Structure-based protein function prediction using graph convolutional networks von Gligorijević, Vladimir, Renfrew, P. Douglas, Kosciolek, Tomasz, Leman, Julia Koehler, Berenberg, Daniel, Vatanen, Tommi, Chandler, Chris, Taylor, Bryn C., Fisk, Ian M., Vlamakis, Hera, Xavier, Ramnik J., Knight, Rob, Cho, Kyunghyun, Bonneau, Richard

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An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data von Cheng, Lu, Ramchandran, Siddharth, Vatanen, Tommi, Lietzén, Niina, Lahesmaa, Riitta, Vehtari, Aki, Lähdesmäki, Harri

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The Super-Donor Phenomenon in Fecal Microbiota Transplantation von Wilson, Brooke C, Vatanen, Tommi, Cutfield, Wayne S, O'Sullivan, Justin M

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Experimental design and quantitative analysis of microbial community multiomics von Mallick, Himel, Ma, Siyuan, Franzosa, Eric A, Vatanen, Tommi, Morgan, Xochitl C, Huttenhower, Curtis

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Temporal development of the gut microbiome in early childhood from the TEDDY study von Stewart, Christopher J., Ajami, Nadim J., O’Brien, Jacqueline L., Hutchinson, Diane S., Smith, Daniel P., Wong, Matthew C., Ross, Matthew C., Lloyd, Richard E., Doddapaneni, HarshaVardhan, Metcalf, Ginger A., Muzny, Donna, Gibbs, Richard A., Vatanen, Tommi, Huttenhower, Curtis, Xavier, Ramnik J., Rewers, Marian, Hagopian, William, Toppari, Jorma, Ziegler, Anette-G., She, Jin-Xiong, Akolkar, Beena, Lernmark, Ake, Hyoty, Heikki, Vehik, Kendra, Krischer, Jeffrey P., Petrosino, Joseph F.

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The human gut microbiome in early-onset type 1 diabetes from the TEDDY study von Vatanen, Tommi, Franzosa, Eric A., Schwager, Randall, Tripathi, Surya, Arthur, Timothy D., Vehik, Kendra, Lernmark, Åke, Hagopian, William A., Rewers, Marian J., She, Jin-Xiong, Toppari, Jorma, Ziegler, Anette-G., Akolkar, Beena, Krischer, Jeffrey P., Stewart, Christopher J., Ajami, Nadim J., Petrosino, Joseph F., Gevers, Dirk, Lähdesmäki, Harri, Vlamakis, Hera, Huttenhower, Curtis, Xavier, Ramnik J.

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Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity von Zhernakova, Alexandra, Kurilshikov, Alexander, Bonder, Marc Jan, Tigchelaar, Ettje F., Schirmer, Melanie, Vatanen, Tommi, Mujagic, Zlatan, Vila, Arnau Vich, Falony, Gwen, Vieira-Silva, Sara, Wang, Jun, Imhann, Floris, Brandsma, Eelke, Jankipersadsing, Soesma A., Joossens, Marie, Cenit, Maria Carmen, Deelen, Patrick, Swertz, Morris A., study, LifeLines cohort, Weersma, Rinse K., Feskens, Edith J. M., Netea, Mihai G., Gevers, Dirk, Jonkers, Daisy, Franke, Lude, Aulchenko, Yurii S., Huttenhower, Curtis, Raes, Jeroen, Hofker, Marten H., Xavier, Ramnik J., Wijmenga, Cisca, Fu, Jingyuan

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Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans von Vatanen, Tommi, Kostic, Aleksandar D., d’Hennezel, Eva, Siljander, Heli, Franzosa, Eric A., Yassour, Moran, Kolde, Raivo, Vlamakis, Hera, Arthur, Timothy D., Hämäläinen, Anu-Maaria, Peet, Aleksandr, Tillmann, Vallo, Uibo, Raivo, Mokurov, Sergei, Dorshakova, Natalya, Ilonen, Jorma, Virtanen, Suvi M., Szabo, Susanne J., Porter, Jeffrey A., Lähdesmäki, Harri, Huttenhower, Curtis, Gevers, Dirk, Cullen, Thomas W., Knip, Mikael, Xavier, Ramnik J.

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The effect of host genetics on the gut microbiome von Bonder, Marc Jan, Kurilshikov, Alexander, Tigchelaar, Ettje F, Mujagic, Zlatan, Imhann, Floris, Vila, Arnau Vich, Deelen, Patrick, Vatanen, Tommi, Schirmer, Melanie, Smeekens, Sanne P, Zhernakova, Daria V, Jankipersadsing, Soesma A, Jaeger, Martin, Oosting, Marije, Cenit, Maria Carmen, Masclee, Ad A M, Swertz, Morris A, Li, Yang, Kumar, Vinod, Joosten, Leo, Harmsen, Hermie, Weersma, Rinse K, Franke, Lude, Hofker, Marten H, Xavier, Ramnik J, Jonkers, Daisy, Netea, Mihai G, Wijmenga, Cisca, Fu, Jingyuan, Zhernakova, Alexandra

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

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Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children von Zhao, Guoyan, Vatanen, Tommi, Droit, Lindsay, Park, Arnold, Kostic, Aleksandar D., Poon, Tiffany W., Vlamakis, Hera, Siljander, Heli, Härkönen, Taina, Hämäläinen, Anu-Maaria, Peet, Aleksandr, Tillmann, Vallo, Ilonen, Jorma, Wang, David, Knip, Mikael, Xavier, Ramnik J., Virgin, Herbert W.

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Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease von Vaughn, Byron P, Vatanen, Tommi, Allegretti, Jessica R, Bai, Aiping, Xavier, Ramnik J, Korzenik, Joshua, Gevers, Dirk, Ting, Amanda, Robson, Simon C, Moss, Alan C

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The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes von Kostic, Aleksandar D., Gevers, Dirk, Siljander, Heli, Vatanen, Tommi, Hyötyläinen, Tuulia, Hämäläinen, Anu-Maaria, Peet, Aleksandr, Tillmann, Vallo, Pöhö, Päivi, Mattila, Ismo, Lähdesmäki, Harri, Franzosa, Eric A., Vaarala, Outi, de Goffau, Marcus, Harmsen, Hermie, Ilonen, Jorma, Virtanen, Suvi M., Clish, Clary B., Orešič, Matej, Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.

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Gut microbiome structure and metabolic activity in inflammatory bowel disease von Franzosa, Eric A., Sirota-Madi, Alexandra, Avila-Pacheco, Julian, Fornelos, Nadine, Haiser, Henry J., Reinker, Stefan, Vatanen, Tommi, Hall, A. Brantley, Mallick, Himel, McIver, Lauren J., Sauk, Jenny S., Wilson, Robin G., Stevens, Betsy W., Scott, Justin M., Pierce, Kerry, Deik, Amy A., Bullock, Kevin, Imhann, Floris, Porter, Jeffrey A., Zhernakova, Alexandra, Fu, Jingyuan, Weersma, Rinse K., Wijmenga, Cisca, Clish, Clary B., Vlamakis, Hera, Huttenhower, Curtis, Xavier, Ramnik J.

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Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads von Lamichhane, Santosh, Härkönen, Taina, Vatanen, Tommi, Hyötyläinen, Tuulia, Knip, Mikael, Orešič, Matej

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The influence of a short-term gluten-free diet on the human gut microbiome von Bonder, Marc Jan, Tigchelaar, Ettje F, Cai, Xianghang, Trynka, Gosia, Cenit, Maria C, Hrdlickova, Barbara, Zhong, Huanzi, Vatanen, Tommi, Gevers, Dirk, Wijmenga, Cisca, Wang, Yang, Zhernakova, Alexandra

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Phages in the Gut Ecosystem von Zuppi, Michele, Hendrickson, Heather L, O'Sullivan, Justin M, Vatanen, Tommi

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High-throughput automated microfluidic sample preparation for accurate microbial genomics von Kim, Soohong, De Jonghe, Joachim, Kulesa, Anthony B., Feldman, David, Vatanen, Tommi, Bhattacharyya, Roby P., Berdy, Brittany, Gomez, James, Nolan, Jill, Epstein, Slava, Blainey, Paul C.

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Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans von Vatanen, Tommi, Kostic, Aleksandar D., d’Hennezel, Eva, Siljander, Heli, Franzosa, Eric A., Yassour, Moran, Kolde, Raivo, Vlamakis, Hera, Arthur, Timothy D., Hämäläinen, Anu-Maaria, Peet, Aleksandr, Tillmann, Vallo, Uibo, Raivo, Mokurov, Sergei, Dorshakova, Natalya, Ilonen, Jorma, Virtanen, Suvi M., Szabo, Susanne J., Porter, Jeffrey A., Lähdesmäki, Harri, Huttenhower, Curtis, Gevers, Dirk, Cullen, Thomas W., Knip, Mikael, Xavier, Ramnik J.

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Sequence-structure-function relationships in the microbial protein universe von Koehler Leman, Julia, Szczerbiak, Pawel, Renfrew, P. Douglas, Gligorijevic, Vladimir, Berenberg, Daniel, Vatanen, Tommi, Taylor, Bryn C., Chandler, Chris, Janssen, Stefan, Pataki, Andras, Carriero, Nick, Fisk, Ian, Xavier, Ramnik J., Knight, Rob, Bonneau, Richard, Kosciolek, Tomasz

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