Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K. CopeRicardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G.I. Langille, Joslynn Lee, Ruth Ley, Yong Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey V. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J.J. van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H.D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J. Gregory Caporaso

Research output: Contribution to journalLetter

64 Citations (Scopus)
Original languageEnglish (US)
Pages (from-to)852-857
Number of pages6
JournalNature Biotechnology
Volume37
Issue number8
DOIs
StatePublished - Aug 1 2019

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Microbiota

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

Cite this

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., ... Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852-857. https://doi.org/10.1038/s41587-019-0209-9

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. / Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R.; Bokulich, Nicholas A.; Abnet, Christian C.; Al-Ghalith, Gabriel A.; Alexander, Harriet; Alm, Eric J.; Arumugam, Manimozhiyan; Asnicar, Francesco; Bai, Yang; Bisanz, Jordan E.; Bittinger, Kyle; Brejnrod, Asker; Brislawn, Colin J.; Brown, C. Titus; Callahan, Benjamin J.; Caraballo-Rodríguez, Andrés Mauricio; Chase, John; Cope, Emily K.; Da Silva, Ricardo; Diener, Christian; Dorrestein, Pieter C.; Douglas, Gavin M.; Durall, Daniel M.; Duvallet, Claire; Edwardson, Christian F.; Ernst, Madeleine; Estaki, Mehrbod; Fouquier, Jennifer; Gauglitz, Julia M.; Gibbons, Sean M.; Gibson, Deanna L.; Gonzalez, Antonio; Gorlick, Kestrel; Guo, Jiarong; Hillmann, Benjamin; Holmes, Susan; Holste, Hannes; Huttenhower, Curtis; Huttley, Gavin A.; Janssen, Stefan; Jarmusch, Alan K.; Jiang, Lingjing; Kaehler, Benjamin D.; Kang, Kyo Bin; Keefe, Christopher R.; Keim, Paul; Kelley, Scott T.; Knights, Dan; Koester, Irina; Kosciolek, Tomasz; Kreps, Jorden; Langille, Morgan G.I.; Lee, Joslynn; Ley, Ruth; Liu, Yong Xin; Loftfield, Erikka; Lozupone, Catherine; Maher, Massoud; Marotz, Clarisse; Martin, Bryan D.; McDonald, Daniel; McIver, Lauren J.; Melnik, Alexey V.; Metcalf, Jessica L.; Morgan, Sydney C.; Morton, Jamie T.; Naimey, Ahmad Turan; Navas-Molina, Jose A.; Nothias, Louis Felix; Orchanian, Stephanie B.; Pearson, Talima; Peoples, Samuel L.; Petras, Daniel; Preuss, Mary Lai; Pruesse, Elmar; Rasmussen, Lasse Buur; Rivers, Adam; Robeson, Michael S.; Rosenthal, Patrick; Segata, Nicola; Shaffer, Michael; Shiffer, Arron; Sinha, Rashmi; Song, Se Jin; Spear, John R.; Swafford, Austin D.; Thompson, Luke R.; Torres, Pedro J.; Trinh, Pauline; Tripathi, Anupriya; Turnbaugh, Peter J.; Ul-Hasan, Sabah; van der Hooft, Justin J.J.; Vargas, Fernando; Vázquez-Baeza, Yoshiki; Vogtmann, Emily; von Hippel, Max; Walters, William; Wan, Yunhu; Wang, Mingxun; Warren, Jonathan; Weber, Kyle C.; Williamson, Charles H.D.; Willis, Amy D.; Xu, Zhenjiang Zech; Zaneveld, Jesse R.; Zhang, Yilong; Zhu, Qiyun; Knight, Rob; Caporaso, J. Gregory.

In: Nature Biotechnology, Vol. 37, No. 8, 01.08.2019, p. 852-857.

Research output: Contribution to journalLetter

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 2019, 'Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2', Nature Biotechnology, vol. 37, no. 8, pp. 852-857. https://doi.org/10.1038/s41587-019-0209-9
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. 2019 Aug 1;37(8):852-857. https://doi.org/10.1038/s41587-019-0209-9
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C. Titus ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Da Silva, Ricardo ; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; van der Hooft, Justin J.J. ; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; von Hippel, Max ; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J. Gregory. / Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. In: Nature Biotechnology. 2019 ; Vol. 37, No. 8. pp. 852-857.
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AU - Rideout, Jai Ram

AU - Dillon, Matthew R.

AU - Bokulich, Nicholas A.

AU - Abnet, Christian C.

AU - Al-Ghalith, Gabriel A.

AU - Alexander, Harriet

AU - Alm, Eric J.

AU - Arumugam, Manimozhiyan

AU - Asnicar, Francesco

AU - Bai, Yang

AU - Bisanz, Jordan E.

AU - Bittinger, Kyle

AU - Brejnrod, Asker

AU - Brislawn, Colin J.

AU - Brown, C. Titus

AU - Callahan, Benjamin J.

AU - Caraballo-Rodríguez, Andrés Mauricio

AU - Chase, John

AU - Cope, Emily K.

AU - Da Silva, Ricardo

AU - Diener, Christian

AU - Dorrestein, Pieter C.

AU - Douglas, Gavin M.

AU - Durall, Daniel M.

AU - Duvallet, Claire

AU - Edwardson, Christian F.

AU - Ernst, Madeleine

AU - Estaki, Mehrbod

AU - Fouquier, Jennifer

AU - Gauglitz, Julia M.

AU - Gibbons, Sean M.

AU - Gibson, Deanna L.

AU - Gonzalez, Antonio

AU - Gorlick, Kestrel

AU - Guo, Jiarong

AU - Hillmann, Benjamin

AU - Holmes, Susan

AU - Holste, Hannes

AU - Huttenhower, Curtis

AU - Huttley, Gavin A.

AU - Janssen, Stefan

AU - Jarmusch, Alan K.

AU - Jiang, Lingjing

AU - Kaehler, Benjamin D.

AU - Kang, Kyo Bin

AU - Keefe, Christopher R.

AU - Keim, Paul

AU - Kelley, Scott T.

AU - Knights, Dan

AU - Koester, Irina

AU - Kosciolek, Tomasz

AU - Kreps, Jorden

AU - Langille, Morgan G.I.

AU - Lee, Joslynn

AU - Ley, Ruth

AU - Liu, Yong Xin

AU - Loftfield, Erikka

AU - Lozupone, Catherine

AU - Maher, Massoud

AU - Marotz, Clarisse

AU - Martin, Bryan D.

AU - McDonald, Daniel

AU - McIver, Lauren J.

AU - Melnik, Alexey V.

AU - Metcalf, Jessica L.

AU - Morgan, Sydney C.

AU - Morton, Jamie T.

AU - Naimey, Ahmad Turan

AU - Navas-Molina, Jose A.

AU - Nothias, Louis Felix

AU - Orchanian, Stephanie B.

AU - Pearson, Talima

AU - Peoples, Samuel L.

AU - Petras, Daniel

AU - Preuss, Mary Lai

AU - Pruesse, Elmar

AU - Rasmussen, Lasse Buur

AU - Rivers, Adam

AU - Robeson, Michael S.

AU - Rosenthal, Patrick

AU - Segata, Nicola

AU - Shaffer, Michael

AU - Shiffer, Arron

AU - Sinha, Rashmi

AU - Song, Se Jin

AU - Spear, John R.

AU - Swafford, Austin D.

AU - Thompson, Luke R.

AU - Torres, Pedro J.

AU - Trinh, Pauline

AU - Tripathi, Anupriya

AU - Turnbaugh, Peter J.

AU - Ul-Hasan, Sabah

AU - van der Hooft, Justin J.J.

AU - Vargas, Fernando

AU - Vázquez-Baeza, Yoshiki

AU - Vogtmann, Emily

AU - von Hippel, Max

AU - Walters, William

AU - Wan, Yunhu

AU - Wang, Mingxun

AU - Warren, Jonathan

AU - Weber, Kyle C.

AU - Williamson, Charles H.D.

AU - Willis, Amy D.

AU - Xu, Zhenjiang Zech

AU - Zaneveld, Jesse R.

AU - Zhang, Yilong

AU - Zhu, Qiyun

AU - Knight, Rob

AU - Caporaso, J. Gregory

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