UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context Autor Hamady Micah, Lozupone Catherine, Knight Rob

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Using the nucleotide substitution rate matrix to detect horizontal gene transfer Autor Betterton M D, Hamady Micah, Knight Rob

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Fast-Find: A novel computational approach to analyzing combinatorial motifs Autor Knight Rob, Peden Erin, Hamady Micah, Singh Ravinder

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Activating and inhibiting connections in biological network dynamics Autor Knight Rob, Waterbury Laura, McDonald Daniel, Betterton M D

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Pathological rate matrices: from primates to pathogens Autor Knight Rob, Easteal Simon, Yap Von, Schranz Harold W, Huttley Gavin A

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Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics Autor Huttley Gavin A, Hunter Lawrence, Easton Brett C, Smit Sandra, Caporaso J Gregory, Knight Rob

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Insights and inferences about integron evolution from genomic data Autor Martin Andrew P, Kysela Robert F, Robeson Michael S, Nemergut Diana R, Schmidt Steven K, Knight Rob

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Comparison of methods for estimating the nucleotide substitution matrix Autor Huttley Gavin A, Yap Von Bing, McDonald Daniel, Oscamou Maribeth, Lladser Manuel E, Knight Rob

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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome Autor McDonald Daniel, Clemente Jose C, Kuczynski Justin, Rideout Jai, Stombaugh Jesse, Wendel Doug, Wilke Andreas, Huse Susan, Hufnagle John, Meyer Folker, Knight Rob, Caporaso J

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Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags Autor Hwang Jennifer, Bittinger Kyle, Knight Rob, Chen Ying-Yu, Hoffmann Christian, Lewis James D, Wu Gary D, Chen Jun, Berkowsky Ronald, Nessel Lisa, Li Hongzhe, Bushman Frederic D

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Tools for the Microbiome: Nano and Beyond Autor Biteen, Julie S., Cardon, Zoe G., Chun, Miyoung, Church, George M., Dorrestein, Pieter C., Fraser, Scott E., Gilbert, Jack A., Jansson, Janet K., Knight, Rob, Miller, Jeff F., Ozcan, Aydogan, Prather, Kimberly A., Quake, Stephen R., Ruby, Edward G., Silver, Pamela A., Taha, Sharif, van den Engh, Ger, Weiss, Paul S., Wong, Gerard C. L., Wright, Aaron T., Young, Thomas D., Blainey, Paul C

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Meeting report for the 1st skin microbiota workshop, Boulder, CO October 15-16 2012 Autor Gilbert, Jack A., Ball, Madeleine, Blainey, Paul C., Blaser, Martin J., Bohannan, Brendan J. M., Bateman, Ashley, Bunge, John, Dominguez-Bello, Maria G., Epstein, Slava, Fierer, Noah, Gevers, Dirk, Grikscheit, Tracy, Hamdan, Leila J., Harvey, James, Huttenhower, Curtis, Kirkup, Benjamin, Kong, Heidi H., Lauber, Christian, Lemon, Katherine P., Lynch, Susan V., Martin, Lance, Mello, Charlene, Palma, Joseph, Parker, Roy, Petrosino, Joseph, Segre, Julia A., Vosshall, Leslie, Yi, Rui, Knight, Rob

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

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microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data Autor Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, Gomes, Paulo Wender P., Caraballo-Rodriguez, Andres M., El Abiead, Yasin, Aron, Allegra T., Gentry, Emily C., Zemlin, Jasmine, Meehan, Michael J., Avalon, Nicole E., Cichewicz, Robert H., Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia-Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte C. M., Jackrel, Sara L., Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A., Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C., Rimal, Bipin, Patterson, Andrew D., Traxler, Matthew F., Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis-Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S., Bandeira, Nuno, Gerwick, William H., Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C., Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva Dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, de León, Arturo Vera Ponce, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M., Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O'Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J., Ding, Su, Sinninghe Damsté, Jaap S., Guan, Xue Li, Cui, Jerry J., Ju, Kou-San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector H. F., Grundmann, Carlismari, Clement, Jason A., Mohimani, Hosein, Broders, Kirk, McPhail, Kerry L., Ober-Singleton, Sidnee E., Rath, Christopher M., McDonald, Daniel, Knight, Rob, Wang, Mingxun, Dorrestein, Pieter C.

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