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.O., Kuo C.C., Malm M., Lundqvist M., Sievertsson Å, Berling A., Tegel H., Hober S., Uhlén M., Grassi L., Hatton D., Rockberg J.‡, Lewis N.E.‡ Deciphering the determinants of recombinant protein yield across the human secretome, bioRxiv (2022).
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)
2025
2024
168. Baghdassarian H.M.*, Dimitrov D.*, Armingol E.*, Saez-Rodriguez J.‡, Lewis N.E‡. Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. Cell Reports Methods, 4:100758 (2024).
166. Armingol E.‡, Baghdassarian H., Lewis N.E.‡ The diversification of methods for studying cell–cell interactions and communication. Nature Reviews Genetics, 25:381-400 (2024).
165. Pong A., Mah C.K., Yeo G.W., Lewis N.E. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment. Current Opinion in Biotechnology, 85:103048 (2024).
2023
159. Aamodt CM, Lewis, NE. Single-cell A/B testing for cell-cell communication, Cell Systems, 14, 428-429 (2023).
157. Baghdassarian H., Blackstone S.A., Clay O.S., Philips R., Matthiasardottir B., Nehrebecky M., Hua V.K., McVicar R., Liu Y., Tucker S.M., Randazzo D., Deuitch N., Rosenzweig S., Mark A., Sasik R., Fisch K.M., Chavan P.P., Eren E., Watts N.R., Gadina M., Schwartz D.M., Sanyal A., Werner G., Murdock D.R., Horita N., Chowdhury S., Dimmock D., Jepsen K., Remmers E.F., Goldbach-Mansky R., Gahl W.A., O’Shea J.J., Milner J.D., Lewis N.E., Chang J., Kastner D.L., Torok K., Oda H., Putnam C.D., Broderick L. Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome. New England Journal of Medicine, 388(24):2241-2252 (2023). doi: 10.1056/NEJMoa2202318
156. 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, Science Advances, 9:eadg0506. (2023).
154. Azadiana S., Doustmohammadi A., Naseri M., Khodarahmi M., Arab S.S., Yazdanifar M., Zahiri J.*, Lewis N.E.* Reconstructing the Cell-Cell Interaction Network Among Mouse Immune Cells. Biotechnology & Bioengineering, 120(9), 2756-2764 (2023). doi: 10.1002/bit.28431
2022
146. 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)
138. 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)
2021
107. 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
2020
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
2019
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
2018
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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 reconstructions. Molecular Systems Biology, 6:422 (2010).
2009
