2019 MICROBIOME RESEARCH PUBLICATIONS BY FRED HUTCH INVESTIGATORS

Navarro SL, Levy L, Curtis KR, Lampe JW, Hullar MAJ. Modulation of gut microbiota by glucosamine and chondroitin in a randomized, double-blind pilot trial in humans. Microorganisms. 2019 Nov 23;7(12). pii: E610. doi: 10.3390/microorganisms7120610. PMID: 31771179

Wang Z, Usyk M, Sollecito CC, Qiu Y, Williams-Nguyen J, Hua S, Gradissimo A, Wang T, Xue X, Kurland IJ, Ley K, Landay AL, Anastos K, Knight R, Kaplan RC, Burk RD, Qi Q. Altered gut microbiota and host metabolite profiles in HIV-infected women. Clin Infect Dis. 2019 Nov 21. pii: ciz1117. doi: 10.1093/cid/ciz1117. [Epub ahead of print]. PMID: 31748797

Willis AD. Rarefaction, alpha diversity, and statistics. Front Microbiol. 2019 Oct 23;10:2407. doi: 10.3389/fmicb.2019.02407. eCollection 2019. PMCID: PMC6819366

Thangavelu G, Du J, Paz KG, Loschi M, Zaiken MC, Flynn R, Taylor PA, Kirchmeier AK, Panoskaltsis-Mortari A, Luznik L, MacDonald KP, Hill GR, Maillard I, Munn DH, Serody JS, Murphy WJ, Miklos D, Cutler CS, Koreth J, Antin JH, Soiffer RJ, Ritz J, et al. Inhibition of inositol kinase B controls acute and chronic graft-versus-host disease. Blood. 2020 Jan 2;135(1):28-40. doi: 10.1182/blood.2019000032. PMCID: PMC6940197

Koyama M, Hill GR. The primacy of gastrointestinal tract antigen presenting cells in lethal graft-versus-host disease. Blood. 2019 Dec 12;134(24):2139-2148. doi: 10.1182/blood.2019000823. PMCID: PMC6908833

Ma J, Shojaie A, Michailidis G. A comparative study of topology-based pathway enrichment analysis methods. BMC Bioinformatics. 2019 Nov 4;20(1):546. doi: 10.1186/s12859-019-3146-1. PMCID: PMC6829999

Pilon AC, Gu H, Raftery D, da Silva Bolzani V, Lopes NP, Castro-Gamboa I, Carnevale Neto F. Correction to mass spectral similarity networking and gas-phase fragmentation reactions in the structural analysis of flavonoid glycoconjugates. Anal Chem. 2019 Nov 19;91(22):14780-14781. doi: 10.1021/acs.analchem.9b04825. Epub 2019 Oct 31. PMID: 31670937

Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD. Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol. 2019 Nov 1;20(1):219. doi: 10.1186/s13059-019-1831-z. PMCID: PMC6824043

Henden AS, Varelias A, Leach J, Sturgeon E, Avery J, Kelly J, Olver S, Samson L, Hartel G, Durrant S, Butler J, Morton AJ, Misra A, Tey SK, Subramoniapillai E, Curley C, Kennedy G, Hill GR. Pegylated interferon-2α invokes graft-versus-leukemia effects in patients relapsing after allogeneic stem cell transplantation. Blood Adv. 2019 Oct 22;3(20):3013-3019. doi: 10.1182/bloodadvances.2019000453. PMCID: PMC6849957

Zhang P, Hill GR. Interleukin-10 mediated immune regulation after stem cell transplantation: Mechanisms and implications for therapeutic intervention. Semin Immunol. 2019 Aug;44:101322. doi: 10.1016/j.smim.2019.101322. Epub 2019 Oct 19. Review. PMID: 31640914

Rose OM, Fredricks DN, Soge OO, Farooq F, Tang G, Ness R, Haggerty CL. Stability of Chlamydia trachomatis RNA after long-term biobank storage. Sex Transm Infect. 2019 Nov;95(7):551. doi: 10.1136/sextrans-2019-054141. PMID: 31628264

Imlay H, Krantz EM, Stohs EJ, Lan KF, Zier J, Kim HN, Rakita RM, Limaye AP, Wald A, Pergam SA, Liu C. Reported beta lactam and other antibiotic allergies in solid organ and hematopoietic cell transplant recipients. Clin Infect Dis. 2019 Oct 17. pii: ciz1025. doi: 10.1093/cid/ciz1025. PMID: 31621829

Hart SFM, Skelding D, Waite AJ, Burton JC, Shou W. High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy. Quant Biol. 2019 Mar;7(1):69-81. doi: 10.1007/s40484-018-0160-7. Epub 2019 Jan 4. PMCID: PMC6785046

Burr RL, Gu H, Cain K, Djukovic D, Zhang X, Han C, Callan N, Raftery D, Heitkemper M. Tryptophan metabolites in irritable bowel syndrome: an overnight time-course study. J Neurogastroenterol Motil. 2019 Oct 30;25(4):551-562. doi: 10.5056/jnm19042. PMCID: PMC6786437

Gartlan KH, Koyama M, Lineburg KE, Chang K, Ensbey KS, Kuns RD, Henden AS, Samson LD, Clouston AD, Lopez AF, MacDonald KPA, Hill GR. Donor T-cell-derived GM-CSF drives alloantigen presentation by dendritic cells in the gastrointestinal tract. Blood Adv. 2019 Oct 8;3(19):2859-2865. doi: 10.1182/bloodadvances.2019000053. PMCID: PMC6784518

Golob JL, DeMeules MM, Loeffelholz T, Quinn ZZ, Dame MK, Silvestri SS, Wu MC, Schmidt TM, Fiedler TL, Hoostal MJ, Mielcarek M, Spence J, Pergam SA, Fredricks DN. Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD. Blood Adv. 2019 Oct 8;3(19):2866-2869. doi: 10.1182/bloodadvances.2019000362. PMCID: PMC6784520

Wilkinson AN, Chang K, Kuns RD, Henden AS, Minnie SA, Ensbey KS, Clouston AD, Zhang P, Koyama M, Hidalgo J, Rose-John S, Varelias A, Vuckovic S, Gartlan KH, Hill GR. IL-6 dysregulation originates in dendritic cells and mediates graft-versus-host disease via classical signaling. Blood. 2019 Dec 5;134(23):2092-2106. doi: 10.1182/blood.2019000396. PMID: 31578204

Munch MM, Chambers LC, Manhart LE, Domogala D, Lopez A, Fredricks DN, Srinivasan S. Optimizing bacterial DNA extraction in urine. PLoS One. 2019 Sep 24;14(9):e0222962. doi: 10.1371/journal.pone.0222962. eCollection 2019. PMCID: PMC6759279

Koyama M, Mukhopadhyay P, Schuster IS, Henden AS, Hülsdünker J, Varelias A, Vetizou M, Kuns RD, Robb RJ, Zhang P, Blazar BR, Thomas R, Begun J, Waddell N, Trinchieri G, Zeiser R, Clouston AD, Degli-Esposti MA, Hill GR. MHC class II antigen presentation by the intestinal epithelium initiates graft-versus-host disease and is influenced by the microbiota. Immunity. 2019 Nov 19;51(5):885-898.e7. doi: 10.1016/j.immuni.2019.08.011. Epub 2019 Sep 18. PMCID: PMC6959419

Koehn BH, Saha A, McDonald-Hyman C, Loschi M, Thangavelu G, Ma L, Zaiken M, Dysthe J, Krepps W, Panthera J, Hippen K, Jameson SC, Miller JS, Cooper MA, Farady CJ, Iwawaki T, Ting JP, Serody JS, Murphy WJ, Hill GR, Murray PJ, Bronte V, et al. Danger-associated extracellular ATP counters MDSC therapeutic efficacy in acute GVHD. Blood. 2019 Nov 7;134(19):1670-1682. doi: 10.1182/blood.2019001950. PMCID: PMC6871306

Spicer JA, Miller CK, O'Connor PD, Jose J, Giddens AC, Jaiswal JK, Jamieson SMF, Bull MR, Denny WA, Akhlaghi H, Trapani JA, Hill GR, Chang K, Gartlan KH. Inhibition of the cytolytic protein perforin prevents rejection of transplanted bone marrow stem cells in vivo. J Med Chem. 2019 Sep 26. doi: 10.1021/acs.jmedchem.9b00881. [Epub ahead of print] PMID: 31525966

Nagana Gowda GA, Raftery D. Overview of NMR spectroscopy-based metabolomics: opportunities and challenges. Methods Mol Biol. 2019;2037:3-14. doi: 10.1007/978-1-4939-9690-2_1. PMID: 31463836

Nagana Gowda GA, Raftery D. Analysis of plasma, serum, and whole blood metabolites using (1)H NMR spectroscopy. Methods Mol Biol. 2019;2037:17-34. doi: 10.1007/978-1-4939-9690-2_2. PMID: 31463837

Chou CK, Turtle CJ. Insight into mechanisms associated with cytokine release syndrome and neurotoxicity after CD19 CAR-T cell immunotherapy. Bone Marrow Transplant. 2019 Aug;54(Suppl 2):780-784. doi: 10.1038/s41409-019-0602-5. Review. PMID: 31431714

Navarro SL, Tarkhan A, Shojaie A, Randolph TW, Gu H, Djukovic D, Osterbauer KJ, Hullar MA, Kratz M, Neuhouser ML, Lampe PD, Raftery D, Lampe JW. Plasma metabolomics profiles suggest beneficial effects of a low-glycemic load dietary pattern on inflammation and energy metabolism. Am J Clin Nutr. 2019 Oct 1;110(4):984-992. doi: 10.1093/ajcn/nqz169. PMCID: PMC6766441

Kreuk LS, Koch MA, Slayden LC, Lind NA, Chu S, Savage HP, Kantor AB, Baumgarth N, Barton GM. B cell receptor and Toll-like receptor signaling coordinate to control distinct B-1 responses to both self and the microbiota. Elife. 2019 Aug 21;8. pii: e47015. doi: 10.7554/eLife.47015. PMCID: PMC6703855

McLean K, Rosenthal CA, Sengupta D, Owens J, Cookson BT, Hoffman NG, Salipante SJ. Improved species-level clinical identification of Enterobacteriaceae through broad-range dnaJ PCR and sequencing. J Clin Microbiol. 2019 Oct 23;57(11). pii: e00986-19. doi: 10.1128/JCM.00986-19. Print 2019 Nov. PMCID: PMC6813017

Maruvada P, Lampe JW, Wishart DS, Barupal D, Chester DN, Dodd D, Djoumbou-Feunang Y, Dorrestein PC, Dragsted LO, Draper J, Duffy LC, Dwyer JT, Emenaker NJ, Fiehn O, Gerszten RE, B Hu F, Karp RW, Klurfeld DM, Laughlin MR, Little AR, Lynch CJ, Moore SC, et al. Perspective: dietary biomarkers of intake and exposure—exploration with omics approaches. Adv Nutr. 2019 Aug 6. pii: nmz075. doi: 10.1093/advances/nmz075. [Epub ahead of print] PMID: 31386148

Minot SS, Willis AD. Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. Microbiome. 2019 Aug 1;7(1):110. doi: 10.1186/s40168-019-0722-6. PMCID: PMC6670193

Chambers LC, Hughes JP, Glick SN, Morgan JL, Lowens MS, Robinson TS, Romano SS, Leipertz GL, Jensen JS, Khosropour CM, Fredricks DN, Golden MR, Manhart LE. Resolution of symptoms and resumption of sex after diagnosis of nongonococcal urethritis among men who have sex with men. Sex Transm Dis. 2019 Oct;46(10):676-682. doi: 10.1097/OLQ.0000000000001040. PMCID: PMC7008972

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K…Willis A et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091. PMCID: PMC7015180

Keller MJ, Wood L, Billingsley JM, Ray LL, Goymer J, Sinclair S, McGinn AP, Marzinke MA, Frank B, Srinivasan S, Liu C, Atrio JM, Espinoza L, Mugo N, Spiegel HML, Anderson PL, Fredricks DN, Hendrix CW, Marrazzo J, Bosinger SE, Herold BC. Tenofovir disoproxil fumarate intravaginal ring for HIV pre-exposure prophylaxis in sexually active women: a phase 1, single-blind, randomised, controlled trial. Lancet HIV. 2019 Aug;6(8):e498-e508. doi: 10.1016/S2352-3018(19)30145-6. Epub 2019 Jul 15. PMCID: PMC6719300

Aitken SL, Nagel JL, Abbo L, Alegria W, Barreto JN, Dadwal S, Freifeld AG, Jain R, Pergam SA, Tverdek FP, Seo SK; Antimicrobial Stewardship in Cancer Consortium ASCC. Antimicrobial stewardship in cancer patients: the time is now. J Natl Compr Canc Netw. 2019 Jul 1;17(7):772-775. doi: 10.6004/jnccn.2019.7318. PMID: 31319394

Pattacini L, Woodward Davis A, Czartoski J, Mair F, Presnell S, Hughes SM, Hyrien O, Lentz GM, Kirby AC, Fialkow MF, Hladik F, Prlic M, Lund JM. A pro-inflammatory CD8+ T-cell subset patrols the cervicovaginal tract. Mucosal Immunol. 2019 Sep;12(5):1118-1129. doi: 10.1038/s41385-019-0186-9. Epub 2019 Jul 16. PMCID: PMC6717561

Lazarus E, Otwombe K, Dietrich J, Andrasik MP, Morgan CA, Kublin JG, Gray GE, Isaacs AJ, Laher F. Vaginal practices among women at risk for HIV acquisition in Soweto, South Africa. South Afr J HIV Med. 2019 Jun 20;20(1):866. doi: 10.4102/sajhivmed.v20i1.866. eCollection 2019. PMCID: PMC6620501

Jarrett OD, Srinivasan S, Richardson BA, Fiedler T, Wallis JM, Kinuthia J, Jaoko W, Mandaliya K, Fredricks DN, McClelland RS. Specific vaginal bacteria are associated with an increased risk of Trichomonas vaginalis acquisition in women. J Infect Dis. 2019 Sep 26;220(9):1503-1510. doi: 10.1093/infdis/jiz354. PMCID: PMC6761949

Garrison CB, Zhang Y, Navarro SL, Randolph TW, Hullar MAJ, Kratz M, Neuhouser ML, Raftery D, Lampe PD, Lampe JW. Proteomic analysis of plasma reveals fat mass influences cancer-related pathways in healthy humans fed controlled diets differing in glycemic load. Cancer Prev Res (Phila). 2019 Sep;12(9):567-578. doi: 10.1158/1940-6207.CAPR-19-0175. Epub 2019 Jul 2. PMCID: PMC6726515

Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR spectroscopy for metabolomics research. Metabolites. 2019 Jun 27;9(7). pii: E123. doi: 10.3390/metabo9070123. Review. PMCID: PMC6680826

Xie L, Yuan AE, Shou W. Simulations reveal challenges to artificial community selection and possible strategies for success. PLoS Biol. 2019 Jun 25;17(6):e3000295. doi: 10.1371/journal.pbio.3000295. eCollection 2019 Jun. PMCID: PMC6658139

Ansaldo E, Slayden LC, Ching KL, Koch MA, Wolf NK, Plichta DR, Brown EM, Graham DB, Xavier RJ, Moon JJ, Barton GM. Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis. Science. 2019 Jun 21;364(6446):1179-1184. doi: 10.1126/science.aaw7479. PMCID: PMC6645389

Taylor JA, Sichel SR, Salama NR. Bent bacteria: a comparison of cell shape mechanisms in Proteobacteria. Annu Rev Microbiol. 2019 Sep 8;73:457-480. doi: 10.1146/annurev-micro-020518-115919. Epub 2019 Jun 14. PMID: 31206344

Sabo MC, Lehman DA, Wang B, Richardson BA, Srinivasan S, Osborn L, Matemo D, Kinuthia J, Fiedler TL, Munch MM, Drake AL, Fredricks DN, Overbaugh J, John-Stewart G, McClelland RS, Graham SM. Associations between vaginal bacteria

implicated in HIV acquisition risk and proinflammatory cytokines and chemokines. Sex Transm Infect. 2020 Feb;96(1):3-9. doi: 10.1136/sextrans-2018-053949. Epub 2019 Jun 13. PMCID: PMC6920574

Maskarinec G, Hullar MAJ, Monroe KR, Shepherd JA, Hunt J, Randolph TW, Wilkens LR, Boushey CJ, Le Marchand L, Lim U, Lampe JW. Fecal microbial diversity and structure are associated with diet quality in the Multiethnic Cohort Adiposity Phenotype Study. J Nutr. 2019 Sep 1;149(9):1575-1584. doi: 10.1093/jn/nxz065. PMCID: PMC6862930

Lampe JW, Kim E, Levy L, Davidson LA, Goldsby JS, Miles FL, Navarro SL, Randolph TW, Zhao N, Ivanov I, Kaz AM, Damman C, Hockenbery DM, Hullar MAJ, Chapkin RS. Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans. Am J Clin Nutr. 2019 Aug 1;110(2):377-390. doi: 10.1093/ajcn/nqy325. PMCID: PMC6669062

Hart SFM, Pineda JMB, Chen CC, Green R, Shou W. Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community. Elife. 2019 Jun 4;8. pii: e44812. doi: 10.7554/eLife.44812. PMCID: PMC6548503

Scoville DK, Li CY, Wang D, Dempsey JL, Raftery D, Mani S, Gu H, Cui JY. Polybrominated diphenyl ethers and gut microbiome modulate metabolic syndrome-related aqueous metabolites in mice. Drug Metab Dispos. 2019 Aug;47(8):928-940. doi: 10.1124/dmd.119.086538. Epub 2019 May 23. PMCID: PMC6657215

Iwaki T, Bennion BG, Stenson EK, Lynn JC, Otinga C, Djukovic D, Raftery D, Fei L, Wong HR, Liles WC, Standage SW. PPARα contributes to protection against metabolic and inflammatory derangements associated with acute kidney injury in experimental sepsis. Physiol Rep. 2019 May;7(10):e14078. doi: 10.14814/phy2.14078. PMCID: PMC6525329

Johnston CD, Cotton SL, Rittling SR, Starr JR, Borisy GG, Dewhirst FE, Lemon KP. Systematic evasion of the restriction-modification barrier in bacteria. Proc Natl Acad Sci USA. 2019 Jun 4;116(23):11454-11459. doi: 10.1073/pnas.1820256116. Epub 2019 May 16. PMCID: PMC6561282

Martínez LE, O'Brien VP, Leverich CK, Knoblaugh SE, Salama NR. Nonhelical Helicobacter pylori mutants show altered gland colonization and elicit less gastric pathology than helical bacteria during chronic infection. Infect Immun. 2019 Jun 20;87(7). pii: e00904-18. doi: 10.1128/IAI.00904-18. Print 2019 Jul. PMCID: PMC6589060

Paudel L, Nagana Gowda GA, Raftery D. Extractive ratio analysis NMR Spectroscopy for metabolite identification in complex biological mixtures. Anal Chem. 2019 Jun 4;91(11):7373-7378. doi: 10.1021/acs.analchem.9b01235. Epub 2019 May 14. PMID: 31059230

Niehaus L, Boland I, Liu M, Chen K, Fu D, Henckel C, Chaung K, Miranda SE, Dyckman S, Crum M, Dedrick S, Shou W, Momeni B. Microbial coexistence through chemical-mediated interactions. Nat Commun. 2019 May 3;10(1):2052. doi: 10.1038/s41467-019-10062-x. PMCID: PMC6499789

Sabo MC, Richardson BA, Lavreys L, Martin HL Jr, Jaoko W, Mandaliya K, Baeten JM, Overbaugh J, McClelland RS. Does bacterial vaginosis modify the effect of hormonal contraception on HIV seroconversion. AIDS. 2019 Jun 1;33(7):1225-1230. doi: 10.1097/QAD.0000000000002167. PMCID: PMC6501800

Fredricks DN. The gut microbiota and graft-versus-host disease. J Clin Invest. 2019 May 1;129(5):1808-1817. doi: 10.1172/JCI125797. Epub 2019 May 1. Review. PMCID: PMC6486325

Da Costa AS, Graham JB, Swarts JL, Lund JM. Regulatory T cells limit unconventional memory to preserve the capacity to mount protective CD8 memory responses to pathogens. Proc Natl Acad Sci USA. 2019 May 14;116(20):9969-9978. doi: 10.1073/pnas.1818327116. Epub 2019 Apr 29. PMCID: PMC6525503

Yang DC, Blair KM, Taylor JA, Petersen TW, Sessler T, Tull CM, Leverich CK, Collar AL, Wyckoff TJ, Biboy J, Vollmer W, Salama NR. A genome-wide Helicobacter pylori morphology screen uncovers a membrane-spanning helical cell shape complex. J Bacteriol. 2019 Jun 21;201(14). pii: e00724-18. doi: 10.1128/JB.00724-18. Print 2019 Jul 15. PMCID: PMC6597387

Sun S, Lulla A, Sioda M, Winglee K, Wu MC, Jacobs DR Jr, Shikany JM, Lloyd-Jones DM, Launer LJ, Fodor AA, Meyer KA. Gut microbiota composition and blood pressure. Hypertension. 2019 May;73(5):998-1006. doi: 10.1161/HYPERTENSIONAHA.118.12109. PMCID: PMC6458072

Minot SS. De novo assembly vastly expands the known microbial universe. Trends Microbiol. 2019 May;27(5):385-386. doi: 10.1016/j.tim.2019.02.007. Epub 2019 Mar 11. PMID: 30871856

Plantinga AM, Chen J, Jenq RR, Wu MC. pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis. Bioinformatics. 2019 Oct 1;35(19):3567-3575. doi: 10.1093/bioinformatics/btz120. PMCID: PMC6761933

Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O'Donovan C, Playdon M, Raftery D, et al. Towards quality assurance and quality control in untargeted metabolomics studies. Metabolomics. 2019 Jan 3;15(1):4. doi: 10.1007/s11306-018-1460-7. PMCID: PMC6443086

Varelias A, Gartlan KH, Wilkinson AN, Olver SD, Samson LD, Tey SK, MacDonald KPA, Hill GR. Expansion of IL-17A-secreting CD8(+) mucosa-associated invariant T cells in peripheral blood following stem cell mobilization. Blood Adv. 2019 Mar 12;3(5):718-723. doi: 10.1182/bloodadvances.2018025601. PMCID: PMC6418493

Fei Q, Wang D, Jasbi P, Zhang P, Nagana Gowda GA, Raftery D, Gu H. Combining NMR and MS with chemical derivatization for absolute quantification with reduced matrix effects. Anal Chem. 2019 Mar 19;91(6):4055-4062. doi: 10.1021/acs.analchem.8b05611. Epub 2019 Mar 11. PMID: 30801179

Hart SFM, Mi H, Green R, Xie L, Pineda JMB, Momeni B, Shou W. Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells. PLoS Biol. 2019 Feb 22;17(2):e3000135. doi: 10.1371/journal.pbio.3000135. eCollection 2019 Feb. PMCID: PMC6402699

Paz K, Fly nn R, Du J, Tannheimer S, Johnson AJ, Dong S, Stark AK, Okkenhaug K, Panoskaltsis-Mortari A, Sage PT, Sharpe AH, Luznik L, Ritz J, Soiffer RJ, Cutler CS, Koreth J, Antin JH, Miklos DB, MacDonald KP, Hill GR, Maillard I, Serody JS, et al. Targeting PI3Kδ function for amelioration of murine chronic graft-versus-host disease. Am J Transplant. 2019 Jun;19(6):1820-1830. doi: 10.1111/ajt.15305. Epub 2019 Mar 19. PMCID: PMC6538456

Jin C, Lagoudas GK, Zhao C, Bullman S, Bhutkar A, Hu B, Ameh S, Sandel D, Liang XS, Mazzilli S, Whary MT, Meyerson M, Germain R, Blainey PC, Fox JG, Jacks T. Commensal microbiota promote lung cancer development via γδ T Cells. Cell. 2019 Feb 21;176(5):998-1013.e16. doi: 10.1016/j.cell.2018.12.040. Epub 2019 Jan 31. PMCID: PMC6691977

Stohs E, Chow VA, Liu C, Bourassa L, Miles-Jay A, Knight J, Sweet A, Storer BE, Mielcarek M, Pergam SA. Limited utility of outpatient surveillance blood cultures in hematopoietic cell transplant recipients on high-dose steroids for treatment of acute graft-versus-host-disease. Biol Blood Marrow Transplant. 2019 Jun;25(6):1247-1252. doi: 10.1016/j.bbmt.2019.01.031. Epub 2019 Feb 1. PMCID: PMC6559865

Chang H, Yao S, Tritchler D, Hullar MA, Lampe JW, Thompson LU, McCann SE. Genetic variation in steroid and xenobiotic metabolizing pathways and enterolactone excretion before and after flaxseed intervention in African American and European American women. Cancer Epidemiol Biomarkers Prev. 2019 Feb;28(2):265-274. doi: 10.1158/1055-9965.EPI-18-0826. PMCID: PMC6363829

Lokken EM, Manguro GO, Abdallah A, Ngacha C, Shafi J, Kiarie J, Jaoko W, Srinivasan S, Fiedler TL, Munch MM, Fredricks DN, McClelland RS, Balkus JE. Association between vaginal washing and detection of Lactobacillus by culture and quantitative PCR in HIV-seronegative Kenyan women: a cross-sectional analysis. Sex Transm Infect. 2019 Sep;95(6):455-461. doi: 10.1136/sextrans-2018-053769. Epub 2019 Jan 29. PMID: 30696752

Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN, McClelland RS. Association between vaginal washing and vaginal bacterial concentrations. PLoS One. 2019 Jan 24;14(1):e0210825. doi: 10.1371/journal.pone.0210825. eCollection 2019. PMCID: PMC6345501

Barber DL, Sakai S, Kudchadkar RR, Fling SP, Day TA, Vergara JA, Ashkin D, Cheng JH, Lundgren LM, Raabe VN, Kraft CS, Nieva JJ, Cheever MA, Nghiem PT, Sharon E. Tuberculosis following PD-1 blockade for cancer immunotherapy. Sci Transl Med. 2019 Jan 16;11(475). pii: eaat2702. doi: 10.1126/scitranslmed.aat2702. PMID: 30651320

McKinnon LR, Achilles SL, Bradshaw CS, Burgener A, Crucitti T, Fredricks DN, Jaspan HB, Kaul R, Kaushic C, Klatt N, Kwon DS, Marrazzo JM, Masson L, McClelland RS, Ravel J, van de Wijgert JHHM, Vodstrcil LA, Tachedjian G. The evolving facets of bacterial vaginosis: implications for HIV transmission. AIDS Res Hum Retroviruses. 2019 Mar;35(3):219-228. doi: 10.1089/AID.2018.0304. PMCID: PMC6434601

Winston McPherson G, Long T, Salipante SJ, Rongitsch JA, Hoffman NG, Stephens K, Penewit K, Greene DN. The vaginal microbiome of transgender men. Clin Chem. 2019 Jan;65(1):199-207. doi: 10.1373/clinchem.2018.293654. PMID: 30602481

Dempsey JL, Wang D, Siginir G, Fei Q, Raftery D, Gu H, Yue Cui J. Pharmacological activation of PXR and CAR downregulates distinct bile acid-metabolizing intestinal bacteria and alters bile acid homeostasis. Toxicol Sci. 2019 Mar 1;168(1):40-60. doi: 10.1093/toxsci/kfy271. PMCID: PMC6821357

Fu BC, Randolph TW, Lim U, Monroe KR, Cheng I, Wilkens LR, Le Marchand L, Lampe JW, Hullar MAJ. Temporal variability and stability of the fecal microbiome: The Multiethnic Cohort Study. Cancer Epidemiol Biomarkers Prev. 2019 Jan;28(1):154-162. doi: 10.1158/1055-9965.EPI-18-0348. Epub 2018 Sep 11. PMCID: PMC6625800

Chambers LC, Srinivasan S, Lukehart SA, Ocbamichael N, Morgan JL, Lowens MS, Fredricks DN, Golden MR, Manhart LE. Primary syphilis in the male urethra: a case report. Clin Infect Dis. 2019 Mar 19;68(7):1231-1234. doi: 10.1093/cid/ciy771. PMCID: PMC6424071

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