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The role of the virome in shaping the gut ecosystem during the first year of life

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Publications

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

Author(s): Trishla Sinha, Arnau Vich Vila, Sanzhima Garmaeva, Soesma A. Jankipersadsing, Floris Imhann, Valerie Collij, Marc Jan Bonder, Xiaofang Jiang, Thomas Gurry, Eric J. Alm, Mauro D’Amato, Rinse K. Weersma, Sicco Scherjon, Cisca Wijmenga, Jingyuan Fu, Alexander Kurilshikov, Alexandra Zhernakova
Published in: Gut Microbes, 2018, Page(s) 1-9, ISSN 1949-0976
DOI: 10.1080/19490976.2018.1528822

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome

Author(s): Daria V. Zhernakova, Trang H. Le, Alexander Kurilshikov, Biljana Atanasovska, Marc Jan Bonder, Serena Sanna, Annique Claringbould, Urmo Võsa, Patrick Deelen, Lude Franke, Rudolf A. de Boer, Folkert Kuipers, Mihai G. Netea, Marten H. Hofker, Cisca Wijmenga, Alexandra Zhernakova, Jingyuan Fu
Published in: Nature Genetics, Issue 50/11, 2018, Page(s) 1524-1532, ISSN 1061-4036
DOI: 10.1038/s41588-018-0224-7

Pharmacomicrobiomics: a novel route towards personalized medicine?

Author(s): Marwah Doestzada, Arnau Vich Vila, Alexandra Zhernakova, Debby P. Y. Koonen, Rinse K. Weersma, Daan J. Touw, Folkert Kuipers, Cisca Wijmenga, Jingyuan Fu
Published in: Protein & Cell, Issue 9/5, 2018, Page(s) 432-445, ISSN 1674-800X
DOI: 10.1007/s13238-018-0547-2

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

Author(s): Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han-na Kim, Tim D. Spector, Jordana T. Bell, Claire J. Steves, Nicolas Timpson, Andre Franke, Cisca Wijmenga, Katie Meyer, Tim Kacprowski, Lude Franke, Andrew D. Paterson, Jeroen Raes, Robert
Published in: Microbiome, Issue 6/1, 2018, ISSN 2049-2618
DOI: 10.1186/s40168-018-0479-3

A system biology perspective on environment–host–microbe interactions

Author(s): Lianmin Chen, Sanzhima Garmaeva, Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga
Published in: Human Molecular Genetics, Issue 27/R2, 2018, Page(s) R187-R194, ISSN 0964-6906
DOI: 10.1093/hmg/ddy137

Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting

Author(s): Bashar Ibrahim, Ksenia Arkhipova, Arno Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene Koonin, Anne Kupczok, Philippe Lemey, Alice McHardy, Dino McMahon, Brett Pickett, David Robertson, Richard Scheuermann, Alexandra Zhernakova, Mark Zwart, Alexander Schönhuth, Bas Dutilh, Manja Marz
Published in: Viruses, Issue 10/5, 2018, Page(s) 256, ISSN 1999-4915
DOI: 10.3390/v10050256

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

Author(s): Matthew A. Jackson, Marc Jan Bonder, Zhana Kuncheva, Jonas Zierer, Jingyuan Fu, Alexander Kurilshikov, Cisca Wijmenga, Alexandra Zhernakova, Jordana T. Bell, Tim D. Spector, Claire J. Steves
Published in: PeerJ, Issue 6, 2018, Page(s) e4303, ISSN 2167-8359
DOI: 10.7717/peerj.4303

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota

Author(s): Floris Imhann, Arnau Vich Vila, Marc Jan Bonder, Ailine G. Lopez Manosalva, Debby P.Y. Koonen, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Rinse K. Weersma
Published in: Gut Microbes, Issue 8/4, 2017, Page(s) 351-358, ISSN 1949-0976
DOI: 10.1080/19490976.2017.1284732

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Author(s): Eric A. Franzosa, Alexandra Sirota-Madi, Julian Avila-Pacheco, Nadine Fornelos, Henry J. Haiser, Stefan Reinker, Tommi Vatanen, A. Brantley Hall, Himel Mallick, Lauren J. McIver, Jenny S. Sauk, Robin G. Wilson, Betsy W. Stevens, Justin M. Scott, Kerry Pierce, Amy A. Deik, Kevin Bullock, Floris Imhann, Jeffrey A. Porter, Alexandra Zhernakova, Jingyuan Fu, Rinse K. Weersma, Cisca Wijmenga, Clary B.
Published in: Nature Microbiology, Issue 4/2, 2019, Page(s) 293-305, ISSN 2058-5276
DOI: 10.1038/s41564-018-0306-4

Studying the gut virome in the metagenomic era: challenges and perspectives

Author(s): Sanzhima Garmaeva, Trishla Sinha, Alexander Kurilshikov, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova
Published in: BMC Biology, Issue 17/1, 2019, ISSN 1741-7007
DOI: 10.1186/s12915-019-0704-y

Structural variation in the gut microbiome associates with host health

Author(s): David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal
Published in: Nature, Issue 568/7750, 2019, Page(s) 43-48, ISSN 0028-0836
DOI: 10.1038/s41586-019-1065-y

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

Author(s): Serena Sanna, Natalie R. van Zuydam, Anubha Mahajan, Alexander Kurilshikov, Arnau Vich Vila, Urmo Võsa, Zlatan Mujagic, Ad A. M. Masclee, Daisy M. A. E. Jonkers, Marije Oosting, Leo A. B. Joosten, Mihai G. Netea, Lude Franke, Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga, Mark I. McCarthy
Published in: Nature Genetics, Issue 51/4, 2019, Page(s) 600-605, ISSN 1061-4036
DOI: 10.1038/s41588-019-0350-x

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk

Author(s): Alexander Kurilshikov, Inge C.L. van den Munckhof, Lianmin Chen, Marc J. Bonder, Kiki Schraa, Joost H.W. Rutten, Niels P. Riksen, Jacqueline de Graaf, Marije Oosting, Serena Sanna, Leo A.B. Joosten, Marinette van der Graaf, Tessa Brand, Debby P.Y. Koonen, Martijn van Faassen, P. Eline Slagboom, Ramnik J. Xavier, Folkert Kuipers, Marten H. Hofker, Cisca Wijmenga, Mihai G. Netea, Alexandra Zhernakov
Published in: Circulation Research, Issue 124/12, 2019, Page(s) 1808-1820, ISSN 0009-7330
DOI: 10.1161/circresaha.118.314642

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author(s): Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondrej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan J. J. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David T. McCarthy, Franklin L. Nobrega, Alejandro Reye
Published in: Nature Microbiology, Issue 4/10, 2019, Page(s) 1727-1736, ISSN 2058-5276
DOI: 10.1038/s41564-019-0494-6

The neuroactive potential of the human gut microbiota in quality of life and depression

Author(s): Mireia Valles-Colomer, Gwen Falony, Youssef Darzi, Ettje F. Tigchelaar, Jun Wang, Raul Y. Tito, Carmen Schiweck, Alexander Kurilshikov, Marie Joossens, Cisca Wijmenga, Stephan Claes, Lukas Van Oudenhove, Alexandra Zhernakova, Sara Vieira-Silva, Jeroen Raes
Published in: Nature Microbiology, Issue 4/4, 2019, Page(s) 623-632, ISSN 2058-5276
DOI: 10.1038/s41564-018-0337-x

SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects

Author(s): Valerie Collij, Floris Imhann, Arnau Vich Vila, Jingyuan Fu, Gerard Dijkstra, Eleonora A. M. Festen, Michiel D. Voskuil, Mark J. Daly, Ramnik J. Xavier, Cisca Wijmenga, Alexandra Zhernakova, Rinse K. Weersma
Published in: PLOS ONE, Issue 14/1, 2019, Page(s) e0211328, ISSN 1932-6203
DOI: 10.1371/journal.pone.0211328

Gut microbiome composition and its relation to joint pain and inflammation

Author(s): C.G. Boer, D. Radjabzadeh, C. Medina-Gomez, S. Garmaeva, D. Schiphof, P. Arp, T. Koet, A. Kurilshikov, J. Fu, A.M. Ikram, S. Bierma-Zeinstra, A.G. Uitterlinden, R. Kraaij, A. Zhernakova, J.B. van Meurs
Published in: Osteoarthritis and Cartilage, Issue 27, 2019, Page(s) S26, ISSN 1063-4584
DOI: 10.1016/j.joca.2019.02.040

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

Author(s): Arnau Vich Vila, Floris Imhann, Valerie Collij, Soesma A. Jankipersadsing, Thomas Gurry, Zlatan Mujagic, Alexander Kurilshikov, Marc Jan Bonder, Xiaofang Jiang, Ettje F. Tigchelaar, Jackie Dekens, Vera Peters, Michiel D. Voskuil, Marijn C. Visschedijk, Hendrik M. van Dullemen, Daniel Keszthelyi, Morris A. Swertz, Lude Franke, Rudi Alberts, Eleonora A. M. Festen, Gerard Dijkstra, Ad A. M. Masclee,
Published in: Science Translational Medicine, Issue 10/472, 2018, Page(s) eaap8914, ISSN 1946-6234
DOI: 10.1126/scitranslmed.aap8914