Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt

Authors: Herman, Chloe, Bolyen, Evan, Simard, Anthony, Gehret, Liz, Caporaso, J. Gregory

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2411.17901

Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis

Authors: Meilander, Jeff, Herman, Chloe, Manley, Andrew, Augustine, Georgia, Birdsell, Dawn, Bolyen, Evan, Celona, Kimberly R., Coffey, Hayden, Cocking, Jill, Donoghue, Teddy, Draves, Alexis, Erickson, Daryn, Foley, Marissa, Gehret, Liz, Hagen, Johannah, Hepp, Crystal, Ingram, Parker, John, David, Kadar, Katarina, Keim, Paul, Lloyd, Victoria, Osterink, Christina, Queeney, Victoria, Ramirez, Diego, Romero, Antonio, Ruby, Megan C., Sahl, Jason W., Soloway, Sydni, Stone, Nathan E., Trottier, Shannon, Van Orden, Kaleb, Painter, Alexis, Wallace, Sam, Wilcox, Larissa, Wood, Colin V., Yancey, Jaiden, Caporaso, J. Gregory

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2411.04148

Facilitating bootstrapped and rarefaction-based microbiome diversity analysis with q2-boots

Authors: Raspet, Isaiah, Gehret, Elizabeth, Herman, Chloe, Meilander, Jeff, Manley, Andrew, Simard, Anthony, Bolyen, Evan, Caporaso, J. Gregory

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2408.05420

Facilitating Bioinformatics Reproducibility

Authors: Keefe, Christopher R., Dillon, Matthew R., Herman, Chloe, Jewell, Mary, Wood, Colin V., Bolyen, Evan, Caporaso, J. Gregory

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2305.11198

PepSIRF + QIIME 2: software tools for automated, reproducible analysis of highly-multiplexed serology data

Authors: Brown, Annabelle M., Bolyen, Evan, Raspet, Isaiah, Altin, John A., Ladner, Jason T.

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2207.11509

Domestic canines do not display evidence of gut microbial dysbiosis in the presence of Clostridioides (Clostridium) difficile, despite cellular susceptibility to its toxins

Authors: Stone, Nathan E., Nunnally, Amalee E., Jimenez, Victor, Jr., Cope, Emily K., Sahl, Jason W., Sheridan, Krystal, Hornstra, Heidie M., Vinocur, Jacob, Settles, Erik W., Headley, Kyle C., Williamson, Charles H.D., Rideout, Jai Ram, Bolyen, Evan, Caporaso, J. Gregory, Terriquez, Joel, Monroy, Fernando P., Busch, Joseph D., Keim, Paul, Wagner, David M.

Source: In Anaerobe August 2019 58:53-72

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

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

Source: Nature biotechnology. 37(8):852-857

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100189364707.0x000001&indx=1&recIds=ETOCvdc_100189364707.0x000001

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Authors: Bokulich, Nicholas, Kaehler, Benjamin, Rideout, Jai, Dillon, Matthew, Bolyen, Evan, Knight, Rob, Huttley, Gavin, Gregory Caporaso, J.

Source: Microbiome. 6(1):1-17

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181180339.0x000001&indx=1&recIds=ETOCvdc_100181180339.0x000001

A longitudinal study of the unique gut microbiota of 3xTg‐AD mice modeling key AD pathologies

Authors: Borsom, Emily M, Keefe, Christopher R, Hirsch, Allyson H, Orsini, Gabrielle M, Conn, Kathryn A, Jaramillo, Sierra A, Testo, George, Avila, Melanie Palma, Bolyen, Evan K, Dillon, Matthew R, Lee, Keehoon, Caporaso, J. Gregory, Cope, Emily K

Source: Alzheimer's & dementia. 17(7)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100138846357.0x000001&indx=1&recIds=ETOCvdc_100138846357.0x000001

Influence of fecal microbiota transplantation on gut microbiota composition and neuroinflammation of 3xTg‐AD mice

Authors: Cope, Emily K, Borsom, Emily M, Bolyen, Evan K, Jaramillo, Sierra A, Conn, Kathryn A, Dillon, Matthew R, Orsini, Gabrielle M, Hirsch, Allyson H, Lee, Keehoon, Caporaso, J. Gregory

Source: Alzheimer's & dementia. 17(7)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100138846361.0x000001&indx=1&recIds=ETOCvdc_100138846361.0x000001

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Authors: Dillon, Matthew R.¹ (AUTHOR), Bolyen, Evan¹ (AUTHOR), Adamov, Anja² (AUTHOR), Belk, Aeriel³ (AUTHOR), Borsom, Emily¹ (AUTHOR), Burcham, Zachary³ (AUTHOR), Debelius, Justine W.⁴ (AUTHOR), Deel, Heather³ (AUTHOR), Emmons, Alex³ (AUTHOR), Estaki, Mehrbod⁵ (AUTHOR), Herman, Chloe¹ (AUTHOR), Keefe, Christopher R.¹ (AUTHOR), Morton, Jamie T.⁶ (AUTHOR), Oliveira, Renato R. M.⁷ (AUTHOR), Sanchez, Andrew¹ (AUTHOR), Simard, Anthony¹ (AUTHOR), Vázquez-Baeza, Yoshiki⁸ (AUTHOR), Ziemski, Michal² (AUTHOR), Miwa, Hazuki E.⁹ (AUTHOR), Kerere, Terry A.⁹ (AUTHOR)

Source: PLoS Computational Biology. 6/24/2021, Vol. 17 Issue 6, p1-18. 18p. 1 Diagram, 2 Charts, 1 Map.

Subject Terms: *COVID-19 pandemic, *COVID-19, *COMPUTER workstation clusters, *BIOINFORMATICS, *PANDEMICS

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay.

Authors: Keefe, Christopher R., Dillon, Matthew R., Gehret, Elizabeth, Herman, Chloe, Jewell, Mary, Wood, Colin V., Bolyen, Evan, Caporaso, J. Gregory

Source: PLoS Computational Biology; 11/27/2023, Vol. 19 Issue 11, p1-9, 9p

Subject Terms: BIOINFORMATICS, BIOINFORMATICS software, BIG data, SOFTWARE development tools

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Authors: Estaki, Mehrbod, Jiang, Lingjing, Bokulich, Nicholas A., McDonald, Daniel, González, Antonio, Kosciolek, Tomasz, Martino, Cameron, Zhu, Qiyun, Birmingham, Amanda, Vázquez‐Baeza, Yoshiki, Dillon, Matthew R., Bolyen, Evan, Caporaso, J. Gregory, Knight, Rob

Source: Current Protocols in Bioinformatics. 70(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100107447678.0x000001&indx=1&recIds=ETOCvdc_100107447678.0x000001

Qiita: rapid, web-enabled microbiome meta-analysis

Authors: Gonzalez, Antonio, Navas-Molina, Jose, Kosciolek, Tomasz, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Ackermann, Gail, DeReus, Jeff, Janssen, Stefan, Swafford, Austin, Orchanian, Stephanie, Sanders, Jon, Shorenstein, Joshua, Holste, Hannes, Petrus, Semar, Robbins-Pianka, Adam, Brislawn, Colin, Wang, Mingxun, Rideout, Jai, Bolyen, Evan, Dillon, Matthew, Caporaso, J., Dorrestein, Pieter, Knight, Rob

Source: Nature methods. 15(10):796-798

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100184092410.0x000001&indx=1&recIds=ETOCvdc_100184092410.0x000001

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

Authors: Bolyen, Evan [and others]

Source: Nature biotechnology. 37(9):1091-1091

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190549651.0x000001&indx=1&recIds=ETOCvdc_100190549651.0x000001

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q²-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data.

Authors: Bokulich, Nicholas A., Dillon, Matthew R., Yilong Zhang, Rideout, Jai Ram, Bolyen, Evan, Huilin Li, Albert, Paul S., Caporaso, J. Gregory

Source: MSystems; Nov/Dec2018, Vol. 3 Issue 6, p1-9, 9p

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