Recent Notable Faculty Publications
2023
Zhang, Y., Zhang, W., Zhao, J., Ito, T., Jin, J., Aparicio, A.O., Zhou, J., Guichard, V., Fang, Y., Que, J., Urban, J.F. Jr., Hanna, J.H., Ghosh, S., Wu, X., Ding, L., Basu, U. and Huang, Y. (2023) m6A RNA modification regulates innate lymphoid cell responses in a lineage-specific manner. Nature Immunology https://doi.org/10.1038/s41590-023-01548-4 (Published online ahead of print, full text available at https://rdcu.be/dfWKv ).
2022
Liu, L., Iketani, S., Guo, Y., Chan, J.F., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M.S., Yu, J., Chik, K.K., Yuen, T.T., Yoon, C., To, K.K., Chen, H., Yin, M.T., Sobieszczyk, M.E., Huang, Y., Wang, H.H., Sheng, Z., Yuen, K.Y. and Ho, D.D. (2022) Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature 602: 676-681. https://doi.org/10.1038/s41586-021-04388-0
2021
Laffleur, B., Lim, J., Zhang, W., Chen, Y., Pefanis, E., Bizarro, J., Batista, C.R., Wu, L., Economides, A.N., Wang, J. and Basu, U. (2021) Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells. Nature Genet. https://doi.org/10.1038/s41588-020-00772-0
Wang, P., Nair, M.S., Liu, L., Iketani, S., Luo, Y., Guo, Y., Wang, M., Yu, J., Zhang, B., Kwong, P.D., Graham, B.S., Mascola, J.R., Chang, J.Y., Yi, M.T., Sobieszczyk, M., Kyratsous, C.A., Shapiro, L., Sheng, Z., Nair, M.S., Huang, Y. and Ho, D.D. (2021) Increased resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 to antibody neutralization. Nature 593: 130-135. https://doi.org/10.21203/rs.3.rs-155394/v1
2020
Weisberg, S.P., Connors, T.J., Zhu, Y. Baldwin, M.R., Lin, W.-H., Wontakal, S., Szabo, P.A., Wells, S.B., Dogra, P., Davis-Porada, J., Matsumoto, R., Poon, M.M.L., Chait, M., Mathieu, C., Horvat, B., Decimo, D., Hudson, K.E., Zotti, F.D., Bitan, Z.C., Carpia, F.L., Ferrara, S.A., Mace, E., Milner, J., Moscona, A., Hod, E., Porotto, M. and Farber, D.L. (2020) Distinct antibody responses to SARS-CoV-2 in children and adults across the COVID-19 clinical spectrum. Nature Immunol. https://doi.org/10.1038/s41590-020-00826-9
2019
Chowdhury, S., Castro, S., Coker, C., Hinchliffe, T.E., Arpaia, N.* and Danino, T.* (2019) Programmable bacteria induce durable tumor regression and systemic antitumor immunity. Nature Medicine 25: 1057–1063. *Co-corresponding
Ladinsky, M.S., Araujo, L.P., Zhang, X., Veltri, J., Galan-Diez, M., Soualhi, S., Lee, C., Irie, K., Pinker, E.Y., Narushima, S., Bandyopadhyay, S., Nagayama, M., Elhenawy, W., Coombes, B.K., Ferraris, R.P., Honda, K., Iliev, I.D., Gao, N., Bjorkman, P.J. and Ivanov, I.I. (2019) Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis. Science 363: eaat4042.
Kim, J., Tan, Y.Z., Wicht, K.J., Erramilli, S.K., Dhingra, S.K., Okombo, J., Vendome, J., Hagenah, L.M., Giacometti, S.I., Warren, A.L., Nosol, K., Roepe, P.D., Potter, C.S., Carragher, B., Kossiakoff, A.A., Quick, M.*, Fidock, D.A.* and Mancia, F.* (2019) Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Nature 576: 315-320. *Co-corresponding
2018
Seeley, J.J., Baker, R.G., Mohamed, G., Bruns, T., Hayden, M.S., Deshmukh, S.D., Freedberg, D.E and Ghosh, S. (2018) Induction of innate immune memory via microRNA targeting of chromatin remodelling factors. Nature 559: 114-119.
Decker, M., Leslie, J., Liu, Q. and Ding, L. (2018) Hepatic thrombopoietin is required for bone marrow hematopoietic stem cell maintenance. Science 360: 106-110.
2017
Grinberg-Bleyer, Y., Oh, H., Desrichard, A., Bhatt, D.M., Caron, R., Chan, T.A., Schmid, R.M., Klein, U., Hayden, M.S. and Ghosh, S. (2017) NF-κB c-Rel is crucial for the regulatory T cell immune checkpoint in cancer. Cell 170: 1096-1108.
Lim, J., Giri, P.K., Kazadi, D., Laffleur, B., Zhang, W., Grinstein, V., Pefanis, E., Brown, L.M., Ladewig, E., Martin, O., Chen, Y., Rabadan, R., Boyer, F., Rothschild, G., Cogne, M., Pinaud, E., Deng, H. and Basu, U. (2017) Nuclear proximity of Mtr4 to RNA exosome restricts DNA mutational asymmetry. Cell 169: 523-537 e515.
Nish, S.A., Zens, K.D., Kratchmarov, R., Lin, W.W., Adams, W.C., Chen, Y.H., Yen, B., Rothman, N.J., Bhandoola, A., Xue, H.H., Farber, D.L. and Reiner, S.L. (2017) CD4+ T cell effector commitment coupled to self-renewal by asymmetric cell divisions. J. Exp. Med. 214: 39-47.
2016
Castellanos-Rubio, A., Fernandez-Jimenez, N., Kratchmarov, R., Luo, X., Bhagat, G., Green, P.H.R., Schneider, R., Kiledjian, M., Bilbao, J.R. and Ghosh, S. (2016) A long noncoding RNA associated with susceptibility to celiac disease. Science 352: 91-95.
Thome, J.J., Bickham, K.L., Ohmura, Y., Kubota, M., Matsuoka, N., Gordon, C., Granot, T., Griesemer, A., Lerner, H., Kato, T. and Farber, D.L. (2016) Early-life compartmentalization of human T cell differentiation and regulatory function in mucosal and lymphoid tissues. Nature Med. 22: 72-77.
Luchsinger, L.L., de Almeida, M.J., Corrigan, D.J., Mumau, M. and Snoeck, H.W. (2016) Mitofusin 2 maintains haematopoietic stem cells with extensive lymphoid potential. Nature 529: 528-531.
2015
Pefanis E., Wang J., Rothschild G., Lim J., Kazadi D., Sun J., Federation A., Chao J., Elliot O., Liu Z-P., Economides A., Bradner J.E., Rabadan R. and Basu U. (2015) RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 161: 774-789.
Dominguez-Sola, D., Kung, J., Holmes, A.B., Wells, V.A., Mo, T., Basso, K. and Dalla-Favera, R. (2015) The FOXO1 transcription factor instructs the germinal center dark zone program. Immunity 43: 1064-1074.
Pereira, S.P.P., Gonzalez, R. and Dworkin, J. (2015) Protein synthesis during cellular quiescence is inhibited by phosphorylation of a translational elongation factor. Proc. Natl. Acad. Sci. U.S.A. 112: e3274-3281.
Metzger, MJ., Reinisch, C., Sherry, J., and Goff, S.P. (2015) Horizontal transmission of clonal cancer cells causes leukemia in soft-shell clams. Cell 161: 255-263.
Straimer, J., Gnadig, N.F., Witkowski, B., Amaratunga, C., Duru, V., Ramadani, A.P., Dacheux, M., Khim, N., Zhang, L., Lam, S., Gregory, P.D., Urnov, F.D., Mercereau-Puijalon, O., Benoit-Vical, F., Fairhurst, R.M., Menard, D. and Fidock, D.A. (2015) Drug resistance. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates. Science 347: 428-431.
Panea, C., Farkas, A.M., Goto, Y., Abdollahi-Roodsaz, S., Lee, C., Koscso, B., Gowda, K., Hohl, T.M., Bogunovic, M. and Ivanov I.I. (2015) Intestinal monocyte-derived macrophages control commensal antigen-specific Th17 responses. Cell Reports 12: 1314-1324.
Morris, H., DeWolf, S., Robins, H., Sprangers, B., Locascio, S.A., Shonts, B., Kawai, T., Wong, W., Yang, S., Zuber, J., Shen, Y. and Sykes, M. (2015) Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients. Science Transl. Med. 7: 272ra10.
2014
Pefanis, E., Wang, J., Rothschild, G., Lim, J., Chao, J., Rabadan, R., Economides, A.N. and Basu, U. (2014) Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature 514: 389-393.
Thome, J.J.C., Yudanin, N.A., Ohmura, Y., Kubota, M., Grinshpun, B., Sathaliyawala, T., Kato, T., Lerner, H., Shen, Y. and Farber, D.L. (2014) Spatial map of human T cell compartmentalization and maintenance over decades of life. Cell 159:814-828.
Goto, Y., Panea, C., Nakato, G., Cebula, A., Lee, C., Diez, M.G., Laufer, T.M., Ignatowicz, L. and Ivanov, I.I. (2014) Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation. Immunity 40: 1-14.
Schoggins, J.W., MacDuff, D.A., Imanaka, N., Gainey, M.D., Shrestha, B., Eitson, J.L., Mar, K.B., Richardson, R.B., Ratushny, A.V., Litvak, V., Dabelic, R., Manicassamy, B., Aitchison, J.D., Aderem, A., Elliott, R.M., Garcia-Sastre, A., Racaniello, V., Snijder, E.J., Yokoyama, W.M., Diamond, M.S., Virgin, H.W. and Rice, C.M. (2014) Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature 505: 691-695.
Huang, S.X., Islam, M.N., O'Neill, J., Hu, Z., Yang, Y.G., Chen, Y.W., Mumau, M., Green, M.D., Vunjak-Novakovic, G., Bhattacharya, J. and Snoeck, H.W. (2014) Efficient generation of lung and airway epithelial cells from human pluripotent stem cells. Nature Biotechnol. 32: 84-91.
Deng, S.K., Gibb, B., Almeida, M.J., Greene, E.C. and Symington, L.S. (2014) RPA antagonizes microhomology-mediated repair of DNA double-strand breaks. Nature Struct. Mol. Biol. 21: 405-412.
2013
Sathaliyawala, T., Kubota, M., Yudanin, N., Turner, D., Camp, P., Thome, J.J.C., Bickham, K.L., Lerner, H., Goldstein, M., Sykes, M., Kato, T. and Farber, D.L. (2013). Distribution and compartmentalization of circulating and tissue-resident memory subsets. Immunity 38: 187-197.
Koblansky, A.A., Jankovic, D., Oh, H., Hieny, S., Sungnak, W., Mathur, R., Hayden, M.S., Akira, S., Sher, A. and Ghosh, S.(2013) Recognition of profilin by Toll-like receptor 12 is critical for host resistance to Toxoplasma gondii. Immunity38: 119-130.
2012
Straimer, J., Lee, M.C., Lee, A.H., Zeitler, B., Williams, A.E., Pearl, J.R., Zhang, L., Rebar, E.J., Gregory, P.D., Llinas, M., Urnov, F.D. and Fidock, D.A. (2012) Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases. Nature Methods 9: 993-998.
Barnett, B.E., Ciocca, M.L., Goenka, R., Barnett, L.G., Wu, J., Laufer, T.M., Burkhardt, J.K., Cancro, M.P. and Reiner, S.L.(2012) Asymmetric B cell division in the germinal center reaction. Science 335: 342-344.
Kalscheuer, H., Danzl, N., Onoe, T., Faust, T., Winchester, R., Goland, R., Greenberg, E., Spitzer, T.R., Savage, D.G., Tahara, H., Choi, G., Yang, Y.-G. and Sykes, M. (2012) A model for personalized in vivo analysis of human immune responsiveness. Science Transl. Med. 4: 125ra30.
2011
Basu, U., Meng, F.L., Keim, C., Grinstein, V., Pefanis, E., Eccleston, J., Zhang, T., Myers, D., Wasserman, C.R., Wesemann, D.R., Januszyk, K., Gregory, R.I., Deng, H., Lima, C.D., Alt. F.W. (2011) The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates. Cell 144: 353-363.
Pasqualucci, L., Dominguez-Sola, D., Chiarenza, A., Fabbri, G., Grunn, A., Trifonov, V., Kasper, L.H., Lerach, S., Tang, H., Ma, J., Rossi, D., Chadburn, A., Murty, V.V., Mullighan, C.G., Gaidano, G., Rabadan, R., Brindle, P.K. and Dalla-Favera, R. (2011) Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature 471: 189-195.
West, A.P., Brodsky, I.E., Rahner, C., Woo, D.K., Erdjument-Bromage, H., Tempst, P., Walsh, M.C., Choi, Y., Shadel, G.S. and Ghosh, S. (2011) TLR signalling augments macrophage bactericidal activity through mitochondrial ROS. Nature472: 476-480.
Washburn, R.S. and Gottesman, M.E. (2011) Transcription termination maintains chromosome integrity. Proc. Natl. Acad. Sci. U.S.A. 108: 792-797.
2010
Rao, P., Hayden, M.S., Long, M., Scott, M.L., Philip West, A., Zhang, D., Oeckinghaus, A., Lynch, C., Hoffmann, A., Baltimore, D. and Ghosh, S. (2010) IkBβ acts to inhibit and activate gene expression during the inflammatory response. Nature 466: 1115-1119.
Hogg, J.R. and Goff, S.P. (2010) Upf1 senses 3' UTR length to potentiate mRNA decay. Cell 143: 379-389.
Burmann, B.M., Schweimer, K., Luo, X., Wahl, M.C., Stitt, B.L., Gottesman, M.E. and Rosch, P. (2010) A NusG: NusE complex links transcription and translation. Science 328: 501-504.