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  • Structure-based protein fun... Structure-based protein function prediction using graph convolutional networks
    Gligorijević, Vladimir; Renfrew, P Douglas; Kosciolek, Tomasz ... Nature communications, 05/2021, Volume: 12, Issue: 1
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    Peer reviewed
    Open access

    The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce ...
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  • An additive Gaussian proces... An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data
    Cheng, Lu; Ramchandran, Siddharth; Vatanen, Tommi ... Nature communications, 04/2019, Volume: 10, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Biomedical research typically involves longitudinal study designs where samples from individuals are measured repeatedly over time and the goal is to identify risk factors (covariates) that are ...
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  • The Super-Donor Phenomenon ... The Super-Donor Phenomenon in Fecal Microbiota Transplantation
    Wilson, Brooke C; Vatanen, Tommi; Cutfield, Wayne S ... Frontiers in cellular and infection microbiology, 2019, Volume: 9
    Journal Article
    Peer reviewed
    Open access

    Fecal microbiota transplantation (FMT) has become a highly effective bacteriotherapy for recurrent infection. Meanwhile the efficacy of FMT for treating chronic diseases associated with microbial ...
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  • Temporal development of the... Temporal development of the gut microbiome in early childhood from the TEDDY study
    Stewart, Christopher J; Ajami, Nadim J; O'Brien, Jacqueline L ... Nature, 10/2018, Volume: 562, Issue: 7728
    Journal Article
    Peer reviewed
    Open access

    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 involved in the pathobiology of later ...
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  • Experimental design and qua... Experimental design and quantitative analysis of microbial community multiomics
    Mallick, Himel; Ma, Siyuan; Franzosa, Eric A ... Genome Biology, 11/2017, Volume: 18, Issue: 1
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    Peer reviewed
    Open access

    Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To ...
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  • The human gut microbiome in... The human gut microbiome in early-onset type 1 diabetes from the TEDDY study
    Vatanen, Tommi; Franzosa, Eric A; Schwager, Randall ... Nature, 10/2018, Volume: 562, Issue: 7728
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    Peer reviewed
    Open access

    Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors , including complex genetic elements , patient exposures and ...
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  • Population-based metagenomi... Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
    Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan ... Science, 04/2016, Volume: 352, Issue: 6285
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    Open access

    Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 ...
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  • Natural history of the infa... Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
    Yassour, Moran; Vatanen, Tommi; Siljander, Heli ... Science translational medicine, 06/2016, Volume: 8, Issue: 343
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    Peer reviewed
    Open access

    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 of environmental factors on the ...
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  • Variation in Microbiome LPS... Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans
    Vatanen, Tommi; Kostic, Aleksandar D.; d’Hennezel, Eva ... Cell, 05/2016, Volume: 165, Issue: 4
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    Open access

    According to the hygiene hypothesis, the increasing incidence of autoimmune diseases in western countries may be explained by changes in early microbial exposure, leading to altered immune ...
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  • The effect of host genetics on the gut microbiome
    Bonder, Marc Jan; Kurilshikov, Alexander; Tigchelaar, Ettje F ... Nature genetics, 11/2016, Volume: 48, Issue: 11
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    Peer reviewed

    The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the ...
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