Graphle: Interactive exploration of large, dense graphs by Huttenhower Curtis, Mehmood Sajid O, Troyanskaya Olga G

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Bioinformatics for the human microbiome project by Gevers, Dirk, Pop, Mihai, Schloss, Patrick D., Huttenhower, Curtis

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GOLEM: an interactive graph-based gene-ontology navigation and analysis tool by Huttenhower Curtis, Hibbs Matthew A, Sealfon Rachel SG, Myers Chad L, Troyanskaya Olga G

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Metagenomic biomarker discovery and explanation by Segata, Nicola, Izard, Jacques, Waldron, Levi, Gevers, Dirk, Miropolsky, Larisa, Garrett, Wendy S., Huttenhower, Curtis

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Microbial Co-occurrence Relationships in the Human Microbiome by Faust, Karoline, Sathirapongsasuti, Jarupon, Izard, Jacques, Segata, Nicola, Gevers, Dirk, Raes, Jeroen, Huttenhower, Curtis

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Host genetic variation and its microbiome interactions within the Human Microbiome Project by Kolde, Raivo, Rahnavard, Gholamali, Vlamakis, Hera, Stevens, Christine, Huttenhower, Curtis, Franzosa, Eric A., Hall, Andrew Brantley, Daly, Mark J., Xavier, Ramnik Joseph

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Genomics in 2011: challenges and opportunities by Berger, Bonnie, Adams, David J., Harismendy, Olivier, Huttenhower, Curtis, Liu, X. Shirley, Myers, Chad L., Oshlack, Alicia, Rinn, John L., Walhout, Albertha J. M.

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Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite by Park, Sun-Yang, Rao, Chitong, Coyte, Katharine Z, Kuziel, Gavin A, Zhang, Yancong, Huang, Wentao, Franzosa, Eric A, Weng, Jing-Ke, Huttenhower, Curtis, Rakoff-Nahoum, Seth

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Nearest Neighbor Networks: clustering expression data based on gene neighborhoods by Olszewski Kellen L, Myers Chad L, Sahi Sauhard, Landis Jessica N, Flamholz Avi I, Huttenhower Curtis, Hibbs Matthew A, Siemers Nathan O, Troyanskaya Olga G, Coller Hilary A

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Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability by Yassour, Moran, Vatanen, Tommi, Siljander, Heli, Hämäläinen, Anu-Maaria, Härkönen, Taina, Ryhänen, Samppa J., Franzosa, Eric A., Vlamakis, Hera, Huttenhower, Curtis, Gevers, Dirk, Knip, Mikael, Lander, Eric Steven, Xavier, Ramnik Joseph

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Delivery Mode Affects Stability of Early Infant Gut Microbiota by Mitchell, Caroline M, Mazzoni, Chiara, Hogstrom, Larson, Bryant, Allison, Bergerat, Agnes, Cher, Avital, Pochan, Shawna, Herman, Penelope, Carrigan, Maureen, Sharp, Karen, Huttenhower, Curtis, Lander, Eric S, Vlamakis, Hera, Xavier, Ramnik J, Yassour, Moran

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Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease by Bhosle, Amrisha, Bae, Sena, Zhang, Yancong, Chun, Eunyoung, Avila-Pacheco, Julian, Geistlinger, Ludwig, Pishchany, Gleb, Glickman, Jonathan N, Michaud, Monia, Waldron, Levi, Clish, Clary B, Xavier, Ramnik J, Vlamakis, Hera, Franzosa, Eric A, Garrett, Wendy S, Huttenhower, Curtis

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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome by Abubucker, Sahar, Segata, Nicola, Goll, Johannes, Schubert, Alyxandria M., Izard, Jacques, Cantarel, Brandi L., Rodriguez-Mueller, Beltran, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T., Methe, Barbara, Schloss, Patrick D., Gevers, Dirk, Mitreva, Makedonka, Huttenhower, Curtis

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Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes by Yassour, Moran, Lim, Mi Young, Yun, Hyun Sun, Tickle, Timothy L., Sung, Joohon, Song, Yun-Mi, Lee, Kayoung, Franzosa, Eric A., Morgan, Xochitl C., Gevers, Dirk, Xavier, Ramnik J., Birren, Bruce W., Ko, GwangPyo, Huttenhower, Curtis, Lander, Eric Steven

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Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life by Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M., Ilonen, Jorma, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Segata, Nicola, Vlamakis, Hera, Lander, Eric Steven, Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.

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A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients by Hall, Andrew Brantley, Yassour, Moran, Sauk, Jenny, Garner, Ashley, Jiang, Xiaofang, Arthur, Timothy, Vatanen, Tommi, Fornelos, Nadine, Wilson, Robin, Bertha, Madeline, Cohen, Melissa, Garber, John, Khalili, Hamed, Gevers, Dirk, Ananthakrishnan, Ashwin N., Kugathasan, Subra, Lander, Eric S., Vlamakis, Hera, Xavier, Ramnik J., Huttenhower, Curtis, Lagoudas, Georgia K, Blainey, Paul C

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Meeting report for the 1st skin microbiota workshop, Boulder, CO October 15-16 2012 by 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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Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine by Geller, Leore T., Barzily-Rokni, Michal, Danino, Tal, Jonas, Oliver H., Shental, Noam, Nejman, Deborah, Gavert, Nancy, Zwang, Yaara, Cooper, Zachary A., Shee, Kevin, Thaiss, Christoph A., Reuben, Alexandre, Livny, Jonathan, Avraham, Roi, Frederick, Dennie T., Ligorio, Matteo, Chatman, Kelly, Johnston, Stephen E., Mosher, Carrie M., Brandis, Alexander, Fuks, Garold, Gurbatri, Candice, Gopalakrishnan, Vancheswaran, Kim, Michael, Hurd, Mark W., Katz, Matthew, Fleming, Jason, Maitra, Anirban, Smith, David A., Skalak, Matthew T., Bu, Jeffrey, Michaud, Monia, Trauger, Sunia A., Barshack, Iris, Golan, Talia, Sandbank, Judith, Flaherty, Keith T., Mandinova, Anna, Garrett, Wendy S., Thayer, Sarah P., Ferrone, Cristina R., Huttenhower, Curtis, Bhatia, Sangeeta N., Gevers, Dirk, Wargo, Jennifer A., Golub, Todd R., Straussman, Ravid

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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

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