Search

Your search keyword '"Naimey AT"' showing total 9 results
Start Over Author "Naimey AT"
9 results on '"Naimey AT"'

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

Author

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, II, 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, and Caporaso, J. Gregory

Published
2019
Full Text
View/download PDF

2. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

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, II, 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, and Caporaso, J. Gregory

Published
2019
Full Text
View/download PDF

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

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, 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, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, 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, and Caporaso, J. Gregory

Published
2020

4. Enabling Reproducible Microbiome Science through Decentralized Provenance Tracking in QIIME 2

Author

Naimey, Ahmad Turan, Keefe, Christopher, Bolyen, Evan, Dillon, Matthew R, and J Gregory Caporaso

Abstract

We demonstrate the ways in which automatic, integrated, decentralized provenance tracking in QIIME 2, a leading microbiome bioinformatics platform, enables reproducible microbiome science. We use sample data from a recent study of arid soil microbiomes (Significant Impacts of Increasing Aridity on the Arid Soil Microbiome; Neilson et al, 2017[2]), to illustrate specific analyses that QIIME 2 supports, and to frame our discussion of the QIIME 2 platform. QIIME 2 actions yield as outputs Artifacts integrating the requested data or visualization with comprehensive data provenance that describes the computational history of that data or visualization, including all methods and parameters involved in its creation. This approach gives users, reviewers, and readers powerful tools for understanding, reproducing, and extending studies. The benefits this approach provides to both the researcher and the scientific community are significant, and provide a useful model for research software developers across disciplines.

Published
2019
Full Text
View/download PDF

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

Author

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

Subjects
Research program, Engineering, Databases, Factual, Bioinformatics, Biomedical Engineering, Library science, Bioengineering, Research initiative, Applied Microbiology and Biotechnology, Article, 03 medical and health sciences, 0302 clinical medicine, Bioinformatica, Humans, Life Science, 030304 developmental biology, National health, 0303 health sciences, business.industry, Extramural, Microbiota, Data Science, Computational Biology, Medical research, Chinese academy of sciences, 3. Good health, Molecular Medicine, Metagenomics, business, Partial support, Engineering research, Software, 030217 neurology & neurosurgery, Biotechnology
Abstract

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.

Published
2019

6. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Author

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

Subjects
Automated data, Computer science, Scalability, Microbiome, Data science, Shotgun metagenomics, Visualization
Abstract

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

Published
2018
Full Text
View/download PDF

7. Author Correction:Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)

Author

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, 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, and Caporaso, J. Gregory

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019

8. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Author

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

Published
2018
Full Text
View/download PDF

9. Comparison of histologic stains in the diagnosis of Pneumocystis carinii

Author

G L, Naimey and R B, Wuerker

Subjects
AIDS-Related Opportunistic Infections, Staining and Labeling, Pneumocystis, Pneumonia, Pneumocystis, Histological Techniques, Humans, Coloring Agents
Abstract

To evaluate commonly used histologic stains used to detect Pneumocystis, including Diff-Quik (DQ), Grocott's Gomori methenamine silver (GMS), Papanicolaou, and hematoxylin and eosin (HE).The study compared the ability of these stains to detect alveolar casts.Although there was a slightly higher average number of casts detected with DQ, the difference between this stain and GMS was not significant. Both Papanicolaou stain and HE showed significantly lower averages. Some differences in HE may be related to differences in preparation.Similar results were obtained with DQ and GMS, but DQ offered the advantage of ease of preparation, rapidity and cost-effectiveness.

Published
1995

Catalog

Books, media, physical & digital resources
See catalog results