Turnbaugh:Publications: Difference between revisions
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== Research == | == Research == | ||
<b>2013</b> | <b>2013</b> | ||
#<b>Maurice, C.F.</b>, <b>Haiser, H.J.</b>, and <b>P.J. Turnbaugh</b>. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50 (2013). [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Maurice_Cell.pdf PDF], [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Maurice_Cell_extended.pdf Extended PDF] | #<b>Maurice, C.F.</b>, <b>Haiser, H.J.</b>, and <b>P.J. Turnbaugh</b>. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50 (2013). [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Maurice_Cell.pdf PDF], [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Maurice_Cell_extended.pdf Extended PDF], [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Fischbach_CHM_preview.pdf CHM Preview] | ||
<b>2012</b> | <b>2012</b> | ||
#Greenblum, S., <b>Turnbaugh, P.J.</b>, and E. Borenstein. Metagenomic systems biology of the human gut microbiome. PNAS 109, 594-599 (2012). Epub 2011 Dec 19. [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Greenblum_PNAS2011.pdf PDF] | #Greenblum, S., <b>Turnbaugh, P.J.</b>, and E. Borenstein. Metagenomic systems biology of the human gut microbiome. PNAS 109, 594-599 (2012). Epub 2011 Dec 19. [http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Greenblum_PNAS2011.pdf PDF] |
Revision as of 08:45, 20 February 2013
the turnbaugh lab
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Research
2013
- 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). PDF, Extended PDF, CHM Preview
2012
- 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
- Reshef, D.N., Reshef, Y.A., Finucane, H.K., Grossman, S.R., McVean, G., Turnbaugh, P.J., Landers, E.S., Mitzenmacher, M., and P.C. Sabeti. Detecting novel associations in large data sets. Science 334, 1518-1524 (2011). MINE_website
- 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
- 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
- Quince, C., Lanzen, A., Davenport, R.J., and P.J. Turnbaugh. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38 (2011). PDF
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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). PDF
2006
- 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
- 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
- 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
- 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
- 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
2012
- Liou, A.P. and P.J. Turnbaugh. Antibiotic exposure promotes fat gain. Cell Metabolism 16, 408-410 (2012). PDF
- Carmody, R.N. and P.J. Turnbaugh. Gut microbes make for fattier fish. Cell Host Microbe 12, 259-261 (2012). PDF
- Haiser, H.J. and P.J. Turnbaugh. Developing a metagenomic view of xenobiotic metabolism. Pharm. Res., Epub ahead of print. PDF
- 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
- P.J. Turnbaugh. Fat, bile and gut microbes. Nature 487, 47–48 (2012). PDF
- Haiser, H.J. and P.J. Turnbaugh. Is it time for a metagenomic basis of therapeutics? Science 336, 1253-1255 (2012). PDF
2011
- 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
- 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
- Swanson, K.S., Suchodolski, J.S., and P.J. Turnbaugh. Companion animals symposium: microbes and health. J. Animal Sci., 5, 1496-1497 (2011). PDF
- 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
- 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
- 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
- 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
- Peterson, D.A. and P.J. Turnbaugh. A microbe-dependent viral key to Crohn’s box. Sci. Transl. Med. 2, 43ps39 (2010). PDF
2009
- 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
- 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). PDF
- Turnbaugh, P.J. and J.I. Gordon. An invitation to the marriage of metagenomics and metabolomics. Cell 134, 708-713 (2008). PDF
2007
- 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