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Catherine A. Lozupone

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-MED

    Collapse Research 
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    K01DK090285     (LOZUPONE, CATHERINE)Feb 1, 2011 - Nov 30, 2015
    NIH
    The Role of Syntrophic Bacteria in Methanogenic Metabolism in the Human Gut
    Role: Principal Investigator

    R01DK104047     (LOZUPONE, CATHERINE)Sep 15, 2014 - Aug 31, 2020
    NIH
    Factors mediating gut microbiota dysbiosis and metabolic disease in HIV patients
    Role: Principal Investigator

    R01DK108366     (PALMER, BRENT E)Sep 21, 2015 - Aug 31, 2021
    NIH
    Diet/gut Microbiome Interaction Influence Inflammatory Disease in HIV Patients
    Role: Co-Principal Investigator

    R01HL138639     (PALMER, BRENT E)Sep 1, 2017 - May 31, 2021
    NIH
    HIV-associated gut microbiome affects lung immunity and pneumococcal immune response
    Role: Co-Principal Investigator

    R21CA245432     (MCCARTER, MARTIN)Mar 1, 2020 - Jan 31, 2022
    NIH
    Improving immunotherapies to melanoma through modulation of MAIT cell activation by the microbiome
    Role: Co-Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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). PMID: 34006628.
      View in: PubMed
    2. 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 07; 11(1):7666. PMID: 33828220.
      View in: PubMed
    3. 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 06; 6(2). PMID: 33824197.
      View in: PubMed
    4. 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. PMID: 33811477.
      View in: PubMed
    5. 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. PMID: 33607938.
      View in: PubMed
    6. Arnolds KL, Martin CG, Lozupone CA. Blood type and the microbiome- untangling a complex relationship with lessons from pathogens. Curr Opin Microbiol. 2020 08; 56:59-66. PMID: 32663769.
      View in: PubMed
    7. Armstrong AJS, Shaffer M, Nusbacher NM, Griesmer C, Fiorillo S, Schneider JM, Neff CP, Li SX, Fontenot AP, Campbell T, Palmer BE, Lozupone CA. Correction to: An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men. Microbiome. 2020 04 06; 8(1):50. PMID: 32252810.
      View in: PubMed
    8. 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 04 01; 66(2):178-186. PMID: 31325361.
      View in: PubMed
    9. 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 06; 14(6):1359-1368. PMID: 32076128.
      View in: PubMed
    10. 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 05 03; 11(3):610-619. PMID: 32036739.
      View in: PubMed
    11. 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 12 20; 64(1). PMID: 31685472.
      View in: PubMed
    12. 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. PMID: 31779604.
      View in: PubMed
    13. 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, 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. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep; 37(9):1091. PMID: 31399723.
      View in: PubMed
    14. 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. PMID: 31429723.
      View in: PubMed
    15. 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, 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 08; 37(8):852-857. PMID: 31341288.
      View in: PubMed
    16. Stanislawski MA, Dabelea D, Lange LA, Wagner BD, Lozupone CA. Gut microbiota phenotypes of obesity. NPJ Biofilms Microbiomes. 2019; 5(1):18. PMID: 31285833.
      View in: PubMed
    17. 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 04; 15(4):e1007611. PMID: 30947289.
      View in: PubMed
    18. Kriss M, Verna EC, Rosen HR, Lozupone CA. Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes. Transplantation. 2019 04; 103(4):668-678. PMID: 30507741.
      View in: PubMed
    19. 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 02 12; 10(1). PMID: 30755504.
      View in: PubMed
    20. Siebert JC, Görg C, Palmer B, Lozupone C. Visualizing microbiome-immune system interplay. Immunotherapy. 2019 02; 11(2):63-67. PMID: 30730269.
      View in: PubMed
    21. 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 11 05; 6(1):198. PMID: 30396369.
      View in: PubMed
    22. 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 10 23; 9(5). PMID: 30352933.
      View in: PubMed
    23. 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 10 08; 34(4):659-673.e6. PMID: 30270124.
      View in: PubMed
    24. Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Curr Opin Microbiol. 2018 08; 44:34-40. PMID: 30036705.
      View in: PubMed
    25. 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 08; 84(2):219-227. PMID: 29538359.
      View in: PubMed
    26. 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. PMID: 29650491.
      View in: PubMed
    27. Lozupone CA. Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease. mSystems. 2018 Mar-Apr; 3(2). PMID: 29556546.
      View in: PubMed
    28. Shaffer M, Lozupone C. Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands. mSystems. 2018 Jan-Feb; 3(1). PMID: 29359197.
      View in: PubMed
    29. 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. PMID: 29274915.
      View in: PubMed
    30. Narrowe A, Miller CS, Lozupone C. Microbial Biodiversity: Straight from the Dolphin's Mouth. Curr Biol. 2017 12 18; 27(24):R1307-R1309. PMID: 29257962.
      View in: PubMed
    31. 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. PMID: 29069100.
      View in: PubMed
    32. 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). PMID: 29034330.
      View in: PubMed
    33. 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. PMID: 28967895.
      View in: PubMed
    34. 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 09 04; 5(1):113. PMID: 28870230.
      View in: PubMed
    35. Shaffer M, Armstrong AJS, Phelan VV, Reisdorph N, Lozupone CA. Microbiome and metabolome data integration provides insight into health and disease. Transl Res. 2017 11; 189:51-64. PMID: 28764956.
      View in: PubMed
    36. Yang IV, Lozupone CA, Schwartz DA. The environment, epigenome, and asthma. J Allergy Clin Immunol. 2017 Jul; 140(1):14-23. PMID: 28673400.
      View in: PubMed
    37. 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 03 06; 7:43741. PMID: 28262770.
      View in: PubMed
    38. 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 03 03; 5(1):27. PMID: 28253908.
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    39. 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 09; 89(3):389-395. PMID: 27698623.
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    40. 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. . 2016 Oct 12; 20(4):535-547. PMID: 27693306.
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    41. 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. PMID: 26940481.
      View in: PubMed
    42. Lozupone CA. Getting to know the microbiome. Nat Microbiol. 2016 03 14; 1:16030. PMID: 27572447.
      View in: PubMed
    43. Palmer BE, Li SX, Lozupone CA. The HIV-Associated Enteric Microbiome Has Gone Viral. . 2016 Mar 09; 19(3):270-2. PMID: 26962936.
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    44. 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 07; 10(7):1669-81. PMID: 26905627.
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    45. Lozupone CA, Knight R. The UniFrac significance test is sensitive to tree topology. BMC Bioinformatics. 2015 Jul 07; 16:211. PMID: 26150095.
      View in: PubMed
    46. 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. PMID: 25769266.
      View in: PubMed
    47. 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. PMID: 25758371.
      View in: PubMed
    48. 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 01; 5(4):562-70. PMID: 25078714.
      View in: PubMed
    49. 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. PMID: 24317696.
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    50. 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. . 2013 Sep 11; 14(3):329-39. PMID: 24034618.
      View in: PubMed
    51. 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. PMID: 23861384.
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    52. 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. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013 May 15; 187(10):1110-7. PMID: 23392441.
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    53. 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. PMID: 23599893.
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    54. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012 Sep 13; 489(7415):220-30. PMID: 22972295.
      View in: PubMed
    55. Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res. 2012 Oct; 22(10):1974-84. PMID: 22665442.
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    56. Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R. RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA. 2012 Jul; 18(7):1319-27. PMID: 22645380.
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    57. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012 May 09; 486(7402):222-7. PMID: 22699611.
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    58. Sullam KE, Essinger SD, Lozupone CA, O'Connor MP, Rosen GL, Knight R, Kilham SS, Russell JA. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol. 2012 Jul; 21(13):3363-78. PMID: 22486918.
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    59. Almodovar S, Knight R, Allshouse AA, Roemer S, Lozupone C, McDonald D, Widmann J, Voelkel NF, Shelton RJ, Suarez EB, Hammer KW, Goujard C, Petrosillo N, Simonneau G, Hsue PY, Humbert M, Flores SC. Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension. AIDS Res Hum Retroviruses. 2012 Jun; 28(6):607-18. PMID: 22066947.
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    60. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med. 2011 Oct 26; 3(106):106ra106. PMID: 22030749.
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    61. Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R. Human-associated microbial signatures: examining their predictive value. . 2011 Oct 20; 10(4):292-6. PMID: 22018228.
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    62. Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends Microbiol. 2011 Oct; 19(10):472-82. PMID: 21872475.
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    63. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 May; 29(5):415-20. PMID: 21552244.
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    64. Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI. Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A. 2011 Mar 15; 108 Suppl 1:4599-606. PMID: 21317366.
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    65. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R. Global patterns in the biogeography of bacterial taxa. Environ Microbiol. 2011 Jan; 13(1):135-144. PMID: 21199253.
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    66. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. The mind-body-microbial continuum. Dialogues Clin Neurosci. 2011; 13(1):55-62. PMID: 21485746.
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    67. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011 Feb; 5(2):169-72. PMID: 20827291.
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    68. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods. 2010 Oct; 7(10):813-9. PMID: 20818378.
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    69. King AJ, Freeman KR, McCormick KF, Lynch RC, Lozupone C, Knight R, Schmidt SK. Biogeography and habitat modelling of high-alpine bacteria. Nat Commun. 2010 Aug 10; 1:53. PMID: 20975720.
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    70. Widmann J, Harris JK, Lozupone C, Wolfson A, Knight R. Stable tRNA-based phylogenies using only 76 nucleotides. RNA. 2010 Aug; 16(8):1469-77. PMID: 20558546.
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    71. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011 Mar 15; 108 Suppl 1:4516-22. PMID: 20534432.
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    72. Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010 Oct; 4(10):1340-51. PMID: 20445636.
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    73. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May; 7(5):335-6. PMID: 20383131.
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    74. Zaneveld JR, Lozupone C, Gordon JI, Knight R. Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Nucleic Acids Res. 2010 Jul; 38(12):3869-79. PMID: 20197316.
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    75. Faith DP, Lozupone CA, Nipperess D, Knight R. The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework. Int J Mol Sci. 2009 Nov 03; 10(11):4723-41. PMID: 20087461.
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    76. Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. . 2009 Sep 17; 6(3):279-89. PMID: 19748469.
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    77. Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010 Jan; 4(1):17-27. PMID: 19710709.
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    78. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008 10; 6(10):776-88. PMID: 18794915.
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    79. Lozupone CA, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI, Knight R. The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A. 2008 Sep 30; 105(39):15076-81. PMID: 18806222.
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    80. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. Evolution of mammals and their gut microbes. Science. 2008 Jun 20; 320(5883):1647-51. PMID: 18497261.
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    81. Lozupone CA, Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev. 2008 Jul; 32(4):557-78. PMID: 18435746.
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    82. Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, Knight R. Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol. 2008 Feb; 12(1):109-14. PMID: 18280814.
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    83. McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog. 2008 Feb 08; 4(2):e20. PMID: 18248093.
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    84. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 2007; 35(18):e120. PMID: 17881377.
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    85. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol. 2007 Nov; 73(21):7059-66. PMID: 17827313.
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    86. D'Souza M, Fontenot AP, Mack DG, Lozupone C, Dillon S, Meditz A, Wilson CC, Connick E, Palmer BE. Programmed death 1 expression on HIV-specific CD4+ T cells is driven by viral replication and associated with T cell dysfunction. J Immunol. 2007 Aug 01; 179(3):1979-87. PMID: 17641065.
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    87. Lozupone CA, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A. 2007 Jul 03; 104(27):11436-40. PMID: 17592124.
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    88. Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 2007 Jul; 5(7):e156. PMID: 17579514.
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    89. Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007 Mar; 73(5):1576-85. PMID: 17220268.
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    90. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. PyCogent: a toolkit for making sense from sequence. Genome Biol. 2007; 8(8):R171. PMID: 17708774.
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    91. Lozupone C, Hamady M, Knight R. UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006 Aug 07; 7:371. PMID: 16893466.
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    92. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005 Dec; 71(12):8228-35. PMID: 16332807.
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    93. Legiewicz M, Lozupone C, Knight R, Yarus M. Size, constant sequences, and optimal selection. RNA. 2005 Nov; 11(11):1701-9. PMID: 16177137.
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    94. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005 Aug 02; 102(31):11070-5. PMID: 16033867.
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    95. Ardell DH, Lozupone CA, Landweber LF. Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea). Genetics. 2003 Dec; 165(4):1761-77. PMID: 14704164.
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    96. Lozupone C, Changayil S, Majerfeld I, Yarus M. Selection of the simplest RNA that binds isoleucine. RNA. 2003 Nov; 9(11):1315-22. PMID: 14561881.
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    97. Lozupone CA, Klein DA. Molecular and cultural assessment of chytrid and Spizellomyces populations in grassland soils. Mycologia. 2002 May-Jun; 94(3):411-20. PMID: 21156512.
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    98. Lozupone CA, Knight RD, Landweber LF. The molecular basis of nuclear genetic code change in ciliates. Curr Biol. 2001 Jan 23; 11(2):65-74. PMID: 11231122.
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