Healthy infants harbor intestinal bacteria that protect against food allergy.
Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R, Nagler CR. Nat Med. Jan 14; pages 448-453 (2019). doi: 10.1038/s41591-018-0324-z.
B cells and the microbiota: a missing connection in food allergy
Campbell E, Hesser LA, Nagler CR. Mucosal Immunol. Oct 26; doi: 10.1038/s41385-020-00350-x.
Kemter AM, Patry RT, Arnold J, Hesser LA, Campbell E, Ionescu E, Mimee M, Wang S, Nagler CR. Cell Rep. 2023 Sep 22;42(10):113153. doi: 10.1016/j.celrep.2023.113153. Online ahead of print. PMID: 37742185
Intestinal Helminth Infection Impairs Oral and Parenteral Vaccine Efficacy.
Zhang Y, Hardy LC, Kapita CM, Hall JA, Arbeeva L, Campbell E, Urban JF, Belkaid Y, Nagler CR, Iweala OI. J Immunol. 2023 Aug 1;211(3):389-402. doi: 10.4049/jimmunol.2300084. PMID: 37272847
Wang R, Cao S, Bashir MEH, Hesser LA, Su Y, Hong SMC, Thompson A, Culleen E, Sabados M, Dylla NP, Campbell E, Bao R, Nonnecke EB, Bevins CL, Wilson DS, Hubbell JA, Nagler CR. Nat Biomed Eng. 2023 Jan;7(1):38-55. doi: 10.1038/s41551-022-00972-5. Epub 2022 Dec 22. PMID: 36550307
Fe, fi, fo, fum, I smell the diet of a healthy human.
Campbell E, Nagler CR. Cell. 2021 Aug 5;184(16):4107-4109. doi: 10.1016/j.cell.2021.07.011. PMID: 34358465
B cells and the microbiota: a missing connection in food allergy.
Campbell E, Hesser LA, Nagler CR. Mucosal Immunol. 2021 Jan;14(1):4-13. doi: 10.1038/s41385-020-00350-x. Epub 2020 Oct 26. PMID: 33106585
Healthy infants harbor intestinal bacteria that protect against food allergy.
Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R, Nagler CR. Nat Med. 2019 Mar;25(3):448-453. doi: 10.1038/s41591-018-0324-z. Epub 2019 Jan 14. PMID: 30643289
Metabolic independence drives gut microbial colonization and resilience in health and disease.
Watson AR, Füssel J, Veseli I, DeLongchamp JZ, Silva M, Trigodet F, Lolans K, Shaiber A, Fogarty E, Runde JM, Quince C, Yu MK, Söylev A, Morrison HG, Lee STM, Kao D, Rubin DT, Jabri B, Louie T, Eren AM. Genome Biol. 2023 Apr 17;24(1):78. doi: 10.1186/s13059-023-02924-x. PMID: 37069665
Runde J, Veseli I, Fogarty EC, Watson AR, Clayssen Q, Yosef M, Shaiber A, Verma R, Quince C, Gerasimidis K, Rubin DT, Eren AM. J Crohns Colitis. 2023 Jul 5;17(7):1103-1113. doi: 10.1093/ecco-jcc/jjad031. PMID: 36934439
A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome.
Chitale P, Lemenze AD, Fogarty EC, Shah A, Grady C, Odom-Mabey AR, Johnson WE, Yang JH, Eren AM, Brosch R, Kumar P, Alland D. Nat Commun. 2022 Nov 18;13(1):7068. doi: 10.1038/s41467-022-34853-x. PMID: 36400796
The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes.
Miranda K, Weigel BL, Fogarty EC, Veseli IA, Giblin AE, Eren AM, Pfister CA. mSystems. 2022 Oct 26;7(5):e0059222. doi: 10.1128/msystems.00592-22. Epub 2022 Aug 22. PMID: 35993708
Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations.
Landis EA, Fogarty E, Edwards JC, Popa O, Eren AM, Wolfe BE. mSystems. 2022 Jun 28;7(3):e0015722. doi: 10.1128/msystems.00157-22. Epub 2022 Jun 7. PMID: 35670539
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes.
Weigel BL, Miranda KK, Fogarty EC, Watson AR, Pfister CA. mSystems. 2022 Jun 28;7(3):e0142221. doi: 10.1128/msystems.01422-21. Epub 2022 Jun 1. PMID: 35642511
High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes.
Trigodet F, Lolans K, Fogarty E, Shaiber A, Morrison HG, Barreiro L, Jabri B, Eren AM. Mol Ecol Resour. 2022 Jul;22(5):1786-1802. doi: 10.1111/1755-0998.13588. Epub 2022 Feb 7. PMID: 35068060
Community-led, integrated, reproducible multi-omics with anvi'o.
Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD. Nat Microbiol. 2021 Jan;6(1):3-6. doi: 10.1038/s41564-020-00834-3. PMID: 33349678
Fogarty E. Science. 2020 Nov 27;370(6520):1130. doi: 10.1126/science.370.6520.1130. PMID: 33243893
Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2.
El-Shennawy L, Hoffmann AD, Dashzeveg NK, McAndrews KM, Mehl PJ, Cornish D, Yu Z, Tokars VL, Nicolaescu V, Tomatsidou A, Mao C, Felicelli CJ, Tsai CF, Ostiguin C, Jia Y, Li L, Furlong K, Wysocki J, Luo X, Ruivo CF, Batlle D, Hope TJ, Shen Y, Chae YK, Zhang H, LeBleu VS, Shi T, Swaminathan S, Luo Y, Missiakas D, Randall GC, Demonbreun AR, Ison MG, Kalluri R, Fang D, Liu H. Nat Commun. 2022 Jan 20;13(1):405. doi: 10.1038/s41467-021-27893-2. PMID: 35058437
Gray LT, Raczy MM, Briquez PS, Marchell TM, Alpar AT, Wallace RP, Volpatti LR, Sasso MS, Cao S, Nguyen M, Mansurov A, Budina E, Watkins EA, Solanki A, Mitrousis N, Reda JW, Yu SS, Tremain AC, Wang R, Nicolaescu V, Furlong K, Dvorkin S, Manicassamy B, Randall G, Wilson DS, Kwissa M, Swartz MA, Hubbell JA. Biomaterials. 2021 Nov;278:121159. doi: 10.1016/j.biomaterials.2021.121159. Epub 2021 Sep 30. PMID: 34634664
Volpatti LR, Wallace RP, Cao S, Raczy MM, Wang R, Gray LT, Alpar AT, Briquez PS, Mitrousis N, Marchell TM, Sasso MS, Nguyen M, Mansurov A, Budina E, Solanki A, Watkins EA, Schnorenberg MR, Tremain AC, Reda JW, Nicolaescu V, Furlong K, Dvorkin S, Yu SS, Manicassamy B, LaBelle JL, Tirrell MV, Randall G, Kwissa M, Swartz MA, Hubbell JA. ACS Cent Sci. 2021 Aug 25;7(8):1368-1380. doi: 10.1021/acscentsci.1c00596. Epub 2021 Jul 21. PMID: 34466656
Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2.
Drayman N, DeMarco JK, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Han KY, O'Brien A, Tomatsidou A, Meyer B, Vignuzzi M, Missiakas D, Botten JW, Brooke CB, Lee H, Baker SC, Mounce BC, Heaton NS, Severson WE, Palmer KE, Dickinson BC, Joachimiak A, Randall G, Tay S. Science. 2021 Aug 20;373(6557):931-936. doi: 10.1126/science.abg5827. Epub 2021 Jul 20. PMID: 34285133
Furlong K, Biering SB, Choi J, Wilen CB, Orchard RC, Wobus CE, Nelson CA, Fremont DH, Baldridge MT, Randall G, Hwang S. J Virol. 2020 Aug 17;94(17):e00837-20. doi: 10.1128/JVI.00837-20. Print 2020 Aug 17. PMID: 32581099
Kandasamy M, Furlong K, Perez JT, Manicassamy S, Manicassamy B. J Virol. 2020 Apr 16;94(9):e00057-20. doi: 10.1128/JVI.00057-20. Print 2020 Apr 16. PMID: 32075925
Gaisina IN, Peet NP, Cheng H, Li P, Du R, Cui Q, Furlong K, Manicassamy B, Caffrey M, Thatcher GRJ, Rong L. J Med Chem. 2020 Mar 26;63(6):3120-3130. doi: 10.1021/acs.jmedchem.9b01900. Epub 2020 Mar 2. PMID: 32069052
Furlong K, Hwang S. Viruses. 2019 Mar 12;11(3):244. doi: 10.3390/v11030244. PMID: 30871000
Virus Impact on Lipids and Membranes.
Ketter E, Randall G. Annu Rev Virol. Sep 29; 6, pages 319-340 (2019). doi: 10.1146/annurev-virology-092818-015748.
Dusting for Flu's Fingerprints.
Riedl W, Gack MU. Nat Micro. Oct 24; 3, pages1196–1197 (2018). doi: 10.1038/s41564-018-0270-z
Riedl W, Acharya D, Lee JH, Liu G, Serman TM, Chiang C, Chan YK, Diamond MS, Gack MU. Cell Host Microbe. 9 Oct; pages 493-503 (2019). doi: 10.1016/j.chom.2019.09.012.
Liu G, Lee JH, Parker ZM, Acharya D, Chiang JJ, van Gent M, Riedl W, Davis-Gardner ME, Wies E, Chiang C, Gack MU. Nat Microbiol. 2021 Apr;6(4):467-478. doi: 10.1038/s41564-021-00884-1. Epub 2021 Mar 16. PMID: 33727702
TRIM25 Binds RNA to Modulate Cellular Anti-viral Defense
Sanchez JG, Sparrer KMJ, Chiang C, Reis RA, Chiang JJ, Zurenski MA, Wan Y, Gack MU, Pornillos O. J Mol Bio. Dec 7; 430, pages 5280-5293 (2018). doi: 10.1016/j.jmb.2018.10.003
Actin cytoskeleton remodeling primes RIG-I-like receptor activation.
Acharya D, Reis R, Volcic M, Liu G, Wang MK, Chia BS, Nchioua R, Groß R, Münch J, Kirchhoff F, Sparrer KMJ, Gack MU. Cell. 2022 Sep 15;185(19):3588-3602.e21. doi: 10.1016/j.cell.2022.08.011. PMID: 36113429
Acetylation of the NS3 helicase by KAT5γ is essential for flavivirus replication.
Serman T, Chiang C, Liu G, Sayyad Z, Pandey S, Volcic M, Lee H, Muppala S, Acharya D, Goins C, Stauffer SR, Sparrer KMJ, Gack MU. Cell Host Microbe. 2023 Aug 9;31(8):1317-1330.e10. doi: 10.1016/j.chom.2023.06.013. Epub 2023 Jul 20. PMID: 37478852
Evasion of Innate and Intrinsic Antiviral Pathways by the Zika Virus.
Serman TM, Gack MU. Viruses. 2019 Oct 22;11(10):970. doi: 10.3390/v11100970. PMID: 31652496
Riedl W, Acharya D, Lee JH, Liu G, Serman T, Chiang C, Chan YK, Diamond MS, Gack MU. Cell Host Microbe. 2019 Oct 9;26(4):493-503.e6. doi: 10.1016/j.chom.2019.09.012. PMID: 31600501
FBXO38 Drives PD-1 to Destruction.
Serman TM, Gack MU. Trends Immunol. 2019 Feb;40(2):81-83. doi: 10.1016/j.it.2018.12.005. Epub 2019 Jan 1. PMID: 30609969
Three-Dimensional Cell Culture Systems for Studying Hepatitis C Virus.
So CW, Randall G. Viruses. 2021 Jan 30;13(2):211. doi: 10.3390/v13020211. PMID: 33573191
A single dominant locus restricts retrovirus replication in YBR/Ei mice.
Beilinson HA, Sevilleja A, Spring J, Benavides F, Beilinson V, Neokosmidis N, Golovkina T. J Virol. 2023 Aug 31;97(8):e0068523. doi: 10.1128/jvi.00685-23. Epub 2023 Aug 14. PMID: 37578238
Spring J, Beilinson V, DeFelice BC, Sanchez JM, Fischbach M, Chervonsky A, Golovkina T. Viruses. 2023 Jan 29;15(2):386. doi: 10.3390/v15020386. PMID: 36851600
Spring J, Beilinson V, DeFelice BC, Sanchez JM, Fischbach M, Chervonsky A, Golovkina T. Viruses. 2023 Jan 29;15(2):386. doi: 10.3390/v15020386. PMID: 36851600
Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus.
Spring J, Khan AA, Lara S, O'Grady K, Wilks J, Gurbuxani S, Erickson S, Fischbach M, Jacobson A, Chervonsky A, Golovkina T. Cell Rep. 2022 Sep 13;40(11):111341. doi: 10.1016/j.celrep.2022.111341.
A Carbonic Anhydrase Pseudogene Sensitizes Select Brucella Lineages to Low CO2 Tension. J Bacteriol
Varesio LM, Willett JW, Fiebig A, Crosson S. 2019 Oct 21;201(22). pii: e00509-19. doi: 10.1128/JB.00509-19.
Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light
Fiebig A, Varesio LM, Alejandro Navarreto X, Crosson S. Mol Microbiol. 2019 Aug;112(2):442-460. doi: 10.1111/mmi.14310.
Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus.
Herrou J, Willett JW, Fiebig A, Varesio LM, Czyż DM, Cheng JX, Ultee E, Briegel A, Bigelow L, Babnigg G, Kim Y, Crosson S. Mol Microbiol. 2019 Mar;111(3):637-661. doi: 10.1111/mmi.14178.
Varesio LM, Fiebig A, Crosson S. Infect Immun. 2021 May 17;89(6):e00808-20. doi: 10.1128/IAI.00808-20. Print 2021 May 17. PMID: 33753413
Delaby M, Varesio LM, Degeorges L, Crosson S, Viollier PH. Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):e2010357118. doi: 10.1073/pnas.2010357118. PMID: 33602809
Broadly Protective Strategies Against Influenza Viruses: Universal Vaccines and Therapeutics.
Vogel OA, Manicassamy B. Front. Microbiol. Feb 7; 11(135), pages 1-14 (2020). doi: 10.3389/fmicb.2020.00135.
Liang CY, Huang I, Han J, Sownthirarajan B, Kulhankova K, Murray NB, Taherzadeh M, Archer-Hartmann S, Pepi L, Manivasagam S, Plung J, Sturtz M, Yu Y, Vogel OA, Kandasamy M, Gourronc FA, Klingelhutz AJ, Choudhury B, Rong L, Perez JT, Azadi P, McCray PB Jr, Neelamegham S, Manicassamy B. J Virol. 2023 Oct 16:e0090623. doi: 10.1128/jvi.00906-23. Online ahead of print. PMID: 37843369
Host factor Rab11a is critical for efficient assembly of influenza A virus genomic segments.
Han J, Ganti K, Sali VK, Twigg C, Zhang Y, Manivasagam S, Liang CY, Vogel OA, Huang I, Emmanuel SN, Plung J, Radoshevich L, Perez JT, Lowen AC, Manicassamy B. PLoS Pathog. 2021 May 10;17(5):e1009517. doi: 10.1371/journal.ppat.1009517. eCollection 2021 May. PMID: 33970958
Vogel OA, Han J, Liang CY, Manicassamy S, Perez JT, Manicassamy B. PLoS Pathog. 2020 Sep 8;16(9):e1008842. doi: 10.1371/journal.ppat.1008842. eCollection 2020 Sep. PMID: 32898178
The Wolbachia mobilome in Culex pipiens includes a putative plasmid.
Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen ÖC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I, Bordenstein SR, Eren AM. Nat Commun. Mar 5; 10(1), pages 1-11 (2019). doi: 10.1038/s41467-019-08973-w.
B cell superantigens in the human intestinal microbiota.
Bunker JJ, Drees C, Watson AR, Plunkett CH, Nagler CR, Schneewind O, Eren AM, Bendelac A. Sci Transl Med. Aug 28; 11(507), page eaau9356 (2019). doi: 10.1126/scitranslmed.aau9356.
Watterson WJ, Tanyeri M, Watson AR, Cham CM, Shan Y, Chang EB, Eren AM, Tay S. bioRxiv. Sept 6; page 759969. doi: 10.1101/759969
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes
Weigel BL, Miranda KK, Fogarty EC, Watson AR, Pfister CA. mSystems. 2022 Jun 28;7(3):e0142221. doi: 10.1128/msystems.01422-21. Epub 2022 Jun 1. PMID: 35642511; PMCID: PMC9238374
Metabolic independence drives gut microbial colonization and resilience in health and disease.
Watson AR, Füssel J, Veseli I, DeLongchamp JZ, Silva M, Trigodet F, Lolans K, Shaiber A, Fogarty E, Runde JM, Quince C, Yu MK, Söylev A, Morrison HG, Lee STM, Kao D, Rubin DT, Jabri B, Louie T, Eren AM. Genome Biol. 2023 Apr 17;24(1):78. doi: 10.1186/s13059-023-02924-x. PMID: 37069665
Runde J, Veseli I, Fogarty EC, Watson AR, Clayssen Q, Yosef M, Shaiber A, Verma R, Quince C, Gerasimidis K, Rubin DT, Eren AM. J Crohns Colitis. 2023 Jul 5;17(7):1103-1113. doi: 10.1093/ecco-jcc/jjad031. PMID: 36934439
Community-led, integrated, reproducible multi-omics with anvi'o.
Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD. Nat Microbiol. 2021 Jan;6(1):3-6. doi: 10.1038/s41564-020-00834-3. PMID: 33349678
Shaiber A, Willis AD, Delmont TO, Roux S, Chen LX, Schmid AC, Yousef M, Watson AR, Lolans K, Esen ÖC, Lee STM, Downey N, Morrison HG, Dewhirst FE, Mark Welch JL, Eren AM. Genome Biol. 2020 Dec 16;21(1):292. doi: 10.1186/s13059-020-02195-w. PMID: 33323122
Watterson WJ, Tanyeri M, Watson AR, Cham CM, Shan Y, Chang EB, Eren AM, Tay S. Elife. 2020 Jun 17;9:e56998. doi: 10.7554/eLife.56998. PMID: 32553109
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes.
Weigel BL, Miranda KK, Fogarty EC, Watson AR, Pfister CA. mSystems. 2022 Jun 28;7(3):e0142221. doi: 10.1128/msystems.01422-21. Epub 2022 Jun 1. PMID: 35642511
Dsouza M, Menon R, Crossette E, Bhattarai SK, Schneider J, Kim YG, Reddy S, Caballero S, Felix C, Cornacchione L, Hendrickson J, Watson AR, Minot SS, Greenfield N, Schopf L, Szabady R, Patarroyo J, Smith W, Harrison P, Kuijper EJ, Kelly CP, Olle B, Bobilev D, Silber JL, Bucci V, Roberts B, Faith J, Norman JM. Cell Host Microbe. 2022 Apr 13;30(4):583-598.e8. doi: 10.1016/j.chom.2022.03.016. PMID: 35421353
B cell superantigens in the human intestinal microbiota.
Bunker JJ, Drees C, Watson AR, Plunkett CH, Nagler CR, Schneewind O, Eren AM, Bendelac A. Sci Transl Med. 2019 Aug 28;11(507):eaau9356. doi: 10.1126/scitranslmed.aau9356. PMID: 31462512
The Wolbachia mobilome in Culex pipiens includes a putative plasmid.
Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen ÖC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I, Bordenstein SR, Eren AM. Nat Commun. 2019 Mar 5;10(1):1051. doi: 10.1038/s41467-019-08973-w. PMID: 30837458
Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization.
Kennedy MS, Zhang M, DeLeon O, Bissell J, Trigodet F, Lolans K, Temelkova S, Carroll KT, Fiebig A, Deutschbauer A, Sidebottom AM, Lake J, Henry C, Rice PA, Bergelson J, Chang EB. Cell Rep. 2023 Aug 29;42(8):113009. doi: 10.1016/j.celrep.2023.113009. Epub 2023 Aug 21. PMID: 37598339