Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

by Langille, Morgan GI, Zaneveld, Jesse, Caporaso, J Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A, Clemente, Jose C, Burkepile, Deron E, Vega Thurber, Rebecca L, Knight, Rob, Beiko, Robert G, Huttenhower, Curtis
Published 2013

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

by Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G, Belda-Ferre, Pedro, Al-Ghalith, Gabriel A, Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B, Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z, Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T, Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, Knight, Rob
Published 2019

Composition of human skin microbiota affects attractiveness to malaria mosquitoes.

by Verhulst, Niels O, Qiu, Yu Tong, Beijleveld, Hans, Maliepaard, Chris, Knights, Dan, Schulz, Stefan, Berg-Lyons, Donna, Lauber, Christian L, Verduijn, Willem, Haasnoot, Geert W, Mumm, Roland, Bouwmeester, Harro J, Claas, Frans HJ, Dicke, Marcel, van Loon, Joop JA, Takken, Willem, Knight, Rob, Smallegange, Renate C
Published 2011

Human gut microbiome viewed across age and geography.

by Yatsunenko, Tanya, Rey, Federico E, Manary, Mark J, Trehan, Indi, Dominguez-Bello, Maria Gloria, Contreras, Monica, Magris, Magda, Hidalgo, Glida, Baldassano, Robert N, Anokhin, Andrey P, Heath, Andrew C, Warner, Barbara, Reeder, Jens, Kuczynski, Justin, Caporaso, J Gregory, Lozupone, Catherine A, Lauber, Christian, Clemente, Jose Carlos, Knights, Dan, Knight, Rob, Gordon, Jeffrey I
Published 2012

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies

by Shields-Cutler, Robin R., Al-Ghalith, Gabe A., Yassour, Moran, Knights, Dan
Published 2018

Moving pictures of the human microbiome.

by Caporaso, J Gregory, Lauber, Christian L, Costello, Elizabeth K, Berg-Lyons, Donna, Gonzalez, Antonio, Stombaugh, Jesse, Knights, Dan, Gajer, Pawel, Ravel, Jacques, Fierer, Noah, Gordon, Jeffrey I, Knight, Rob
Published 2011

A Guide to Diet-Microbiome Study Design.

by Johnson, Abigail J, Zheng, Jack Jingyuan, Kang, Jea Woo, Saboe, Anna, Knights, Dan, Zivkovic, Angela M
Published 2020

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst

by Graham, Daniel B., Becker, Christine E., Doan, Aivi, Goel, Gautam, Villablanca, Eduardo J., Knights, Dan, Mok, Amanda, Ng, Aylwin C.Y., Doench, John G., Root, David E., Clish, Clary B., Xavier, Ramnik J.
Published 2015

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice

by Schulfer, Anjelique F., Battaglia, Thomas, Alvarez, Yelina, Bijnens, Luc, Ruiz, Victoria E., Ho, Melody, Robinson, Serina, Ward, Tonya, Cox, Laura M., Rogers, Arlin B., Knights, Dan, Sartor, R. Balfour, Blaser, Martin J.
Published 2018

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

by Langille, Morgan G. I., Zaneveld, Jesse, Caporaso, J. Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A., Clemente, Jose C., Burkepile, Deron E., Vega Thurber, Rebecca L., Knight, Rob, Beiko, Robert G., Huttenhower, Curtis
Published 2014

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

by Weingarden, Alexa, González, Antonio, Vázquez-Baeza, Yoshiki, Weiss, Sophie, Humphry, Gregory, Berg-Lyons, Donna, Knights, Dan, Unno, Tatsuya, Bobr, Aleh, Kang, Johnthomas, Khoruts, Alexander, Knight, Rob, Sadowsky, Michael J
Published 2015

Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.

by Manichanh, Chaysavanh, Eck, Anat, Varela, Encarna, Roca, Joaquim, Clemente, José C, González, Antonio, Knights, Dan, Knight, Rob, Estrella, Sandra, Hernandez, Carlos, Guyonnet, Denis, Accarino, Anna, Santos, Javier, Malagelada, Juan-R, Guarner, Francisco, Azpiroz, Fernando
Published 2014

Evaluating the Information Content of Shallow Shotgun Metagenomics.

by Hillmann, Benjamin, Al-Ghalith, Gabriel A, Shields-Cutler, Robin R, Zhu, Qiyun, Gohl, Daryl M, Beckman, Kenneth B, Knight, Rob, Knights, Dan
Published 2018

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

by 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
Published 2020

Complex host genetics influence the microbiome in inflammatory bowel disease

by Knights, Dan, Silverberg, Mark S, Weersma, Rinse K, Gevers, Dirk, Dijkstra, Gerard, Huang, Hailiang, Tyler, Andrea D, van Sommeren, Suzanne, Imhann, Floris, Stempak, Joanne M, Huang, Hu, Vangay, Pajau, Al-Ghalith, Gabriel A, Russell, Caitlin, Sauk, Jenny, Knight, Jo, Daly, Mark J, Huttenhower, Curtis, Xavier, Ramnik J
Published 2015

A Framework for Human Microbiome Research

by Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Vivien Bonazzi, J., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Deych, Elena, Dooling, David J., Dugan, Shannon P., Farmer, Candace N., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huse, Susan M., Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, R. Dwayne, Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Pamela Sankar, J., Sathirapongsasuti, Fah, Schloss, Jeffery A., Schloss, Patrick D., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., White, Owen, Huttenhower, Curtis, FitzGerald, Michael G., Martin, John C., Young, Sarah K., Anderson, Scott, Chu, Ken, Dewhirst, Floyd Everett, Ding, Yan, Dunne, Wm. Michael, Durkin, A. Scott, Edgar, Robert C., Erlich, Rachel L., Farrell, Ruth M., Goldberg, Jonathan M., Harris, Emily L., Huang, Katherine H., Izard, Jacques Georges, Knights, Dan, Lee, Sandra L., Lemon, Katherine Paige, Lennon, Niall, Liu, Bo, Liu, Yue, McDonald, Daniel, Miller, Jason R., Pearson, Matthew, Schmidt, Thomas M., Smillie, Chris Scott, Sykes, Sean M., Wang, Lu, White, James R., Ye, Liang, Zhang, Lan, Zucker, Jeremy Daniel Hofeld, Wilson, Richard K.
Published 2013