome using a novel meta-analysis workflow Biotechnology Advances, 34(5):621–633 (2016). DOI:10.1016/j.biotechadv.2016.02.011 * equal contribution, listed alphabetically The CHO Bibliome website

40. King, Z.A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J., Ebrahim, A., Palsson, B.O., Lewis, N.E.‡ BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models.  Nucleic Acids Research, 44(D1):D515-22 (2016). DOI: 10.1093/nar/gkv1049 BiGG Models website

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

38. Pramparo, T., Campbell, K., Barnes, C.C., Marinero, S., Solso, S., Young, J., Mayo, M., Dale, A., Ahrens-Barbeau, C., Murray, S.S., Lopez, L., Lewis, N.E., Pierce, K., Courchesne, E. Cell Cycle Networks link Gene Expression Dysregulation, Mutation and Brain Maldevelopment in Autistic ToddlersMolecular Systems Biology,  11: 841 (2015). DOI:10.15252/msb.20156108

37. Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Dräger, A., Famili, I., Feist, A.M., Fleming, R.M.T., Fong, S.S., Hatzimanikatis, V., Herrgård, M.J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S.Y., Le Novère, N., Lerman, J.A., Lewis, N.E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L.K., Nogales, J., Noronha, A., Pal, C., Palsson, B.O., Papin, J.A., Patil, K.R., Price, N.D., Reed, J., Saunders, M., Senger, R.S., Sonnenschein, N., Sun, Y., Thiele, I.  Do genome‐scale models need exact solvers or clearer standards?Molecular Systems Biology, 11: 831 (2015). DOI: 10.15252/msb.20156157

36. Kumar, A., Baycin-Hizal, D., Wolozny, D., Pedersen, L.E., Lewis, N.E., Heffner, K., Chaerkady, R., Cole, R.N., Shiloach, J., Zhang, H., Bowen, M.A., Betenbaugh, M.J. Elucidation of the CHO Super-Ome (CHO-SO) by ProteoInfomatics.  Journal of Proteome Research, 14 (11), pp 4687–4703 (2015). DOI: 10.1021/acs.jproteome.5b00588

35. King, Z.A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N.E., Palsson, B.O. Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways.  PLoS Computational Biology, 11:e1004321 (2015). DOI: 10.1371/journal.pcbi.1004321

34. Swann, J., Jamshidi, N., Lewis, N.E., Winzeler, E.A.. Systems analysis of host–parasite interactions. WIREs: Systems Biology and Medicine, 7(6), 381–400 (2015). DOI: 10.1002/wsbm.1311

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

32. Rodriguez, R.*, Thomas, A.*, Watanabe, L., Vazirabad, I.Y., Kofia, V., Gómez, H.F., Mittag, F., Matthes, J.,  Rudolph, J., Wrzodek, F., Netz, E., Diamantikos, A., Eichner, J., Keller, R., Wrzodek, C., Fröhlich, S., Lewis, N.E., Myers, C.J., Le Novère, N., Palsson, B.O., Hucka, M., Dräger,  A. JSBML 1.0: providing a smorgasbord of options to encode systems biology modelsBioinformatics, 31(20):3383-3386 (2015). DOI: 10.1093/bioinformatics/btv341

31. Lee, J.S., Grav, L.M., Lewis, N.E., Kildegaard, H.F. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnology Journal, 10:979–994 (2015). DOI: 10.1002/biot.201500082.

2014

30. Busskamp, V.*, Lewis, N.E.*, Guye, P.*, Ng, A.H.M., Shipman, S.L., Byrne, S.M., Sanjana, N.E., Murn, J., Li, Y., Li, S., Stadler, M., Weiss, R., Church, G.M. Rapid neurogenesis through transcriptional activation in human stem cellsMolecular Systems Biology, 10:760 (2014). DOI: 10.15252/msb.20145508. * equal contribution

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

28. Hefzi, H., Lewis, N.E.‡ From random mutagenesis to systems biology in metabolic engineering of mammalian cellsPharmaceutical Bioprocessing, 2:355-358 (2014). DOI: 10.4155/pbp.14.36

27. Kumar, A., Harrelson, T., Lewis, N.E., Gallagher, E., LeRoith, D., Shiloach, J., Betenbaugh, M.J.Multi-tissue computational modeling analyzes pathophysiology of Type 2 Diabetes in MKR micePLoS One, 9(7): e102319. DOI: 10.1371/journal.pone.0102319

26. Bordbar, A., Nagarajan, H., Lewis, N.E., Schellenberger, J., Latif, H., Federowicz, S., Ebrahim, A., Palsson, B.O. Minimal metabolic pathway structure is consistent with associated biomolecular interactionsMolecular Systems Biology, 10:737 (2014). DOI: 10.15252/msb.20145243

25. Robasky, K.*, Lewis, N.E.‡*, Church, G.M. The Role of Replicates for Error Mitigation in Next-Generation SequencingNature Reviews Genetics. 15:56–62 (2014). DOI: 10.1038/nrg3655  corresponding author, * equal contribution

2013

evo graphic

24. Lewis, N.E.‡, Abdel-Haleem, A.M. The evolution of genome-scale models of cancer metabolismFront. Physiol. 4:237 (2013). DOI: 10.3389/fphys.2013.00237    corresponding author

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

22. Kildegaard, H.F., Baycin-Hizal, D., Lewis, N.E., Betenbaugh, M.J. The Emerging CHO Systems Biology Era: Harnessing the ‘Omics Revolution for BiotechnologyCurrent Opinion in Biotechnology. S0958-1669(13):00021-9 (2013). doi: 10.1016/j.copbio.2013.02.007

21. Hyduke, D.R., Lewis, N.E., Palsson, B.Ø. Analysis of omics data with genome-scale models of metabolismMolecular BioSystems, 9:167 (2013). doi: 10.1039/c2mb25453k

2012

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20. Nam, H.J.*, Lewis, N.E.‡*, Lerman, J.A., Lee, D.H., Chang, R.L., Kim, D., Palsson, B.Ø.‡ Network context and selection in the evolution to enzyme specificityScience. 337:1101-1104 (2012).   corresponding author, * equal contribution

19. Noor, E.‡, Lewis, N.E.‡, Milo, R. A proof for loop-law constraints in stoichiometric metabolic networksBMC Systems Biology. 6:140 (2012). Highly Accessed corresponding author

18. Baycin-Hizal, D., Tabb, D.L., Chaerkady, R., Chen, L., Lewis, N.E., Nagarajan, H., Sarkaria, V., Kumar, A., Wolozny, D., Colao, J., Jacobson, E., Tian, Y., O’Malley, R.N., Krag, S., Cole, R.N., Palsson, B.O., Zhang, H., Betenbaugh, M.J. Proteomic analysis of Chinese hamster ovary cellsJournal of Proteome Research. 11:5265-76 (2012).

17. Hefzi, H., Palsson, B.Ø., Lewis, N.E.‡Reconstruction of genome-scale metabolic networks. In Handbook of Systems Biology. 229 (2013). doi:10.1016/B978-0-12-385944-0.00012-5  corresponding author

16. Lerman, J.A., Hyduke, D.R., Latif, H., Portnoy, V.A., Lewis, N.E., Orth, J.D., Schrimpe-Rutledge, A.C., Smith, R.D., Adkins, J.N., Zengler, K.A., Palsson, B.Ø. In silico method for modelling metabolism and gene product expression at genome scaleNature Communications. 3:929 (2012).

15. Lewis, N.E., Nagarajan, H., Palsson, B.Ø. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methodsNature Reviews Microbiology.10:291-305 (2012). Click here for accompanying website with a catalog of constraint-based methods.

2011

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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

13. Schellenberger, J., Que, R., Fleming, R.T., Thiele, I., Orth, J., Feist, A.M., Zielinski , D.C., Bordbar, A., Lewis, N.E., Rahmanian, S., Kang, J., Hyduke, D., Palsson, B.Ø. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0Nature Protocols, 6:1290-307 (2011).

12. Nam, H.J.*, Conrad, T.M., Lewis, N.E.*‡The role of cellular objectives and selective pressures in metabolic pathway evolutionCurrent Opinion in Biotechnology, 22:595-600 (2011). * equal contribution corresponding author

11. Conrad, T.M., Lewis, N.E., Palsson, B.Ø. Microbial Laboratory Evolution in the Era of Genome-Scale ScienceMolecular Systems Biology, 7:509 (2011).

10. Schellenberger, J., Lewis, N.E., Palsson, B.Ø. Elimination of thermodynamically infeasible loops in steady state metabolic modelsBiophysical Journal, 100:544-53 (2011).

2010

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9. Lewis, N.E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M.P., Cheng, J.K., Patel, N., Yee, A., Lewis, R.A., Eils, R., König, R., Palsson, B.Ø. Large-scale in silico modeling of metabolic interactions between cell types in the human brainNature Biotechnology, 28:1279–1285 (2010). Paper highlighted by Nature Methods (January 2011).

8. Conrad, T.M., Frazier, M., Joyce, A.R., Cho, B. K., Knight, E. M., Lewis, N.E., Landick, R., Palsson, B.Ø. RNA polymerase mutants found through adaptive evolution re-program Escherichia coli K-12 MG1655 for optimal growth in minimal mediaProc. Nat. Acad. Sci. USA, 107:20500-5 (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).

6. Portnoy, V.A., Scott, D.A., Lewis, N.E., Tarasova, Y., Osterman, A.L., Palsson, B.Ø. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655Appl. Environ. Microbiol., 76:6529-40 (2010).

5. Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez-Ferrer, D., Weitz, K.K., Eils, R., König, R., Smith, R.D., Palsson, B.Ø. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale modelsMolecular Systems Biology, 6:390 (2010).

4. Bar-Even, A., Noor, E., Lewis, N.E., Milo, R. Design and analysis of synthetic carbon fixation pathwaysProc. Natl. Acad. Sci. USA., 107:8889-8894 (2010).

2009

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3. Lewis, N.E., Cho, B.K., Knight, E.M. Palsson, B. Ø. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for contentJ. Bacteriol., 191:3437-44 (2009).

2. Lewis, N.E., Jamshidi, N., Thiele, I. & Palsson, B.Ø. Metabolic systems biology: a constraint-based approach. In Encyclopedia of Complexity and Systems Science 5535 (Springer, New York, 2009). DOI:10.1007/978-3-642-27737-5_329-2

2004

1. Merrell, K., Southwick, K., Graves, S.W., Esplin, M.S., Lewis, N.E., Thulin, C.D. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometryJ. Biomol. Tech., 15:238-48 (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 pending – provisional.

11. Hefzi, H., Lewis, N.E., la Cour Karottki, K.J., Kildegaard, H. Selection System for Heterologous Protein Expression in Mammalian Cells. 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. 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.

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

5. Lewis, N.E., Chiang, W.T., Puig, M., Zhang, Y., Rosenberg, A.  Method to Suppress Viral Infection of Mammalian Cells. Patent PCT/US2019/048361.

4. Lewis, N.E., Gazestani, V., Pramparo, T., Courchesne, E. Expression-based diagnosis, prognosis, and treatment of complex diseases. Patent PCT/US2019/041618.

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.