Publications
Preprints
2020
2019
2018
2017
2016 and earlier
Preprints
Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology
Hughes, TK.*, Wadsworth, MH.*, Gierahn, TM.*, Do, T., Weiss, D., Andrade P.R., Ma, F., de Andrade Silva, B.J., Shao, S., Tsoi, L.C., Ordovas-Montanes, J., Gudjonsson, J.E., Modlin, R.L., Love, J.C.^#, Shalek, A.K.^#
* Co-main authors, ^ Co-senior authors, # Co-corresponding authors
bioRxiv
Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
Huang, S.*, Ziegler, C.G.K.*, Austin, J., Mannoun, N., Vukovic, M., Ordovas-Montanes, J., Shalek, A.K.^#, von Andrian, U.H.^#.
* Co-main authors, ^ Co-senior authors, # Co-corresponding authors
bioRxiv
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
Cao, Y.*, Guo, Z.*, Vangala, P., Donnard, E., Liu, P., McDonel, P., Ordovas-Montanes, J., Shalek, A.K., Finberg, R.W., Wang, J.P., Garber, M.
* Co-main authors
bioRxiv
2020
Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
Mitsialis V., Wall S., Liu P., Ordovas-Montanes, J., Parmet, T., Vukovic, M., Spencer, D., Field, M., McCourt, C., Tthaker, J., Bousvaros, A., BCH IBD Center, BWH Crohn’s and Colitis Center, Shalek. A., Kean, L., Horwitz, B., Goldsmith, J., Tseng, G., Snapper, S.B.^#, and Konnikova, L^#.
^ Co-senior authors, # Co-corresponding authors
Gastroenterology (in press)
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
Ziegler, C.G.K.*, Allon, S.J.*, Nyquist, S.K.*, Mbano, I.M.*, Miao, V.N., Tzouanas, C.N., Cao, Y., Yousif, A.S., Bals, J., Hauser, B.M., Feldman, J., Muus, C., Wadsworth II, M.H., Kazer, S.W., Hughes, T.K., Doran, B., Gatter, G.J., Vukovic, M., Taliaferro, F., Mead, B.E., Guo, Z., Wang, J.P., Gras, D., Plaisant, M., Ansari, M., Angelidis, I., Adler, H., Sucre, J.M.S., Taylor, C.J., Lin, B., Waghray, A., Mitsialis, V., Dwyer, D.F., Buchheit, K.M., Boyce, J.A., Barrett, N.A., Laidlaw, T.M., Carroll, S.L., Colonna, L., Tkachev, V., Peterson, C.W., Yu, A., Zheng, H.B., Gideon, H.P., Winchell, C.G., Lin, P.L., Bingle, C.D., Snapper, S.B., Kropski, J.A., Theis, F.J., Schiller, H.B., Zaragosi, L.-E., Barbry, P., Leslie, A., Kiem, H.-P., Flynn, J.L., Fortune, S.M., Berger, B., Finberg, R.W., Kean, L.S., Garber, M., Schmidt, A.G., Lingwood, D., Shalek, A.K.#, Ordovas-Montanes, J.#, HCA Lung Biological Network
* Co-main authors, # Co-corresponding authors
Cell
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PDF
Distribution and Storage of Inflammatory Memory in Barrier Tissue
Ordovas-Montanes, J., Beyaz, S., Rakoff-Nahoum S., Shalek, A.K.
Nature Reviews Immunology
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PDF
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Kazer, SW., Aicher, TP., Muema, DM., Carroll, SL., Ordovas-Montanes, J., Miao, VN., Tu, AA., Ziegler, CGK., Nyquist, SK., Wong, EB., Ismail, N., Moodly, A., Berger, B., Love, JC., Dong, K., Leslie, A., Ndhlovu, ZM., Ndung’u T., Walker, BD., Shalek, AK.
bioRxiv
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Nature Medicine
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PDF
2019
Sensory Neurons Innervate Peripheral Lymph Nodes and Locally Regulate Gene Expression in Postsynaptic Endothelium, Stromal Cells, and Innate Leukocytes
Huang, S.*, Ziegler, CGK.*, Austin, J., Mannoun, N., Vukovic, M., Ordovas-Montanes, J., Shalek, AK^#, von Andrian, UH^#.
* Co-main authors, ^ Co-senior authors, # Co-corresponding authors
bioRxiv
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PDF
Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
Smillie, CS.*, Biton, M.*, Ordovas-Montanes, J.*, Sullivan, K., Burgin, G., Graham, DB., Herbst, RH., Rogel, N., Slyper, M., Waldman, J., Sud, M., Andrews, EA., Haber, AL., Vickovic, S., Dionne, D., Nguyen, LT., Villani, AC., Hofree, M., Creasey, EA., Huang, H., Rozenblatt-Rosen, O., Garber, JJ., Khalili, H., Desch, AN., Daly, MJ., Ananthakrishnan, AN.#, Shalek, AK.#, Xavier, RJ.#, Regev, A.#.
* Co-main authors, # Co-corresponding authors
bioRxiv
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Cell
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PDF
Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration.
Pepe-Mooney, BJ.*, Dill, MT.*, Alemany, A., Ordovas-Montanes, J., Matsushita, Y., Rao, A., Sen, A., Miyazaki, M, Anakk, S., Dawson, PA., Ono, N., Shalek, AK., van Oudenaarden, A., Camargo, FD.#
* Co-main authors, # Corresponding author
Cell Stem Cell
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PDF
2018
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
Biton, M.*, Haber, AL.*, Beyaz, S., Rogel, N., Smillie, C., Sh*ekhar, K., Chen, Z., Wu, C., Ordovas-Montanes, J., Alvarez, D., Herbst, RH., Tirosh, I., Burgin, G., Dionne, D., Zhang, M., Rozenblatt-Rosen, O., Shi, HN., Kuchroo, V., Yilmaz, O., Regev, A.^, Xavier, RJ.*#
* Co-main authors, ^ Senior author, # Corresponding author
bioRxiv
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Cell
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PDF
Allergic inflammatory memory in human respiratory epithelial progenitor cells
Ordovas-Montanes, J.*, Dwyer, DF.*, Nyquist, SK., Buchheit, KM., Vukovic, M., Deb, C., Wadsworth, MH., Hughes, TK., Kazer, SW., Yoshimoto, E., Bhattacharyya, N., Cahill, KN., Katz, HR., Laidlaw, TM., Boyce, JA., Barrett, NA#. Shalek, AK#.
* Co-main authors, # Co-corresponding authors
bioRxiv
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Nature
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PDF
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Mead, BE.*#, Ordovas-Montanes, J.*, Braun, AP., Levy, L., Szucs, MJ, MacMullan, M., Ammendolia, D., Zheng, Y., Bhargava, P., Yin, X., Hughes, TK., Wadsworth III, MH., Ahmad, R., Rakoff-Nahoum, S., Carr, S., Langer, R., Collins JJ., Shalek, AK., Karp, JM.#
* Co-main authors, # Co-corresponding authors
BMC Biology
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PDF
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
Martin-Gayo, E., Cole, M., Kolb, KE., Ouyang, Z., Cronin, J., Kazer, SW., Ordovas-Montanes, J., Lichterfeld, M., Walker, BD., Yosef, N.#, Shalek, AK.#, Yu, XG.#
# Co-corresponding authors
Genome Biology
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PDF
2017
Novel in vitro booster vaccination to rapidly generate antigen-specific fully human monoclonal antibodies from healthy individuals
Nandin, IS.*, Fong, C.*, Deantonio, C., Torreno-Pina, JA., Pecetta, S., Maldonado, P., Gasparrini, F., Ordovas-Montanes, J., Kazer, SW., Kjaer, S., Borley, DW., Nair, U., Coleman, JA., Lingwood, D., Shalek, AK., Meffre, E., Poignard, P., Burton, DR., Batista, FD.#
* Co-main authors, # Corresponding author
Journal of Experimental Medicine
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PDF
2016
The Whiteboard Revolution: Illuminating Science Communication in the Digital Age
Mar, FA., Ordovas-Montanes, J., Oksenberg, N., Olson, AM.
Trends in Immunology
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PDF
2015
The regulation of immunological processes by peripheral neurons in homeostasis and disease
Ordovas-Montanes, J., Rakoff-Nahoum, S., Huang, S., Riol-Blanco, L., Barreiro, O., von Andrian, UH.
Trends in Immunology
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PDF
2014
2012
Impaired intrinsic immunity to HSV-1 in human iPSC-derived TLR3-deficient CNS cells
Lafaille, FG., Pessach, IM., Zhang, SY., Ciancanelli, M., Herman, M., Mostoslavsky, G., Ordovas-Montanes, J., Jouanguy, E., Plancoulaine, S., Tu, E., Elkabetz, Y., Schlaeger, TM., Daley, GQ., Tardieu, M., Abel, L., Casanova, JL., Studer, L., Notarangelo, LD.
Nature
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PDF
2011