Publications

Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics. 2024;25(1):5.

Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics. 2024;25(1):5.

Wheeler MA, Clark IC, Lee H-G, Li Z, Linnerbauer M, Rone JM, Blain M, Akl CFaust, Piester G, Giovannoni F, Charabati M, Lee J-H, Kye Y-C, Choi J, Sanmarco LM, Srun L, Chung EN, Flausino LE, Andersen BM, Rothhammer V, Yano H, Illouz T, Zandee SEJ, Daniel C, Artis D, Prinz M, Abate AR, Kuchroo VK, Antel JP, Prat A, Quintana FJ. Droplet-based forward genetic screening of astrocyte-microglia cross-talk. Science. 2023;379(6636):1023-1030.

Ma Y, Sannino D, Linden JR, Haigh S, Zhao B, Grigg JB, Zumbo P, Dündar F, Butler D, Profaci CP, Telesford K, Winokur PN, Rumah KR, Gauthier SA, Fischetti VA, McClane BA, Uzal FA, Zexter L, Mazzucco M, Rudick R, Danko D, Balmuth E, Nealon N, Perumal J, Kaunzner U, Brito IL, Chen Z, Xiang JZ, Betel D, Daneman R, Sonnenberg GF, Mason CE, Vartanian T. Epsilon toxin-producing Clostridium perfringens colonize the multiple sclerosis gut microbiome overcoming CNS immune privilege. J Clin Invest. 2023;133(9).

Venturelli OS, Wang HH, Estrela S, Huang KCasey, Ledesma-Amaro R, Fedorec AJH, Stecher B, Lawson CE, Zarrinpar A, Guo C-J, Soyer OS. What is the key challenge in engineering microbiomes?. Cell Syst. 2023;14(2):85-90.

Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, N Glass L, Gow NAR, Gurr SJ, Hittinger CTodd, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (Bethesda). 2022;.

Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, N Glass L, Gow NAR, Gurr SJ, Hittinger CTodd, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (Bethesda). 2022;.

Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, N Glass L, Gow NAR, Gurr SJ, Hittinger CTodd, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (Bethesda). 2022;.

Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, N Glass L, Gow NAR, Gurr SJ, Hittinger CTodd, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (Bethesda). 2022;.

Zhou L, Zhou W, Joseph AM, Chu C, Putzel GG, Fang B, Teng F, Lyu M, Yano H, Andreasson KI, Mekada E, Eberl G, Sonnenberg GF. Group 3 innate lymphoid cells produce the growth factor HB-EGF to protect the intestine from TNF-mediated inflammation. Nat Immunol. 2022;.

Göktuna SI, Canli O, Bollrath J, Fingerle AA, Horst D, Diamanti MA, Pallangyo C, Bennecke M, Nebelsiek T, Mankan AK, Lang R, Artis D, Hu Y, Patzelt T, Ruland J, Kirchner T, M Taketo M, Chariot A, Arkan MC, Greten FR. IKKα Promotes Intestinal Tumorigenesis by Limiting Recruitment of M1-like Polarized Myeloid Cells. Cell Rep. 2022;38(9):110471.

Lyu M, Suzuki H, Kang L, Gaspal F, Zhou W, Goc J, Zhou L, Zhou J, Zhang W, Shen Z, Fox JG, Sockolow RE, Laufer TM, Fan Y, Eberl G, Withers DR, Sonnenberg GF. ILC3s select microbiota-specific regulatory T cells to establish tolerance in the gut. Nature. 2022;.

Lyu M, Suzuki H, Kang L, Gaspal F, Zhou W, Goc J, Zhou L, Zhou J, Zhang W, Shen Z, Fox JG, Sockolow RE, Laufer TM, Fan Y, Eberl G, Withers DR, Sonnenberg GF. ILC3s select microbiota-specific regulatory T cells to establish tolerance in the gut. Nature. 2022;.

Li XV, Leonardi I, Putzel GG, Semon A, Fiers WD, Kusakabe T, Lin W-Y, Gao IH, Doron I, Gutierrez-Guerrero A, DeCelie MB, Carriche GM, Mesko M, Yang C, Naglik JR, Hube B, Scherl EJ, Iliev ID. Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature. 2022;603(7902):672-678.

Leonardi I, Gao IH, Lin W-Y, Allen M, Li XV, Fiers WD, De Celie MBialt, Putzel GG, Yantiss RK, Johncilla M, Colak D, Iliev ID. Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity. Cell. 2022;.

Goc J, Lv M, Bessman NJ, Flamar A-L, Sahota S, Suzuki H, Teng F, Putzel GG, Eberl G, Withers DR, Arthur JC, Shah MA, Sonnenberg GF. Dysregulation of ILC3s unleashes progression and immunotherapy resistance in colon cancer. Cell. 2021;184(19):5015-5030.e16.

Lima-Junior DS, Krishnamurthy SR, Disease CBiblio _ T, Collins N, Han S-J, Chen EY, Constantinides MG, Link VM, Lim AIng, Enamorado M, Cataisson C, Gil L, Rao I, Farley TK, Koroleva G, Attig J, Yuspa SH, Fischbach MA, Kassiotis G, Belkaid Y. Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota. Cell. 2021;184(14):3794-3811.e19.

Lima-Junior DS, Krishnamurthy SR, Disease CBiblio _ T, Collins N, Han S-J, Chen EY, Constantinides MG, Link VM, Lim AIng, Enamorado M, Cataisson C, Gil L, Rao I, Farley TK, Koroleva G, Attig J, Yuspa SH, Fischbach MA, Kassiotis G, Belkaid Y. Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota. Cell. 2021;184(14):3794-3811.e19.

Doron I, Leonardi I, Li XV, Fiers WD, Semon A, Bialt-DeCelie M, Migaud M, Gao IH, Lin W-Y, Kusakabe T, Puel A, Iliev ID. Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies. Cell. 2021;.

Doron I, Mesko M, Li XV, Kusakabe T, Leonardi I, Shaw DG, Fiers WD, Lin W-Y, Bialt-DeCelie M, Román E, Longman RS, Pla J, Wilson PC, Iliev ID. Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn's disease. Nat Microbiol. 2021;6(12):1493-1504.

Offit K, Tkachuk KA, Stadler ZK, Walsh MF, Diaz-Zabala H, Levin JD, Steinsnyder Z, Ravichandran V, Sharaf RN, Frey MK, Lipkin SM, Robson ME, Hamilton JG, Vijai J, Mukherjee S. Cascading After Peridiagnostic Cancer Genetic Testing: An Alternative to Population-Based Screening. J Clin Oncol. 2020;:JCO1902010.

Tummers B, Mari L, Guy CS, Heckmann BL, Rodriguez DA, Rühl S, Moretti J, Crawford JChase, Fitzgerald P, Kanneganti T-D, Janke LJ, Pelletier S, J Blander M, Green DR. Caspase-8-Dependent Inflammatory Responses Are Controlled by Its Adaptor, FADD, and Necroptosis. Immunity. 2020;52(6):994-1006.e8.

Bessman NJ, Mathieu JRR, Renassia C, Zhou L, Fung TC, Fernandez KC, Austin C, Moeller JB, Zumerle S, Louis S, Vaulont S, Ajami NJ, Sokol H, Putzel GG, Arvedson T, Sockolow RE, Lakhal-Littleton S, Cloonan SM, Arora M, Peyssonnaux C, Sonnenberg GF. Dendritic cell-derived hepcidin sequesters iron from the microbiota to promote mucosal healing. Science. 2020;368(6487):186-189.

Bessman NJ, Mathieu JRR, Renassia C, Zhou L, Fung TC, Fernandez KC, Austin C, Moeller JB, Zumerle S, Louis S, Vaulont S, Ajami NJ, Sokol H, Putzel GG, Arvedson T, Sockolow RE, Lakhal-Littleton S, Cloonan SM, Arora M, Peyssonnaux C, Sonnenberg GF. Dendritic cell-derived hepcidin sequesters iron from the microbiota to promote mucosal healing. Science. 2020;368(6487):186-189.

Fiers WD, Leonardi I, Iliev ID. From Birth and Throughout Life: Fungal Microbiota in Nutrition and Metabolic Health. Annu Rev Nutr. 2020;.