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Tommi Vatanen
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Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
A Zhernakova, A Kurilshikov, MJ Bonder, EF Tigchelaar, M Schirmer, ...
Science 352 (6285), 565-569, 2016
16962016
Temporal development of the gut microbiome in early childhood from the TEDDY study
CJ Stewart, NJ Ajami, JL O’Brien, DS Hutchinson, DP Smith, MC Wong, ...
Nature 562 (7728), 583-588, 2018
14792018
Pushing stochastic gradient towards second-order methods–backpropagation learning with transformations in nonlinearities
T Vatanen, T Raiko, H Valpola, Y LeCun
International Conference on Neural Information Processing, 442-449, 2013
12562013
Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans
T Vatanen, AD Kostic, E d’Hennezel, H Siljander, EA Franzosa, ...
Cell 165 (4), 842-853, 2016
12502016
Gut microbiome structure and metabolic activity in inflammatory bowel disease
EA Franzosa, A Sirota-Madi, J Avila-Pacheco, N Fornelos, HJ Haiser, ...
Nature microbiology 4 (2), 293-305, 2019
12422019
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes
AD Kostic, D Gevers, H Siljander, T Vatanen, T Hyötyläinen, ...
Cell host & microbe 17 (2), 260-273, 2015
11832015
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
M Yassour, T Vatanen, H Siljander, AM Hämäläinen, T Härkönen, ...
Science translational medicine 8 (343), 343ra81-343ra81, 2016
8912016
The effect of host genetics on the gut microbiome
MJ Bonder, A Kurilshikov, EF Tigchelaar, Z Mujagic, F Imhann, AV Vila, ...
Nature genetics 48 (11), 1407-1412, 2016
7442016
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study
T Vatanen, EA Franzosa, R Schwager, S Tripathi, TD Arthur, K Vehik, ...
Nature 562 (7728), 589-594, 2018
6942018
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
AB Hall, M Yassour, J Sauk, A Garner, X Jiang, T Arthur, GK Lagoudas, ...
Genome medicine 9, 1-12, 2017
5562017
Structure-based protein function prediction using graph convolutional networks
V Gligorijević, PD Renfrew, T Kosciolek, JK Leman, D Berenberg, ...
Nature communications 12 (1), 3168, 2021
4822021
The super-donor phenomenon in fecal microbiota transplantation
BC Wilson, T Vatanen, WS Cutfield, JM O'Sullivan
Frontiers in cellular and infection microbiology 9, 2, 2019
3212019
Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children
G Zhao, T Vatanen, L Droit, A Park, AD Kostic, TW Poon, H Vlamakis, ...
Proceedings of the National Academy of Sciences 114 (30), E6166-E6175, 2017
2752017
Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease
KA Shaw, M Bertha, T Hofmekler, P Chopra, T Vatanen, A Srivatsa, ...
Genome medicine 8, 1-13, 2016
2702016
The influence of a short-term gluten-free diet on the human gut microbiome
MJ Bonder, EF Tigchelaar, X Cai, G Trynka, MC Cenit, B Hrdlickova, ...
Genome medicine 8, 1-11, 2016
2692016
Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn's disease
BP Vaughn, T Vatanen, JR Allegretti, A Bai, RJ Xavier, J Korzenik, ...
Inflammatory bowel diseases 22 (9), 2182-2190, 2016
2232016
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life
T Vatanen, DR Plichta, J Somani, PC Münch, TD Arthur, AB Hall, S Rudolf, ...
Nature microbiology 4 (3), 470-479, 2019
1902019
Elevated rates of horizontal gene transfer in the industrialized human microbiome
M Groussin, M Poyet, A Sistiaga, SM Kearney, K Moniz, M Noel, J Hooker, ...
Cell 184 (8), 2053-2067. e18, 2021
1822021
Experimental design and quantitative analysis of microbial community multiomics
H Mallick, S Ma, EA Franzosa, T Vatanen, XC Morgan, C Huttenhower
Genome biology 18, 1-16, 2017
1692017
Language Identification of Short Text Segments with N-gram Models.
T Vatanen, JJ Väyrynen, S Virpioja
LREC, 2010
1272010
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