Catherine Lozupone, PhD

Department

Biomedical Informatics

Publications

O'Connor JB, Fouquier J, Neff CP, Sterrett JD, Marden T, Fiorillo S, Siebert JC, Scheinder J, Nusbacher N, Noe AT, Fennimore B, Higgins J, Campbell TB, Palmer B, Lozupone C. Agrarian Diet Improves Metabolic Health in HIV-positive Men with Prevotella-Rich Microbiomes: Results from a Randomized Trial. Res Sq. 2024 Nov 15. PubMed PMID: 39606458
Sterrett JD, Quinn KD, Doenges KA, Nusbacher NM, Levens CL, Armstrong ML, Reisdorph RM, Smith H, Saba LM, Kuhn KA, Lozupone CA, Reisdorph NA. Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice. bioRxiv. 2024 Nov 13. PubMed PMID: 39605610
Fouquier J, Stanislawski M, O'Connor J, Scadden A, Lozupone C. EXPLANA: A user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies. bioRxiv. 2024 Aug 15. PubMed PMID: 39185201
Lippincott RA, O'Connor J, Neff CP, Lozupone C, Palmer BE. Deciphering HIV-associated inflammation: microbiome's influence and experimental insights. Curr Opin HIV AIDS. 2024 Sep 1;19(5):228-233. PubMed PMID: 38884255
Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Front Microbiol. 2024;15:1351678. PubMed PMID: 38638909
Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE, Lozupone C. Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe. Microbiome. 2024 Feb 3;12(1):18. PubMed PMID: 38310301
Carneiro VL, Littlefield KM, Watson R, Palmer BE, Lozupone C. Inflammation-associated gut microbiome in postacute sequelae of SARS-CoV-2 points towards new therapeutic targets. Gut. 2024 Jan 5;73(2):376-378. PubMed PMID: 36717218
Carneiro VL, Littlefield KM, Watson R, Palmer BE, Lozupone C. Inflammation-associated gut microbiome in postacute sequelae of SARS-CoV-2 points towards new therapeutic targets. Gut. 2024 Jan 5;73(2):376-378. PubMed PMID: 36717218
Shaffer M, Thurimella K, Sterrett JD, Lozupone CA. SCNIC: Sparse correlation network investigation for compositional data. Mol Ecol Resour. 2023 Jan;23(1):312-325. PubMed PMID: 36001047
Arnolds KL, Yamada E, Neff CP, Schneider JM, Palmer BE, Lozupone CA. Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors. Microb Ecol. 2023 May;85(4):1620-1629. PubMed PMID: 35596750
Shaffer M, Thurimella K, Sterrett JD, Lozupone CA. SCNIC: Sparse correlation network investigation for compositional data. Mol Ecol Resour. 2023 Jan;23(1):312-325. PubMed PMID: 36001047
Arnolds KL, Yamada E, Neff CP, Schneider JM, Palmer BE, Lozupone CA. Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors. Microb Ecol. 2023 May;85(4):1620-1629. PubMed PMID: 35596750
Santangelo B, Hunter L, Lozupone C. Characterization of methods for mechanistic inference of the gut microbiome in disease. bioRxiv. 2023 Dec 1. PubMed PMID: 38076987
Santangelo B, Bada M, Hunter L, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. bioRxiv. 2023 Dec 4. PubMed PMID: 38106100
Shaffer M, Thurimella K, Sterrett JD, Lozupone CA. SCNIC: Sparse correlation network investigation for compositional data. Mol Ecol Resour. 2023 Jan;23(1):312-325. PubMed PMID: 36001047
Santangelo B, Bada M, Hunter L, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. bioRxiv. 2023 Dec 4. PubMed PMID: 38106100
Santangelo B, Hunter L, Lozupone C. Characterization of methods for mechanistic inference of the gut microbiome in disease. bioRxiv. 2023 Dec 1. PubMed PMID: 38076987
Lazzaro A, Colorado ASB, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert J, Campbell T, Borok M, Palmer B, Lozupone C. Antiretroviral treatment is less effective at reducing gut microbiome-associated inflammation and T cell activation in people living with HIV in rural versus urban Zimbabwe. Res Sq. 2023 Aug 31. PubMed PMID: 37693491
Kozik AJ, Holguin F, Segal LN, Chatila TA, Dixon AE, Gern JE, Lozupone C, Lukacs N, Lumeng C, Molyneaux PL, Reisdorph N, Vujkovic-Cvijin I, Togias A, Huang YJ. Microbiome, Metabolism, and Immunoregulation of Asthma: An American Thoracic Society and National Institute of Allergy and Infectious Diseases Workshop Report. Am J Respir Cell Mol Biol. 2022 Aug;67(2):155-163. PubMed PMID: 35914321
Darcy JL, Amend AS, Swift SOI, Sommers PS, Lozupone CA. specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data. Environ Microbiome. 2022 Jun 25;17(1):34. PubMed PMID: 35752802
Arnolds KL, Yamada E, Neff CP, Schneider JM, Palmer BE, Lozupone CA. Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors. Microb Ecol. 2022 May 21. [Epub ahead of print] PubMed PMID: 35596750
Hazleton KZ, Martin CG, Orlicky DJ, Arnolds KL, Nusbacher NM, Moreno-Huizar N, Armstrong M, Reisdorph N, Lozupone CA. Dietary fat promotes antibiotic-induced Clostridioides difficile mortality in mice. NPJ Biofilms Microbiomes. 2022 Apr 1;8(1):15. PubMed PMID: 35365681
Vorwald VM, Davis DM, Van Gulick RJ, Torphy RJ, Borgers JS, Klarquist J, Couts KL, Amato CM, Cogswell DT, Fujita M, Castleman MJ, Davis T, Lozupone C, Medina TM, Robinson WA, Gapin L, McCarter MD, Tobin RP. Circulating CD8( ) mucosal-associated invariant T cells correlate with improved treatment responses and overall survival in anti-PD-1-treated melanoma patients. Clin Transl Immunology. 2022;11(1):e1367. PubMed PMID: 35028137
Sherrill-Mix S, Yang M, Aldrovandi GM, Brenchley JM, Bushman FD, Collman RG, Dandekar S, Klatt NR, Lagenaur LA, Landay AL, Paredes R, Tachedjian G, Turpin JA, Serrano-Villar S, Lozupone CA, Ghosh M. A Summary of the Sixth International Workshop on Microbiome in HIV Pathogenesis, Prevention, and Treatment. AIDS Res Hum Retroviruses. 2022 Mar;38(3):173-180. PubMed PMID: 34969255
Littlefield KM, Schneider JM, Neff CP, Soesanto V, Siebert JC, Nusbacher NM, Moreno-Huizar N, Cartwright IM, Armstrong AJS, Colgen SP, Lozupone CA, Palmer BE. Elevated inflammatory fecal immune factors in men who have sex with men with HIV associate with microbiome composition and gut barrier function. Front Immunol. 2022;13:1072720. PubMed PMID: 36605218
Sherrill-Mix S, Yang M, Aldrovandi GM, Brenchley J, Bushman F, Collman R, Dandekar S, Klatt NR, Lagenaur LA, Landay A, Paredes R, Tachedjian G, Turpin JA, Serrano-Villar S, Lozupone C, Ghosh M. A summary of the sixth International Workshop on Microbiome in HIV Pathogenesis, Prevention and Treatment. AIDS Res Hum Retroviruses. 2021 Dec 30. [Epub ahead of print] PubMed PMID: 34969255
Yamada E, Martin CG, Moreno-Huizar N, Fouquier J, Neff CP, Coleman SL, Schneider JM, Huber J, Nusbacher NM, McCarter M, Campbell TB, Lozupone CA, Palmer BE. Intestinal microbial communities and Holdemanella isolated from HIV /- men who have sex with men increase frequencies of lamina propria CCR5( ) CD4( ) T cells. Gut Microbes. 2021 Jan-Dec;13(1):1997292. PubMed PMID: 34818131
Armstrong AJS, Quinn K, Fouquier J, Li SX, Schneider JM, Nusbacher NM, Doenges KA, Fiorillo S, Marden TJ, Higgins J, Reisdorph N, Campbell TB, Palmer BE, Lozupone CA. Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations. mSystems. 2021 May 18;6(3). PubMed PMID: 34006628
Abange WB, Martin C, Nanfack AJ, Yatchou LG, Nusbacher N, Nguedia CA, Kamga HG, Fokam J, Kennedy SP, Ndjolo A, Lozupone C, Nkenfou CN. Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon. Sci Rep. 2021 Apr 7;11(1):7666. PubMed PMID: 33828220
Fouquier J, Moreno Huizar N, Donnelly J, Glickman C, Kang DW, Maldonado J, Jones RA, Johnson K, Adams JB, Krajmalnik-Brown R, Lozupone C. The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change. mSystems. 2021 Apr 6;6(2). PubMed PMID: 33824197
Siebert JC, Stanislawski MA, Zaman A, Ostendorf DM, Konigsberg IR, Jambal P, Ir D, Bing K, Wayland L, Scorsone JJ, Lozupone CA, Görg C, Frank DN, Bessesen D, MacLean PS, Melanson EL, Catenacci VA, Borengasser SJ. Multiomic Predictors of Short-Term Weight Loss and Clinical Outcomes During a Behavioral-Based Weight Loss Intervention. Obesity (Silver Spring). 2021 May;29(5):859-869. PubMed PMID: 33811477
Siebert JC, Saint-Cyr M, Borengasser SJ, Wagner BD, Lozupone CA, Görg C. CANTARE: finding and visualizing network-based multi-omic predictive models. BMC Bioinformatics. 2021 Feb 19;22(1):80. PubMed PMID: 33607938
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
Shaffer M, Thurimella K, Quinn K, Doenges K, Zhang X, Bokatzian S, Reisdorph N, Lozupone CA. AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data. BMC Bioinformatics. 2019 Nov 28;20(1):614. PubMed PMID: 31779604
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, Lange LA, Wagner BD, Lozupone CA. Gut microbiota phenotypes of obesity. NPJ Biofilms Microbiomes. 2019;5:18. PubMed PMID: 31285833
Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, Shaffer M, Armstrong AJS, Severs E, Kuhn K, Neff CP, McCarter M, Campbell T, Lozupone CA, Palmer BE. Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection. PLoS Pathog. 2019 Apr;15(4):e1007611. PubMed PMID: 30947289
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
Siebert JC, Görg C, Palmer B, Lozupone C. Visualizing microbiome-immune system interplay. Immunotherapy. 2019 Feb;11(2):63-67. PubMed PMID: 30730269
Kriss M, Verna EC, Rosen HR, Lozupone CA. Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes. Transplantation. 2019 Apr;103(4):668-678. PubMed PMID: 30507741
Kriss M, Verna EC, Rosen HR, Lozupone CA. Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes. Transplantation. 2018 Nov 30. [Epub ahead of print] PubMed PMID: 30507741
Armstrong AJS, Shaffer M, Nusbacher NM, Griesmer C, Fiorillo S, Schneider JM, Preston Neff C, Li SX, Fontenot AP, Campbell T, Palmer BE, Lozupone CA. An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men. Microbiome. 2018 Nov 5;6(1):198. PubMed PMID: 30396369
Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M. Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort. MBio. 2018 Oct 23;9(5). PubMed PMID: 30352933
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
Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Curr Opin Microbiol. 2018 Aug;44:34-40. PubMed PMID: 30036705
Neff CP, Krueger O, Xiong K, Arif S, Nusbacher N, Schneider JM, Cunningham AW, Armstrong A, Li S, McCarter MD, Campbell TB, Lozupone CA, Palmer BE. Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals. EBioMedicine. 2018 Apr;30:192-202. PubMed PMID: 29650491
Lozupone CA. Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease. mSystems. 2018 Mar-Apr;3(2). PubMed PMID: 29556546
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
Shaffer M, Lozupone C. Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands. mSystems. 2018 Jan-Feb;3(1). PubMed PMID: 29359197
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
Arnolds KL, Lozupone CA. Striking a Balance with Help from our Little Friends - How the Gut Microbiota Contributes to Immune Homeostasis. Yale J Biol Med. 2016 Sep 30;89(3):389-395. PubMed PMID: 27698623
Neff CP, Rhodes ME, Arnolds KL, Collins CB, Donnelly J, Nusbacher N, Jedlicka P, Schneider JM, McCarter MD, Shaffer M, Mazmanian SK, Palmer BE, Lozupone CA. Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties. Cell Host Microbe. 2016 Oct 12;20(4):535-547. PubMed PMID: 27693306
Lozupone CA. Getting to know the microbiome. Nat Microbiol. 2016 Mar 14;1:16030. PubMed PMID: 27572447
Palmer BE, Li SX, Lozupone CA. The HIV-Associated Enteric Microbiome Has Gone Viral. Cell Host Microbe. 2016 Mar 9;19(3):270-2. PubMed PMID: 26962936
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
Leao Carneiro,V., K.M. Littlefield, R.O. Watson, B.E. Palmer, and C. Lozupone. Inflammation-associated gut microbiome in post-acute sequelae of SARS-CoV-2 points towards new therapeutic targets. In Press. Gut.
Shaffer, M. and C.A. Lozupone. The Prevalence and Source of Fecal and Oral Bacteria on Infant, Child and Adult Hands. MSystems. In Press.
Lozupone, C. Unraveling interactions between the microbiome and the host immune system to decipher mechanisms of disease. mSystems. In Press.

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Internal Medicine

Professor, Biomedical Informatics

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School of Medicine

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