Yomogida K, Trsan T, Sudan R, Rodrigues PF, Ulezko Antonova A, Ingle H, Luccia BD, Collins PL, Cella M, Gilfillan S, Baldridge MT, Oltz EM, Colonna M (2024). The transcription factor Aiolos restrains the activation of intestinal intraepithelial lymphocytes. Nature Immunology. 25(1):77-87. 

Ingle H, Makimaa H, Aggarwal S, Deng H, Foster L, Li Y, Kennedy EA, Peterson ST, Wilen CB, Lee S, Suthar MS, Baldridge MT (2023). IFN-λ derived from nonsusceptible enterocytes acts on tuft cells to limit persistent norovirus. Science Advances. 9(37):eadi2562.

Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Schriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD (2023). Microbiota-produced indole metabolites disrupt mitochondrial function and inhibit Cryptosporidium parvum growth. Cell Reports. 42(7):112680.

Kennedy EA, Aggarwal S, Dhar A, Karst SM, Wilen CB, Baldridge MT (2023). Age-associated features of norovirus infection analysed in mice. Nature Microbiology. 8(6):1095-1107.

Nadjsombati MS, Niepoth N, Webeck LM, Kennedy EA, Jones DL, Billipp TE, Baldridge MT, Bendesky A, von Moltke J (2023). Genetic mapping reveals Pou2af2/OCA-T1-dependent tuning of tuft cell differentiation and intestinal type 2 immunity. Science Immunology. 8(83):eade5019.

Peiper AM, Helm EW, Nguyen Q, Phillips M, Williams CG, Shah D, Tatum S, Iyer N, Grodzki M, Eurell LB, Nasir A, Baldridge MT, Karst SM (2023). Infection of neonatal mice with the murine norovirus strain WU23 is a robust model to study norovirus pathogenesis. Lab Animal. 52(6):119-129.

Campbell DE, Li Y, Ingle H, Baldridge MT (2023). Impact of the Microbiota on Viral Infections. Annual Reviews of Virology.

Li Y, Baldridge MT (2023). Modelling human immune responses using microbial exposures in rodents. Nature Microbiology. 8(3):363-366.

Helm EW, Peiper AM, Phillips M, Williams CG, Sherman MB, Kelley T, Smith HQ, Jacobs SO, Shah D, Tatum SM, Iyer N, Grodzki M, Morales Aparicio JC, Kennedy EA, Manzi MS, Baldridge MT, Smith TJ, Karst SM (2022). Environmentally-triggered contraction of the norovirus virion determines diarrheagenic potential. Frontiers in Immunology. 13:1043746.

Strine MS, Alfajaro MM, Graziano VR, Song J, Hsieh LL, Hill R, Guo J, VanDussen KL, Orchard RC, Baldridge MT, Lee S, Wilen CB (2022). Tuft-cell-intrinsic and -extrinsic mediators of norovirus tropism regulate viral immunity. Cell Reports. 41(6):111593.

Celorrio Navarro M, Shumilov K, Rodgers R, Schriefer L, Li Y, Baldridge MT, Friess S (2022). Innate and peripheral immune alterations after TBI are regulated in a gut microbiota-dependent manner in mice. Journal of Neurotrauma.

Sullender ME, Pierce LR, Annaswamy Srinivas M, Crockett SL, Dunlap BF, Rodgers R, Schriefer LA, Kennedy EA, Stewart BM, Doench JG, Baldridge MT#, Orchard RC# (2022). Selective Polyprotein Processing Determines Norovirus Sensitivity to Trim7. Journal of Virology. 96(17):e0070722. #co-corresponding

Nolan LS, Baldridge MT (2022). Advances in understanding interferon-mediated immune responses to enteric viruses in intestinal organoids. Frontiers in Immunology. 13:943334.

Kennedy EA, Baldridge MT (2022). Norovirus from the mouths of babes. Nature. 607(7918):247-248.

Yan H, Walker FC, Ali A, Han H, Tan L, Veillon L, Lorenzi PL, Baldridge MT#, King KY# (2022). The bacterial microbiota regulates normal hematopoiesis via metabolite-induced type 1 interferon signaling. Blood Advances. 6(6):1754-1765. #co-corresponding

Van Winkle JA, Peterson ST, Kennedy EA, Wheadon MJ, Ingle H, Desai C, Rodgers R, Constant DA, Wright AP, Li L, Artyomov MN, Lee S, Baldridge MT#, Nice TJ# (2022). Homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium. Elife. 11:e74072. #co-corresponding

Wirusanti NI, Baldridge MT, Harris VC (2022). Microbiota regulation of viral infections through interferon signaling. Trends Microbiol. S0966-842X(22)00007-5.

Lawrence D, Campbell DE, Schriefer LA, Rodgers R, Walker FC, Turkin M, Droit L, Parkes M, Handley SA, Baldridge MT (2022). Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry. Gut Microbes. 14(1):2029673.

Kim AH, Armah G, Dennis F, Wang L, Rodgers R, Droit L, Baldridge MT, Handley SA, Harris VC (2022). Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants. Cell Host Microbe. 30(1):110-123.e5.

Walker FC, Sridhar PR, Baldridge MT (2021). Differential roles of interferons in innate responses to mucosal viral infections. Trends Immunol. 42(11):1009-1023.

Lee S, Kalugotla G, Ingle H, Rodgers R, Wu C, Wang Y, Li Y, Yang X, Zhang J, Borella NR, Deng H, Droit L, Hill R, Peterson ST, Desai C, Lawrence D, Lu Q, Baldridge MT (2021). Intestinal antiviral signaling is controlled by autophagy gene Epg5 independent of the microbiota. Autophagy. 1-16.

Saraav I, Cervantes-Barragan L, Olias P, Fu Y, Wang Q, Wang L, Wang Y, Mack M, Baldridge MT, Stappenbeck T, Colonna M, Sibley LD (2021). Chronic Toxoplasma gondii infection enhances susceptibility to colitis. PNAS. 118(36):e2106730118.

Schnepf D, Hernandez P, Mahlakõiv T, Crotta S, Sullender ME, Peterson ST, Ohnemus A, Michiels C, Gentle I, Dumoutier L, Reis CA, Diefenbach A, Wack A, Baldridge MT, Staeheli P (2021). Rotavirus susceptibility of antibiotic-treated mice ascribed to diminished expression of interleukin-22. PLoS One. 16(8):e0247738.

Campbell DE, Baldridge MT (2021). Enteric viruses seize their immunomodulatory niche. Cell Host Microbe. 29(6):858-861. 

Aggarwal S, Hassan E, Baldridge MT (2021). Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses. Viruses. 13(6):975.

Platt DJ, Lawrence D, Rodgers R, Schriefer L, Qian W, Miner CA, Menos AM, Kennedy EA, Peterson ST, Stinson WA, Baldridge MT, Miner JJ (2021). Transferrable protection by gut microbes against STING-associated lung disease. Cell Reports. 35(6):109113. 

Li Y, Handley SA, Baldridge MT (2021). The dark side of the gut: Virome-host interactions in intestinal homeostasis and disease. Journal of Experimental Medicine. 218(5):e20201044.

Walker FC*, Hassan E*, Peterson ST, Rodgers R, Schriefer LA, Thompson CE, Li Y, Kalugotla G, Blum-Johnston C, Lawrence D, McCune BT, Graziano VR, Lushniak L, Lee S, Roth AN, Karst SM, Nice TJ, Miner JJ, Wilen CB#, Baldridge MT# (2021). Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid. PLoS Pathogens. 17(3):e1009402. #co-corresponding

Ingle H, Hassan E, Gawron J, Mihi B, Li Y, Kennedy EA, Kalugotla G, Makimaa H, Lee S, Desai P, McDonald KG, Diamond MS, Newberry RD, Good M, Baldridge MT (2021). Murine astrovirus tropism for goblet cells and enterocytes facilitates an IFN-λ response in vivo and in enteroid cultures. Mucosal Immunology. doi: 10.1038/s41385-021-00387-6.

Celorrio M, Abellanas MA, Rhodes J, Goodwin V, Moritz J, Vadivelu S, Wang L, Rodgers R, Xiao S, Anabayan I, Payne C, Perry AM, Baldridge MT, Aymerich MS, Steed A, Friess SH (2021). Gut microbial dysbiosis after traumatic brain injury modulates the immune response and impairs neurogenesis. Acta Neuropathologica Communications. 9(1):40.

Desai P, Janova H, White JP, Reynoso GV, Hickman HD, Baldridge MT, Urban JF, Stappenbeck TS, Thackray LB, Diamond MS (2021). Enteric helminth coinfection enhances host susceptibility to neurotropic flaviviruses via a tuft cell-IL-4 receptor signaling axis in gut epithelium. Cell.184(5):1214-1231.e16.

Lee S, Baldridge MT (2021). Crossing the T’s on Norovirus. Cellular and Molecular Gastroenterology and Hepatology. S2352-345X(21)00027-8.

Kim AH, Hogarty MP, Harris VC, Baldridge MT (2021).The Complex Interactions Between Rotavirus and the Gut Microbiota. Frontiers in Cellular and Infection Microbiology. 10:586751.

Graziano VR, Alfajaro MM, Schmitz CO, Filler RB, Strine MS, Wei J, Hsieh LL, Baldridge MT, Nice TJ, Lee S, Orchard RC, Wilen CB (2020). CD300lf conditional knockout mouse reveals strain-specific cellular tropism for murine norovirus. Journal of Virology. JVI.01652-20.

Makimaa H, Ingle H, Baldridge MT (2020). Enteric Viral Co-Infections: Pathogenesis and Perspective. Viruses. 12(8):904.

Furlong K, Biering S, Choi J, Wilen CB, Orchard RC, Wobus CE, Fremont D, Baldridge MT, Randall G, and Hwang S (2020). CD300LF polymorphisms of inbred mouse strains confer resistance to murine norovirus infection in a cell type-dependent manner. Journal of Virology. JVI.00837-20.

Graziano VR, Walker FC, Kennedy EA, Wei J, Ettayebi K, Strine MS, Filler RB, Hassan E, Hsieh LL, Kim AS, Kolawole AO, Wobus CE, Lindesmith LC, Baric RS, Estes MK, Orchard RC, Baldridge MT#, Wilen CB# (2020). CD300lf is the primary physiologic receptor of murine norovirus but not human norovirus. PLoS Pathogens. 16(4):e1008242. #co-corresponding

Crock L, Baldridge MT (2020). A Role for the Microbiota in Complex Regional Pain Syndrome? Neurobiology of Pain. 8:100054.

Lee AG, Scott JM, Fabbrizi MR, Jiang X, Sojka DK, Miller MJ, Baldridge MT, Yokoyama WM, Shin H (2020). T cell response kinetics determines neuroinfection outcomes during murine HSV infection. JCI Insight. 5(5). pii: 134258.

Wang YT, Zaitsev K, Lu Q, Li S, Schaiff WT, Kim KW, Droit L, Wilen CB, Desai C, Balce DR, Orchard RC, Orvedahl A, Park S, Kreamalmeyer D, Handley SA, Pfeifer JD, Baldridge MT, Artyomov MN, Stallings CL, Virgin HW (2020). Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes. Nature Microbiology. doi: 10.1038/s41564-019-0633-0.

Grau KR, Zhu S, Peterson ST, Helm EW, Philip D, Phillips M, Hernandez A, Turula H, Frasse P, Graziano VR, Wilen CB, Wobus CE, Baldridge MT#, Karst SM# (2020). The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon. Nature Microbiology. 5(1):84-92. #co-corresponding

Lee S, Baldridge MT (2019). Viruses RIG up intestinal immunity. Nature Immunology. 20(12):1563-1564.

Shi Z, Zou J, Zhang Z, Zhao X, Noriega J, Zhang B, Zhao C, Ingle H, Bittinger K, Mattei LM, Pruijssers AJ, Plemper RK, Nice TJ, Baldridge MT, Dermody TS, Chassaing B, and Gewirtz AT (2019). Segmented filamentous bacteria prevent and cure rotavirus infection. Cell. 179(3):644-658

Hassan E, Baldridge MT (2019). Norovirus encounters in the gut: multifaceted interactions and disease outcomes. Mucosal Immunology, 12(6): 1259-1267.

Peterson ST*, Kennedy E*, Brigleb P, Taylor G, Urbanek K, Bricker T, Lee S, Shin H, Dermody T, Boon ACM, and Baldridge MT (2019). Disruption of type III interferon genes Ifnl2 and Ifnl3 recapitulates loss of the type III IFN receptor in the mucosal antiviral response. Journal of Virology, 93(22). *equal contribution

Lawrence D, Baldridge MT#, Handley SA# (2019). Phages and Human Health: More Than Idle Hitchhikers. Viruses, 11(7). pii: E587. #co-corresponding

Qian W, Miner CA, Ingle H, Platt DJ, Baldridge MT, Miner JJ (2019). A human STAT1 gain-of-function mutation impairs CD8+ T cell responses against gammaherpesvirus-68. Journal of Virology, 93(19).

Wilke G, Funkhouser-Jones LJ, Wang Y, Ravindran S, Wang Q, Beatty WL, Baldridge MT, VanDussen KL, Shen B, Kuhlenschmidt MS, Kuhlenschmidt TB, Witola WH, Stappenbeck TS, Sibley LD (2019). A Stem-Cell-Derived Platform Enables Complete Cryptosporidium Development In Vitro and Genetic Tractability. Cell Host & Microbe, 26(1):123-134.

Lee S, Liu H, Wilen CB, Sychev ZE, Desai C, Hykes BL, Orchard RC, McCune BT, Kim K, Nice TJ, Handley SA, Baldridge MT, Amarasinghe GK, Virgin HW (2019). A Secreted Viral Nonstructural Protein Determines Intestinal Norovirus Pathogenesis. Cell Host & Microbe, 25(6):845-857.

Walker FC, Baldridge MT (2019). Interactions between noroviruses, the host, and the microbiota. Current Opinion in Virology, 37:1-9.

Ingle H*, Lee S*, Ai T, Orvedahl A, Rodgers R, Zhao G, Sullender M, Peterson ST, Locke M, Liu TC, Yokoyama CC, Sharp B, Schultz-Cherry S, Miner JJ, Baldridge MT (2019). Viral complementation of immunodeficiency confers protection against enteric pathogens via interferon-λ. Nature Microbiology, 4(7):1120-1128. *equal contribution

Bennion BG*, Ingle H*, Ai TL, Miner CA, Platt DJ, Smith AM, Baldridge MT#, Miner JJ(2018). A human gain-of-function STING mutation causes immunodeficiency and gammaherpesvirus-induced pulmonary fibrosis in mice. Journal of Virology, 93(4). *equal contribution, #co-corresponding

Kennedy EA, King KY, Baldridge MT (2018). Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria. Frontiers in Physiology, 9:1534.

MacDuff DA*, Baldridge MT*, Qaqish AM, Nice TJ, Darbandi AD, Hartley VL, Peterson ST, Miner JJ, Iwai K, Virgin HW (2018). HOIL1 is essential for the induction of type I and III interferons by MDA5 and regulates persistent murine norovirus infection. Journal of Virology, 92(23). *equal contribution

Sullender ME, Baldridge MT (2018). Norovirus interactions with the commensal microbiota. PLoS Pathogens14(9):e1007183.

Yan H, Baldridge MT, King KY (2018). Hematopoiesis and the bacterial microbiomeBlood,132(6):559-564.

Wilen CB, Lee S, Hsieh LL, Orchard RC, Desai C, Hykes BL Jr., McAllaster MR, Balce DR, Feehley T, Brestoff JR, Hickey CA, Yokoyama CC, Wang YT, MacDuff DA, Kreamalmayer D, Howitt MR, Neil JA, Cadwell K, Allen PM, Handley SA, van Lookeren Campagne M, Baldridge MT, Virgin HW (2018). Tropism for tuft cells determines immune promotion of norovirus pathogenesis. Science, 360(6385):204-208.

Ingle H*, Peterson ST*, Baldridge MT (2018). Distinct effects of type I and III interferons on enteric virusesViruses, 10(1), 46. *equal contribution

Lee S, Wilen CB, Orvedahl A, McCune BT, Kim K, Orchard RC, Peterson ST, Nice TJ, Baldridge MT#, Virgin HW# (2017). Norovirus cell tropism is determined by combinatorial action of a viral non-structural protein and host cytokine. Cell Host & Microbe, 22(4):449-459. #co-corresponding

Lee S and Baldridge MT. (2017). Interferon-lambda: A potent regulator of intestinal viral infections. Frontiers in Immunology, 8:749.

Baldridge MT*, Lee S*, Brown JJ, McAllister N, Urbanek K, Dermody TS, Nice TJ, Virgin HW. (2017). Expression of Ifnlr1 on intestinal epithelial cells is critical to the antiviral effects of IFN-lambda against norovirus and reovirus. Journal of Virology, 13;91(7). *equal contribution

Josefsdottir, KS, Baldridge MT, Kadmon CS, King KY. (2017). Antibiotics impair murine hematopoiesis by depleting intestinal microbiota. Blood, 129(6):729-739.

Baldridge MT, Turula H, Wobus CE. (2016). Norovirus regulation by host and microbe. Trends in Molecular Medicine, 22(12):1047-1059.

Orchard RC*, Wilen CB*, Doench JG, Baldridge MT, McCune BT, Lee YCJ, Lee S, Pruett-Miller S, Nelson CA, Fremont DH, Virgin HW. (2016). Discovery of a proteinaceous cellular receptor for a norovirus. Science, 353(6302):933-6. *equal contribution

Liu T, Gurram B, Baldridge MT, Head R, Lam V, Luo C, Cao Y, Simpson P, Hayward M, Holtz ML, Bousounis P, Noe J, Lerner D, Cabrera J, Biank V, Stephens M, Huttenhower C, McGovern DPB, Xavier RJ, Stappenbeck TS, Salzman NH. (2016). Paneth cell defects in Crohn’s disease patients promote dysbiosis. JCI Insight, 1(8):e86907.

Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW. (2016). Altered virome and bacterial microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host & Microbe, 19(3):311-22.

Lu Q, Yokoyama CC, Williams JW, Baldridge MT, Jin X, DesRochers B, Bricker T, Wilen CB, Bagaitkar J, Loginicheva E, Sergushichev A, Kreamalmeyer D, Keller BC, Zhao Y, Kambal A, Green DR, Martinez J, Dinauer MC, Holtzman MJ, Crouch EC, Beatty W, Boon ACM, Zhang H, Randolph GJ, Artyomov MN, Virgin HW (2016). Homeostatic control of innate lung inflammation by Vici Syndrome gene Epg5 and additional autophagy genes promotes influenza pathogenesis. Cell Host & Microbe, 19(1):102–113.

Moon C*, Baldridge MT*, Wallace MA, Burnham CD, Virgin HW, Stappenbeck TS. (2015). Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation. Nature, 521(7550):90-3. *equal contribution

Baldridge MT, Nice TJ, McCune BT, Yokoyama C, Kambal A, Wheadon M, Lazear HM, Diamond MS, Ivanova Y, Artyomov M, Virgin HW. (2015). Commensal microbes and interferon-λ determine persistence off enteric murine norovirus infection. Science, 347(6219):266-9.

Nice TJ, Baldridge MT, McCune BT, Norman JM, Lazear HM, Artyomov M, Diamond MS, Virgin HW. (2015). Interferon λ cures persistent murine norovirus infection in the absence of adaptive immunity. Science, 347(6219):269-73.

Norman JM*, Handley SA*, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW. (2015). Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease. Cell, 160(3):447-60. *equal contribution

Nelson AM, Elftman MD, Pinto AK, Baldridge M, Hooper P, Kuczynski J, Petrosino JF, Young VB and Wobus CE. (2013). Murine norovirus infection does not cause major disruptions in the murine intestinal microbiota. Microbiome; 1:7.

Baldridge MT, King KY, Goodell MA. (2011). Inflammatory signals regulate hematopoietic stem cells. Trends in Immunology; 32(2):57-65.

King KY*, Baldridge MT*, Weksberg DC, Chambers SM, Lukov GL, Wu S, Boles NC, Jung SY, Qin J, Liu D, Songyang Z, Eissa NT, Taylor GA, and Goodell MA. (2011). Irgm1 protects hematopoietic stem cells by negative regulation of interferon signaling. Blood, 118(6):1525-33. *equal contribution

Baldridge MT*, King KY*, Boles NC, Weksberg DC, and Goodell MA. Quiescent hematopoietic stem cells are activated by IFN-gamma in response to chronic infection. (2010). Nature, 465: 793-797. *equal contribution