Turnbaugh:Publications

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Research

2013

1. David, L.A., Maurice, C.M., Carmody, R.N., Gootenberg, D.B., Button, J.E., Wolfe, B.E., Ling, A.V., Devlin, A.S., Varma, Y., Fischbach, M.A., Biddinger, S.B., Dutton, R.J., and P.J. Turnbaugh. Diet rapidly and reproducibly alters the human gut microbiome. Nature, Epub ahead of print, Nov 2013. doi:10.1038/nature12820. PDF
2. Amir, A., Zeisel, A., Zuk, O., Elgart, M., Stern, S., Shamir, O., Turnbaugh, P.J., Soen, Y., and N. Shental. High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions. Nucleic Acids Research Epub 2013 Nov 7. PDF
3. Haiser, H.J., Gootenberg, D.B., Chatman, K., Sirasani, G., Balskus, E.P., and P.J. Turnbaugh. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 341, 295-298 (2013). PDF
4. Liou, A.P., Paziuk, M., Leuvano, J.M., Machineni, S., Turnbaugh, P.J., and L.M. Kaplan. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci. Transl. Med. 5, 178ra41 (2013). PDF
5. Maurice, C.F., Haiser, H.J., and P.J. Turnbaugh. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50 (2013). URL

2012

1. Greenblum, S., Turnbaugh, P.J., and E. Borenstein. Metagenomic systems biology of the human gut microbiome. PNAS 109, 594-599 (2012). Epub 2011 Dec 19. PDF

2011

1. Reshef, D.N., Reshef, Y.A., Finucane, H.K., Grossman, S.R., McVean, G., Turnbaugh, P.J., Lander, E.S., Mitzenmacher, M., and P.C. Sabeti. Detecting novel associations in large data sets. Science 334, 1518-1524 (2011). MINE_website
2. Jumpertz, R., Le, D.S., Turnbaugh, P.J., Trinidad, C., Bogardus, C., Gordon, J.I., and J. Krakoff. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. AJCN 94, 58-65 (2011). Epub 2011 May 4. PDF
3. Patil, K.R., Haider, P., Pope, P.B., Turnbaugh, P.J., Morrison, M., Scheffer, T., and A.C. McHardy. Taxonomic metagenome sequence assignment with structured output models. Nat. Methods 8, 191-192 (2011). PDF
4. Quince, C., Lanzen, A., Davenport, R.J., and P.J. Turnbaugh. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38 (2011). PDF
5. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., Fierer, N., and R. Knight. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS 108, 4516-4522 (2011). Epub 2010 Jun 3. PDF

2010

1. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zanefeld, J., and R. Knight. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010). PDF
2. Turnbaugh, P.J., Quince, C., Faith, J.J., McHardy, A.C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R., and J.I. Gordon. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. PNAS 107, 7503-7508 (2010). PDF

2009

1. Turnbaugh, P.J., Ridaura, V.K., Faith, J.J., Rey, F.E., Knight, R., and J.I. Gordon. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14 (2009). PDF
2. Mahowald, M.A., Rey, F.E., Seedorf, H., Turnbaugh, P.J., Fulton, R.S., Wollam, A., Shah, N., Wang, C., Magrini, V., Wilson, R.K., Cantarel, B.L., Coutinho, P.M., Henrissat, B., Crock, L.W., Russell, A., Verberkmoes, N.C., Hettich, R., and J.I. Gordon. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. PNAS 106, 5859-5864 (2009). Epub 2009 Mar 24. PDF
3. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C., Knight, R., and J.I. Gordon. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009). Epub 2008 Nov 30. PDF

2008

1. Ley, R.E.,Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., and J.I. Gordon. Evolution of mammals and their gut microbes. Science 320, 1647-1651 (2008). PDF
2. Turnbaugh, P.J., Backhed, F., Fulton, L., and J.I. Gordon. Diet-induced obesity in linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3, 213-223 (2008). URL

2006

1. Turnbaugh, P.J., Ley, R.E., Mahowald, M., Magrini, V., Mardis, E.R., and J.I. Gordon. An obesity-associated microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006). PDF
2. Ley, R.E., Turnbaugh, P.J., Klein, S., and J.I. Gordon. Human gut microbes associated with obesity. Nature 444, 1022-1023 (2006). PDF

2005

1. Gill, S.R., Pop, M., DeBoy, R.T., Eckburg, P., Turnbaugh, P.J., Samuel, B., Gordon, J.I., Relman, D., Fraser-Ligett, C.M., and K.E. Nelson. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006). PDF
2. Gertz, J., Riles, L., Turnbaugh, P., Ho, S., and B.A. Cohen. Discovery, Validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. Genome Research 15, 1145-1152 (2005). PDF
3. Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C., Knight, R. and J. I. Gordon. Obesity alters gut microbial ecology. PNAS 102, 11070-11075 (2005). PDF

Reviews, Commentaries, and Book Chapters

2014

1. Haiser, H.J., Seim, K.L., Balskus, E.P. and P.J. Turnbaugh. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes 5, 1-6 (2014). PDF
2. Ursell, L.K., Haiser, H.J., Treuren, W.V., Garg, N., Reddivari, L., Vanamala, J., Dorresttein, P.C., Turnbaugh, P.J. and R. Knight. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology, Epub ahead of print (2014). PDF

2013

1. Maurice, C.F. and P.J. Turnbaugh. Quantifying and identifying the active and damaged subsets of indigenous microbial communities. Methods Enzymol 531, 91-107 (2013). URL
2. Devkota, S. and P.J. Turnbaugh. An acidic link. Nature 499, 37-38 (2013). PDF
3. Maurice, C.F. and P.J. Turnbaugh. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. FEMS Micro. Rev. 37, 830-848 (2013). PDF
4. Brown, J., deVos, W.M., DiStefano, P.S., Dore, J., Huttenhower, C., Knight, R., Lawley, T.D., Raes, J. and P. Turnbaugh. Translating the human microbiome. Nature Biotech 31, 304-308 (2013). PDF

2012

1. Liou, A.P. and P.J. Turnbaugh. Antibiotic exposure promotes fat gain. Cell Metabolism 16, 408-410 (2012). URL
2. Carmody, R.N. and P.J. Turnbaugh. Gut microbes make for fattier fish. Cell Host Microbe 12, 259-261 (2012). URL
3. Haiser, H.J. and P.J. Turnbaugh. Developing a metagenomic view of xenobiotic metabolism. Pharm. Res., Epub ahead of print. URL
4. Dutton, R.J. and P.J Turnbaugh. Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care 15, 448-454 (2012). Download here
5. P.J. Turnbaugh. Fat, bile and gut microbes. Nature 487, 47–48 (2012). PDF
6. Haiser, H.J. and P.J. Turnbaugh. Is it time for a metagenomic basis of therapeutics? Science 336, 1253-1255 (2012). PDF

2011

1. Babayan, S.A., Allen, J.E., Bradley, J.E., Geuking, M.B., Graham, A.L., Grencis, R.K., Kaufman, J., McCoy, K.D., Paterson, S., Smith, K.G.C., Turnbaugh, P.J., Viney, M.E., Maizels, R.M. and A.B. Petersen. Wild immunology: converging on the ‘real world’. Annals NY Acad. Sci., 1236, 17-29 (2011). PDF
2. Turnbaugh, P.J. and A. Stintzi. Human health and disease in a microbial world. Front. Microbio. 2:190. doi: 10.3389/fmicb.2011.00190 (2011). PDF
3. Swanson, K.S., Suchodolski, J.S., and P.J. Turnbaugh. Companion animals symposium: microbes and health. J. Animal Sci., 5, 1496-1497 (2011). PDF
4. Gonzalez, A., Stombaugh, J., Lozupone, C., Turnbaugh, P.J., Gordon, J.I., and R. Knight. The mind-body microbial continuum. Diag. Clin. Neuro. 13, 55-62 (2011). PDF
5. Maurice, C.F. and P.J. Turnbaugh. The human microbiome: exploring and manipulating our microbial selves. In Metagenomics: Current Innovations and Future Trends. Caister Academic Press (2011). Get a copy here
6. Gootenberg, D.B. and P.J. Turnbaugh. Humanized animal models of the microbiome. J. Animal Sci. 89, 1531-1537 (2011). Epub 2010 Sep 10. PDF

2010

1. Turnbaugh, P.J., Henrissat, B., and J.I. Gordon. Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Cryst. F. 66, 1261-1264 (2010). PDF
2. Peterson, D.A. and P.J. Turnbaugh. A microbe-dependent viral key to Crohn’s box. Sci. Transl. Med. 2, 43ps39 (2010). PDF

2009

1. Turnbaugh, P.J. and J.I. Gordon. The core gut microbiome, energy balance, and obesity. J. Phys. 587, 4153-4158 (2009). Epub 2009 June 2. PDF

2008

1. Zanefeld, J., Turnbaugh, P.J., Lozupone, C., Ley, R.E., Hamady, M., Gordon, J.I., and R. Knight. Host-bacterial coevolution and the search for new drug targets. Curr. Op. Chem. Bio. 12, 1-6 (2008). URL
2. Turnbaugh, P.J. and J.I. Gordon. An invitation to the marriage of metagenomics and metabolomics. Cell 134, 708-713 (2008). URL

2007

1. Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R. & J.I. Gordon. The human microbiome project. Nature 449, 804-810 (2007). PDF