Tommi Vatanen

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Curtis HuttenhowerDepartment of Biostatistics, Harvard School of Public HealthVerified email at hsph.harvard.edu
Aleksandar David KosticAssistant Professor, Harvard Medical School & Joslin Diabetes CenterVerified email at joslin.harvard.edu
Vallo TillmannUniversity of TartuVerified email at ut.ee
Eric Alan FranzosaSenior Research Scientist / Harvard T. H. Chan School of Public HealthVerified email at hsph.harvard.edu
Moran YassourThe Hebrew University of JerusalemVerified email at mail.huji.ac.il
Tapani RaikoPrincipal research scientist, AppleVerified email at apple.com
Matej OrešičProfessor of Medicine (Systems Medicine), Örebro University & University of TurkuVerified email at oru.se
Clary ClishSenior Director, Metabolomics, Broad Institute of MIT and HarvardVerified email at broadinstitute.org
kugathasan, sProfessor of Pediatrics and Human Genetics, Marcus Professor of Pediatric GastroenterologyVerified email at emory.edu
Outi VaaralaRIA IMED AstraZenecaVerified email at astrazeneca.com
Ismo MattilaResearch Scientist, Steno Diabetes CenterVerified email at steno.dk
Paul C BlaineyBroad Institute and MIT, Department of Biological EngineeringVerified email at broadinstitute.org
Yann LeCunChief AI Scientist at Facebook & Silver Professor at the Courant Institute, New York UniversityVerified email at cs.nyu.edu
Harri ValpolaSystem 2 AIVerified email at system2ai.com
Timo HonkelaUniversity of HelsinkiVerified email at helsinki.fi
Eric MalmiStaff Research Scientist, Google DeepMindVerified email at google.com
Mikael KuuselaCarnegie Mellon UniversityVerified email at andrew.cmu.edu
Alexandra (Sasha) ZhernakovaProfessor of Human Genome and Exposome, University Medical Centre Groningen, The NetherlandsVerified email at umcg.nl
Cisca Wijmenga, PhDERC advanced investigator; Professor of Human Genetics, Dept Genetics (MGE), UMCG, Groningen, theVerified email at umcg.nl
Marc Jan BonderPostdoctoral researcher UMCGVerified email at umcg.nl

Tommi Vatanen

Associate Professor, University of Helsinki

Verified email at helsinki.fi - Homepage

Human microbiome Bioinformatics Machine learning Computational systems biology Bayesian statistics


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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	1919	2016
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	1811	2018
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	1584	2019
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	1397	2016
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	1284	2015
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	1264	2013
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	1031	2016
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	831	2016
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	829	2018
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	759	2021
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	688	2017
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	375	2019
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	316	2016
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	304	2017
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	301	2016
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	249	2016
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	246	2021
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	224	2019
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	186	2017
Self-organization and missing values in SOM and GTM T Vatanen, M Osmala, T Raiko, K Lagus, M Sysi-Aho, M Orešič, T Honkela, ... Neurocomputing 147, 60-70, 2015	137	2015

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