Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells
Hernando-Herraez, Irene, Evano, Brendan, Stubbs, Thomas, Commere, Pierre-Henri, Jan Bonder, Marc, Clark, Stephen, Andrews, Simon, Tajbakhsh, Shahragim, Reik, Wolf
Published in Nature communications (25.09.2019)
Published in Nature communications (25.09.2019)
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Journal Article
Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats
Jakubosky, David, Smith, Erin N., D’Antonio, Matteo, Jan Bonder, Marc, Young Greenwald, William W., D’Antonio-Chronowska, Agnieszka, Matsui, Hiroko, Stegle, Oliver, Montgomery, Stephen B., DeBoever, Christopher, Frazer, Kelly A.
Published in Nature communications (10.06.2020)
Published in Nature communications (10.06.2020)
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Journal Article
The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults
Kraneveld, Eefje A, Buijs, Mark J, Bonder, Marc J, Visser, Marjolein, Keijser, Bart J F, Crielaard, Wim, Zaura, Egija
Published in PloS one (10.08.2012)
Published in PloS one (10.08.2012)
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Journal Article
Properties of structural variants and short tandem repeats associated with gene expression and complex traits
Jakubosky, David, D’Antonio, Matteo, Bonder, Marc Jan, Smail, Craig, Donovan, Margaret K. R., Young Greenwald, William W., Matsui, Hiroko, D’Antonio-Chronowska, Agnieszka, Stegle, Oliver, Smith, Erin N., Montgomery, Stephen B., DeBoever, Christopher, Frazer, Kelly A.
Published in Nature communications (10.06.2020)
Published in Nature communications (10.06.2020)
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Journal Article
Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study
Kurilshikov, Alexander, van den Munckhof, Inge C.L, Chen, Lianmin, Bonder, Marc J, Schraa, Kiki, Rutten, Joost H.W, Riksen, Niels P, de Graaf, Jacqueline, Oosting, Marije, Sanna, Serena, Joosten, Leo A.B, van der Graaf, Marinette, Brand, Tessa, Koonen, Debby P.Y, van Faassen, Martijn, Slagboom, P Eline, Xavier, Ramnik J, Kuipers, Folkert, Hofker, Marten H, Wijmenga, Cisca, Netea, Mihai G, Zhernakova, Alexandra, Fu, Jingyuan
Published in Circulation research (07.06.2019)
Published in Circulation research (07.06.2019)
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Journal Article
DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels: a systematic review and replication in a case–control sample of the Lifelines study
Walaszczyk, Eliza, Luijten, Mirjam, Spijkerman, Annemieke M. W., Bonder, Marc J., Lutgers, Helen L., Snieder, Harold, Wolffenbuttel, Bruce H. R., van Vliet-Ostaptchouk, Jana V.
Published in Diabetologia (01.02.2018)
Published in Diabetologia (01.02.2018)
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Journal Article
Comparing clustering and pre-processing in taxonomy analysis
BONDER, Marc J, ABELN, Sanne, ZAURA, Egija, BRANDT, Bernd W
Published in Bioinformatics (15.11.2012)
Published in Bioinformatics (15.11.2012)
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Journal Article
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
D'Antonio, Matteo, Reyna, Joaquin, Jakubosky, David, Donovan, Margaret Kr, Bonder, Marc-Jan, Matsui, Hiroko, Stegle, Oliver, Nariai, Naoki, D'Antonio-Chronowska, Agnieszka, Frazer, Kelly A
Published in eLife (20.11.2019)
Published in eLife (20.11.2019)
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Journal Article
Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases
Cai, Na, Gomez-Duran, Aurora, Yonova-Doing, Ekaterina, Kundu, Kousik, Burgess, Annette I., Golder, Zoe J., Calabrese, Claudia, Bonder, Marc J., Camacho, Marta, Lawson, Rachael A., Li, Lixin, Williams-Gray, Caroline H., Di Angelantonio, Emanuele, Roberts, David J., Watkins, Nick A., Ouwehand, Willem H., Butterworth, Adam S., Stewart, Isobel D., Pietzner, Maik, Wareham, Nick J., Langenberg, Claudia, Danesh, John, Walter, Klaudia, Rothwell, Peter M., Howson, Joanna M. M., Stegle, Oliver, Chinnery, Patrick F., Soranzo, Nicole
Published in Nature medicine (01.09.2021)
Published in Nature medicine (01.09.2021)
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Journal Article
A linear mixed-model approach to study multivariate gene–environment interactions
Moore, Rachel, Casale, Francesco Paolo, Jan Bonder, Marc, Horta, Danilo, Franke, Lude, Barroso, Inês, Stegle, Oliver
Published in Nature genetics (01.01.2019)
Published in Nature genetics (01.01.2019)
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Journal Article
Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration
Deelen, Patrick, Bonder, Marc Jan, van der Velde, K Joeri, Westra, Harm-Jan, Winder, Erwin, Hendriksen, Dennis, Franke, Lude, Swertz, Morris A
Published in BMC research notes (11.12.2014)
Published in BMC research notes (11.12.2014)
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Journal Article
Genetic and epigenetic regulation of gene expression in fetal and adult human livers
Bonder, Marc Jan, Kasela, Silva, Kals, Mart, Tamm, Riin, Lokk, Kaie, Barragan, Isabel, Buurman, Wim A, Deelen, Patrick, Greve, Jan-Willem, Ivanov, Maxim, Rensen, Sander S, van Vliet-Ostaptchouk, Jana V, Wolfs, Marcel G, Fu, Jingyuan, Hofker, Marten H, Wijmenga, Cisca, Zhernakova, Alexandra, Ingelman-Sundberg, Magnus, Franke, Lude, Milani, Lili
Published in BMC genomics (04.10.2014)
Published in BMC genomics (04.10.2014)
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Journal Article
Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
Bonder, Marc Jan, Smail, Craig, Gloudemans, Michael J., Frésard, Laure, Jakubosky, David, D’Antonio, Matteo, Li, Xin, Ferraro, Nicole M., Carcamo-Orive, Ivan, Mirauta, Bogdan, Seaton, Daniel D., Cai, Na, Vakili, Dara, Horta, Danilo, Zhao, Chunli, Zastrow, Diane B., Bonner, Devon E., Wheeler, Matthew T., Kilpinen, Helena, Knowles, Joshua W., Smith, Erin N., Frazer, Kelly A., Montgomery, Stephen B., Stegle, Oliver
Published in Nature genetics (01.03.2021)
Published in Nature genetics (01.03.2021)
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Journal Article
Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes
McCarthy, Davis J., Rostom, Raghd, Huang, Yuanhua, Kunz, Daniel J., Danecek, Petr, Bonder, Marc Jan, Hagai, Tzachi, Lyu, Ruqian, Wang, Wenyi, Gaffney, Daniel J., Simons, Benjamin D., Stegle, Oliver, Teichmann, Sarah A.
Published in Nature methods (01.04.2020)
Published in Nature methods (01.04.2020)
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Journal Article
Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations
Shah, Sonia, Bonder, Marc J., Marioni, Riccardo E., Zhu, Zhihong, McRae, Allan F., Zhernakova, Alexandra, Harris, Sarah E., Liewald, Dave, Henders, Anjali K., Mendelson, Michael M., Liu, Chunyu, Joehanes, Roby, Liang, Liming, Heijmans, Bastiaan T., ’t Hoen, Peter A.C., van Meurs, Joyce, Isaacs, Aaron, Jansen, Rick, Franke, Lude, Boomsma, Dorret I., Pool, René, van Dongen, Jenny, Hottenga, Jouke J., van Greevenbroek, Marleen M.J., Stehouwer, Coen D.A., van der Kallen, Carla J.H., Schalkwijk, Casper G., Wijmenga, Cisca, Zhernakova, Sasha, Tigchelaar, Ettje F., Slagboom, P. Eline, Beekman, Marian, Deelen, Joris, van Heemst, Diana, Veldink, Jan H., van den Berg, Leonard H., van Duijn, Cornelia M., Hofman, Bert A., Uitterlinden, André G., Jhamai, P. Mila, Verbiest, Michael, Suchiman, H. Eka D., Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, van ’t Hof, Peter, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Zhernakova, Dasha V., Luijk, René, Bonder, Marc Jan, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon M., Swertz, Morris A., van Zwet, Erik W., Levy, Daniel, Martin, Nicholas G., Starr, John M., Wijmenga, Cisca, Wray, Naomi R., Yang, Jian, Montgomery, Grant W., Franke, Lude, Deary, Ian J., Visscher, Peter M.
Published in American journal of human genetics (02.07.2015)
Published in American journal of human genetics (02.07.2015)
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Journal Article
Tobacco smoking is associated with DNA methylation of diabetes susceptibility genes
Ligthart, Symen, Steenaard, Rebecca V., Peters, Marjolein J., van Meurs, Joyce B. J., Sijbrands, Eric J. G., Uitterlinden, André G., Bonder, Marc J., Hofman, Albert, Franco, Oscar H., Dehghan, Abbas
Published in Diabetologia (01.05.2016)
Published in Diabetologia (01.05.2016)
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Journal Article
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity
Schirmer, Melanie, Smeekens, Sanne P., Vlamakis, Hera, Jaeger, Martin, Oosting, Marije, Franzosa, Eric A., ter Horst, Rob, Jansen, Trees, Jacobs, Liesbeth, Bonder, Marc Jan, Kurilshikov, Alexander, Fu, Jingyuan, Joosten, Leo A.B., Zhernakova, Alexandra, Huttenhower, Curtis, Wijmenga, Cisca, Netea, Mihai G., Xavier, Ramnik J.
Published in Cell (03.11.2016)
Published in Cell (03.11.2016)
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Journal Article
Genetic, parental and lifestyle factors influence telomere length
Andreu-Sánchez, Sergio, Aubert, Geraldine, Ripoll-Cladellas, Aida, Henkelman, Sandra, Zhernakova, Daria V., Sinha, Trishla, Kurilshikov, Alexander, Cenit, Maria Carmen, Jan Bonder, Marc, Franke, Lude, Wijmenga, Cisca, Fu, Jingyuan, van der Wijst, Monique G. P., Melé, Marta, Lansdorp, Peter, Zhernakova, Alexandra
Published in Communications biology (09.06.2022)
Published in Communications biology (09.06.2022)
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Journal Article
Hematopoietic Npc1 mutation shifts gut microbiota composition in Ldlr−/− mice on a high-fat, high-cholesterol diet
Houben, Tom, Penders, John, Oligschlaeger, Yvonne, dos Reis, Inês A. Magro, Bonder, Marc-Jan, Koonen, Debby P., Fu, Jingyuan, Hofker, Marten H., Shiri-Sverdlov, Ronit
Published in Scientific reports (18.10.2019)
Published in Scientific reports (18.10.2019)
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Journal Article
Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease
Imhann, Floris, Vich Vila, Arnau, Bonder, Marc Jan, Fu, Jingyuan, Gevers, Dirk, Visschedijk, Marijn C, Spekhorst, Lieke M, Alberts, Rudi, Franke, Lude, van Dullemen, Hendrik M, Ter Steege, Rinze W F, Huttenhower, Curtis, Dijkstra, Gerard, Xavier, Ramnik J, Festen, Eleonora A M, Wijmenga, Cisca, Zhernakova, Alexandra, Weersma, Rinse K
Published in Gut (01.01.2018)
Published in Gut (01.01.2018)
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