Search Results - "Vatanen, Tommi"

Structure-based protein function prediction using graph convolutional networks by 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

“…The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated…”
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An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data by Cheng, Lu, Ramchandran, Siddharth, Vatanen, Tommi, Lietzén, Niina, Lahesmaa, Riitta, Vehtari, Aki, Lähdesmäki, Harri

“…Biomedical research typically involves longitudinal study designs where samples from individuals are measured repeatedly over time and the goal is to identify…”
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The Super-Donor Phenomenon in Fecal Microbiota Transplantation by Wilson, Brooke C, Vatanen, Tommi, Cutfield, Wayne S, O'Sullivan, Justin M

“…Fecal microbiota transplantation (FMT) has become a highly effective bacteriotherapy for recurrent infection. Meanwhile the efficacy of FMT for treating…”
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Experimental design and quantitative analysis of microbial community multiomics by Mallick, Himel, Ma, Siyuan, Franzosa, Eric A, Vatanen, Tommi, Morgan, Xochitl C, Huttenhower, Curtis

“…Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for…”
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Temporal development of the gut microbiome in early childhood from the TEDDY study by 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.

“…The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial–immune crosstalk during this time thought to be…”
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The human gut microbiome in early-onset type 1 diabetes from the TEDDY study by 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.

“…Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors 1 , including…”
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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, Lander, Eric S, Knip, Mikael, Xavier, Ramnik J

“…The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact…”
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Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity by 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

“…Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and…”
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Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans by 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.

“…According to the hygiene hypothesis, the increasing incidence of autoimmune diseases in western countries may be explained by changes in early microbial…”
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The effect of host genetics on the gut microbiome by 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

“…Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga and colleagues perform genome-wide association analysis for microbiome characteristics in a cohort with fully…”
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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, 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

“…Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome…”
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Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children by 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.

“…Viruses have long been considered potential triggers of autoimmune diseases. Here we defined the intestinal virome from birth to the development of…”
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Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease by 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

“…The microbiota in the lumen of patients with Crohn's disease (CD) is characterized by reduced diversity, particularly Firmicutes and Bacteroidetes. It is…”
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The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes by 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.

“…Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the…”
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Gut microbiome structure and metabolic activity in inflammatory bowel disease by 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.

“…The inflammatory bowel diseases (IBDs), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the…”
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Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads by Lamichhane, Santosh, Härkönen, Taina, Vatanen, Tommi, Hyötyläinen, Tuulia, Knip, Mikael, Orešič, Matej

“…There is growing evidence suggesting that chemical exposure alters gut microbiota composition. However, not much is known about the impact of per- and…”
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The influence of a short-term gluten-free diet on the human gut microbiome by 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

“…A gluten-free diet (GFD) is the most commonly adopted special diet worldwide. It is an effective treatment for coeliac disease and is also often followed by…”
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Phages in the Gut Ecosystem by Zuppi, Michele, Hendrickson, Heather L, O'Sullivan, Justin M, Vatanen, Tommi

“…Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored…”
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High-throughput automated microfluidic sample preparation for accurate microbial genomics by 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.

“…Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting…”
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Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans by 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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