Arnolds KL, Martin CG, Lozupone CA. Blood type and the microbiome- untangling a complex relationship with lessons from pathogens. Curr Opin Microbiol. 2020 Aug;56:59-66. PubMed PMID: 32663769
Darcy JL, Washburne AD, Robeson MS, Prest T, Schmidt SK, Lozupone CA. A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome. ISME J. 2020 Jun;14(6):1359-1368. PubMed PMID: 32076128
Coleman SL, Neff CP, Li SX, Armstrong AJS, Schneider JM, Sen S, Fennimore B, Campbell TB, Lozupone CA, Palmer BE. Can gut microbiota of men who have sex with men influence HIV transmission?. Gut Microbes. 2020 May 3;11(3):610-619. PubMed PMID: 32036739
Abange WB, Nkenfou CN, Gonsu Kamga H, Nguedia CA, Kamgaing N, Lozupone C, Sosso SM, Kamgaing R, Fosso S, Essomba A, Ndjolo A, Koki P. Intestinal Parasites Infections among HIV Infected Children Under Antiretrovirals Treatment in Yaounde, Cameroon. J Trop Pediatr. 2020 Apr 1;66(2):178-186. PubMed PMID: 31325361
Lomeli BK, Galbraith H, Schettler J, Saviolakis GA, El-Amin W, Osborn B, Ravel J, Hazleton K, Lozupone CA, Evans RJ, Bell SJ, Ochsner UA, Jarvis TC, Baqar S, Janjic N. Multiple-Ascending-Dose Phase 1 Clinical Study of the Safety, Tolerability, and Pharmacokinetics of CRS3123, a Narrow-Spectrum Agent with Minimal Disruption of Normal Gut Microbiota. Antimicrob Agents Chemother. 2019 Dec 20;64(1). PubMed PMID: 31685472
Siebert JC, Neff CP, Schneider JM, Regner EH, Ohri N, Kuhn KA, Palmer BE, Lozupone CA, Görg C. VOLARE: visual analysis of disease-associated microbiome-immune system interplay. BMC Bioinformatics. 2019 Aug 20;20(1):432. PubMed PMID: 31429723
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, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Aug;37(8):852-857. PubMed PMID: 31341288
Abange WB, Nkenfou CN, Gonsu Kamga H, Nguedia CA, Kamgaing N, Lozupone C, Sosso SM, Kamgaing R, Fosso S, Essomba A, Ndjolo A, Koki P. Intestinal Parasites Infections among HIV Infected Children Under Antiretrovirals Treatment in Yaounde, Cameroon. J Trop Pediatr. 2019 Jul 20. [Epub ahead of print] PubMed PMID: 31325361
Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M. Reply to Moossavi and Azad, "Quantifying and Interpreting the Association between Early-Life Gut Microbiota Composition and Childhood Obesity". mBio. 2019 Feb 12;10(1). PubMed PMID: 30755504
Ye H, Adane B, Khan N, Alexeev E, Nusbacher N, Minhajuddin M, Stevens BM, Winters AC, Lin X, Ashton JM, Purev E, Xing L, Pollyea DA, Lozupone CA, Serkova NJ, Colgan SP, Jordan CT. Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells. Cancer Cell. 2018 Oct 8;34(4):659-673.e6. PubMed PMID: 30270124
Stanislawski MA, Lozupone CA, Wagner BD, Eggesbø M, Sontag MK, Nusbacher NM, Martinez M, Dabelea D. Gut microbiota in adolescents and the association with fatty liver: the EPOCH study. Pediatr Res. 2018 Aug;84(2):219-227. PubMed PMID: 29538359
Kang DW, Ilhan ZE, Isern NG, Hoyt DW, Howsmon DP, Shaffer M, Lozupone CA, Hahn J, Adams JB, Krajmalnik-Brown R. Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders. Anaerobe. 2018 Feb;49:121-131. PubMed PMID: 29274915
Kang DW, Ilhan ZE, Isern NG, Hoyt DW, Howsmon DP, Shaffer M, Lozupone CA, Hahn J, Adams JB, Krajmalnik-Brown R. Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders. Anaerobe. 2017 Dec 21. [Epub ahead of print] PubMed PMID: 29274915
Narrowe A, Miller CS, Lozupone C. Microbial Biodiversity: Straight from the Dolphin's Mouth. Curr Biol. 2017 Dec 18;27(24):R1307-R1309. PubMed PMID: 29257962
Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, Knight R, Stigum H, Eggesbø M. Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. PLoS One. 2017;12(10):e0184336. PubMed PMID: 29069100
Reddivari L, Veeramachaneni DNR, Walters WA, Lozupone C, Palmer J, Hewage MKK, Bhatnagar R, Amir A, Kennett MJ, Knight R, Vanamala JKP. Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. mSystems. 2017 Sep-Oct;2(5). PubMed PMID: 29034330
Liu C, Frank DN, Horch M, Chau S, Ir D, Horch EA, Tretina K, van Besien K, Lozupone CA, Nguyen VH. Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors. Bone Marrow Transplant. 2017 Dec;52(12):1643-1650. PubMed PMID: 28967895
Stanislawski MA, Dabelea D, Wagner BD, Sontag MK, Lozupone CA, Eggesbø M. Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants. Microbiome. 2017 Sep 4;5(1):113. PubMed PMID: 28870230
Shaffer M, Armstrong AJS, Phelan VV, Reisdorph N, Lozupone CA. Microbiome and metabolome data integration provides insight into health and disease. Transl Res. 2017 Nov;189:51-64. PubMed PMID: 28764956
Yang IV, Lozupone CA, Schwartz DA. The environment, epigenome, and asthma. J Allergy Clin Immunol. 2017 Jul;140(1):14-23. PubMed PMID: 28673400
Pinto-Cardoso S, Lozupone C, Briceño O, Alva-Hernández S, Téllez N, Adriana A, Murakami-Ogasawara A, Reyes-Terán G. Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens. Sci Rep. 2017 Mar 6;7:43741. PubMed PMID: 28262770
Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017 Mar 3;5(1):27. PubMed PMID: 28253908
Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016 Feb 23. [Epub ahead of print] PubMed PMID: 26905627
Li SX, Armstrong A, Neff CP, Shaffer M, Lozupone CA, Palmer BE. Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy. Clin Pharmacol Ther. 2016 Jun;99(6):600-11. PubMed PMID: 26940481
Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016 Jul;10(7):1669-81. PubMed PMID: 26905627
Lozupone CA, Knight R. The UniFrac significance test is sensitive to tree topology. BMC Bioinformatics. 2015 Jul 7;16:211. PubMed PMID: 26150095
Krajmalnik-Brown R, Lozupone C, Kang DW, Adams JB. Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease. Microb Ecol Health Dis. 2015;26:26914. PubMed PMID: 25769266
McDonald D, Hornig M, Lozupone C, Debelius J, Gilbert JA, Knight R. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microb Ecol Health Dis. 2015;26:26555. PubMed PMID: 25758371
Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM. Muc5b is required for airway defence. Nature. 2014 Jan 16;505(7483):412-6. PubMed PMID: 24317696
Lozupone CA, Rhodes ME, Neff CP, Fontenot AP, Campbell TB, Palmer BE. HIV-induced alteration in gut microbiota: driving factors, consequences, and effects of antiretroviral therapy. Gut Microbes. 2014 Jul 1;5(4):562-70. PubMed PMID: 25078714
Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM. Muc5b is required for airway defence. Nature. 2014 Jan 16;505(7483):412-6. PubMed PMID: 24317696
Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, Knight R, Fontenot AP, Palmer BE. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe. 2013 Sep 11;14(3):329-39. PubMed PMID: 24034618
Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R. Meta-analyses of studies of the human microbiota. Genome Res. 2013 Oct;23(10):1704-14. PubMed PMID: 23861384
Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013 Apr 16;2:e00458. PubMed PMID: 23599893
Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP, Lung HIV Microbiome Project. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013 May 15;187(10):1110-7. PubMed PMID: 23392441