Recent Notable Faculty Publications

2026

Yang-Fischer, R., Shearer, A., Zhao, J., Nelson, T., Santin, I., Leão, F.B., Castellanos-Rubio, A., Bhagat, G., Basu, U. and Ghosh, S. (2026) An inflammatory bowel disease-linked lncRNA suppresses transcription factor T-BET expression in T cells to limit intestinal inflammation. Immunity 10.1016/j.immuni.2026.07.019 https://doi.org/10.1016/j.immuni.2026.07.019 (Advance online publication, free download, video abstract)

Lauring, M.C., Yang, M., Sarode, A., Wang, J., Ni, Z., Froehlich, K.A., Zhang, W., Wahed, S., Zheng, S., Goff, S.P., Wang, J. and Basu, U. (2026) Co-option of retrotransposons promotes antibody diversification. Cell S0092-8674(26)00819-6. https://doi.org/10.1016/j.cell.2026.07.021 (Advance online publication)

Kanai, M., Mok, S., Yeo, T., Shears, M.J., Jeon, J.H., Narwal, S.K., Ross, L. S., Wiradiputri, K., Haile, M.T., Tripathi, A.K., Mlambo, G., Kim, J., Gil-Iturbe, E., Park, H., Ndiaye, T., Okombo, J., Ward, K. E., Rozenberg, F. D., Fairhurst, K.J., Gavula, S.M., Bloxham, T.S., Bridgford, J.L., Sheth, T., Llinás, M., Lee, M.C.S., Small-Saunders, J.L., Mancia, F., Quick, M., Uhlemann, A.C., Sinnis, P. and Fidock, D.A. (2026) Identification of genetic markers of quinine partial resistance in Plasmodium falciparum. Nature Microbiol. 11: 2213–2231. https://doi.org/10.1038/s41564-026-02410-7 (Cover article)

Haile, M.T., Kaxiras, D.A., Zhen, J., Lee, C.L., Jiang, B., Small-Saunders, J.L. and Ho, C.M. (2026) Structural basis for host membrane binding and remodeling by invading malaria parasites. Cell S0092-8674(26)00699-9. https://doi.org/10.1016/j.cell.2026.06.012 (Advance online publication)

Ringham, O.R., Rivera, M., Loffredo, L.F., Ozsoy, M.A., Healy, C.M., Cheng, M.F., Jin, Y., Chen, N., de Los Santos-Alexis, K., Azizi, E., Saqi, A., Buechler, M.B., Concepcion-Crisol, C. P. and Arpaia, N. (2026). A novel CAF population coordinates hyper-suppressive regulatory T cell recruitment and localization in lung cancer. Nature Immunology 10.1038/s41590-026-02607-2. https://doi.org/10.1038/s41590-026-02607-2 (Advance online publication)

Yang-Fischer, R., Shearer, A., Leão, F.B., Pascual-Gonzalez, I., Han, A., Castellanos-Rubio, A., Bhagat, G. and Ghosh, S. (2026) The long noncoding RNA lnc13 restrains inflammatory responses to maintain oral tolerance to gluten. Nature Immunology 10.1038/s41590-026-02506-6. https://doi.org/10.1038/s41590-026-02506-6 (Advance online publication featured in CUIMC News).

2025

Guichard, V., Leão, F.B., Zhao, J., Zhang, Y., Ito, T., Shirley, S., Postler, T.S., Tian, R., Huang, Y. and Ghosh, S. (2025) Pre-existing epigenetic state and differential NF-κB activation shape type 2 immune cell responses. Immunity 58: 1422–1437.e6. https://doi.org/10.1016/j.immuni.2025.04.016

Lam, N., Angel, J.C., Buchholz, B.A., Lee, Y.-S., Weisberg, S.P., Brown, B.H., Davis-Porada, J., Caron, D.P., Jensen, I.J., Lee Y., Szabo, P.A., Ural, B.B., Wells, S,B., Kubota, M., Matsumoto, R., Brusko, M., Brusko, T.M., Lu, C., Yates, A.J. and Farber D.L. (2025) Asynchronous aging and turnover of human circulating and tissue-resident memory T cells across sites. Immunity 58: 2271-2288.e6. https://doi.org/10.1016/j.immuni.2025.07.001

Gelsinger, D.R., Ronda, C., Ma, J., Kar, O.B., Edwards, M., Huang, Y., Mavros, C.F., Sun, Y., Perdue, T., Vo, P. L., Ivanov, I.I.*, Sternberg, S.H.* and Wang, H.H.* (2025) Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases. Science 390: eadx7604. (*Co-corresponding authors) https://doi.org/10.1126/science.adx7604

2024

Araujo, L.P., Edwards, M., Irie, K., Huang, Y., Kawano, Y., Tran, A., De Michele, S., Bhagat, G., Wang, H.H. and Ivanov, I.I. (2024) Context-dependent role of group 3 innate lymphoid cells in mucosal protection. Science Immunology 9: eade7530. https://doi.org/10.1126/sciimmunol.ade7530 (Cover article)

Small-Saunders, J.L., Sinha, A., Bloxham, T.S., Hagenah, L.M., Sun, G., Preiser, P.R., Dedon, P.C. and Fidock, D.A. (2024) tRNA modification reprogramming contributes to artemisinin resistance in Plasmodium falciparum. Nature Microbiol. 6: 1483-1498. PMC11153160.

Redenti, A., Im, J., Redenti, B., Li, F., Rouanne, M., Sheng, Z., Sun, W., Gurbatri, C.R., Huang, S., Komaranchath, M., Jang, Y., Hahn, J., Ballister, E.R., Vincent, R.L., Vardoshivilli, A., Danino, T. and Arpaia, N. (2024) Probiotic neoantigen delivery vectors for precision cancer immunotherapy. Nature 635: 453-461. https://doi: 10.1038/s41586-024-08033-4 PMC11560847

Davis-Porada J., George A., Lam N., Caron D., Gray J.I., Huang J., Hwu J., Wells S.B., Matsumoto R., Kubota M., Lee Y.S., Morrison-Colvin R., Jensen I.J., Ural B.B., Shaabani N., Weiskopf D., Grifoni A., Sette A., Szabo P.A., Teijaro J.R., Sims P.A. and Farber D.L. (2024) Maintenance and functional regulation of immmune memory to COVID-19 vaccines in tissues. Immunity 57: 2895-2913.e8. https://doi.org/10.1016/j.immuni.2024.10.003

Gao, L., Lee, H., Goodman, J. and Ding, L. (2024) Hematopoietic stem cell niche generation and maintenance are distinguishable by an epitranscriptomic program. Cell 187: 2801-2816. https://doi.org/10.1016/j.cell.2024.03.032

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 24: 1256–1264. https://doi.org/10.1038/s41590-023-01548-4 (Full text available at https://rdcu.be/dfWKv )

Leeman-Neill, R.J., Song, D., Bizarro, J., Wacheul, L., Rothschild, G., Singh, S., Yang, Y., Sarode, A.Y., Gollapalli, K., Wu, L., Zhang, W., Chen, Y., Lauring, M.C., Whisenant, D.E., Bhavsar, S., Lim, J., Swerdlow, S.H., Bhagat, G., Zhao, Q., Berchowitz, L.E., Wang, J. and Basu, U. (2023) Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression. Nature Genetics 55: 2160-2174. https://doi.org/10.1038/s41588-023-01561-1

Iketani, S., Mohri, H., Culbertson, B., Hong, S.J., Duan, Y., Luck, M.I., Annavajhala, M.K., Guo, Y., Sheng, Z., Uhlemann, A.C., Goff, S.P., Sabo, Y., Yang, H., Chavez, A., and Ho, D.D. (2023). Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir. Nature 613: 558–564. https://doi.org/10.1038/s41586-022-05514-2

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

Laffleur, B., Batista, C. R., Zhang, W., Lim, J., Yang, B., Rossille, D., Wu, L., Estrella, J., Rothschild, G., Pefanis, E. and Basu, U. (2022) RNA exosome drives early B cell development via noncoding RNA processing mechanisms. Science Immunology 7: eabn2738. https://doi.org/10.1126/sciimmunol.abn2738 (Cover article)

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 Genetics 53: 230–242. 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. 22: 25–31. 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.