Biological interpretation of genome-wide association studies using predicted gene functions
Pers, Tune H, Karjalainen, Juha M, Chan, Yingleong, Westra, Harm-Jan, Wood, Andrew R, Yang, Jian, Lui, Julian C, Vedantam, Sailaja, Gustafsson, Stefan, Esko, Tonu, Frayling, Tim, Speliotes, Elizabeth K, Boehnke, Michael, Raychaudhuri, Soumya, Fehrmann, Rudolf S N, Hirschhorn, Joel N, Franke, Lude
Published in Nature communications (19.01.2015)
Published in Nature communications (19.01.2015)
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Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids
van der Graaf, Adriaan, Claringbould, Annique, Rimbert, Antoine, Heijmans, Bastiaan T., Hoen, Peter A. C.’t, van Meurs, Joyce B. J., Jansen, Rick, Franke, Lude, Westra, Harm-Jan, Li, Yang, Wijmenga, Cisca, Sanna, Serena
Published in Nature communications (01.10.2020)
Published in Nature communications (01.10.2020)
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Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure
Oelen, Roy, de Vries, Dylan H, Brugge, Harm, Gordon, M Grace, Vochteloo, Martijn, Ye, Chun J, Westra, Harm-Jan, Franke, Lude, van der Wijst, Monique G P
Published in Nature communications (07.06.2022)
Published in Nature communications (07.06.2022)
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Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells
Kasela, Silva, Kisand, Kai, Tserel, Liina, Kaleviste, Epp, Remm, Anu, Fischer, Krista, Esko, Tõnu, Westra, Harm-Jan, Fairfax, Benjamin P, Makino, Seiko, Knight, Julian C, Franke, Lude, Metspalu, Andres, Peterson, Pärt, Milani, Lili
Published in PLoS genetics (01.03.2017)
Published in PLoS genetics (01.03.2017)
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Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes
Westra, Harm-Jan, Martínez-Bonet, Marta, Onengut-Gumuscu, Suna, Lee, Annette, Luo, Yang, Teslovich, Nikola, Worthington, Jane, Martin, Javier, Huizinga, Tom, Klareskog, Lars, Rantapaa-Dahlqvist, Solbritt, Chen, Wei-Min, Quinlan, Aaron, Todd, John A, Eyre, Steve, Nigrovic, Peter A, Gregersen, Peter K, Rich, Stephen S, Raychaudhuri, Soumya
Published in Nature genetics (01.10.2018)
Published in Nature genetics (01.10.2018)
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IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors
Amariuta, Tiffany, Luo, Yang, Gazal, Steven, Davenport, Emma E., van de Geijn, Bryce, Ishigaki, Kazuyoshi, Westra, Harm-Jan, Teslovich, Nikola, Okada, Yukinori, Yamamoto, Kazuhiko, Price, Alkes L., Raychaudhuri, Soumya
Published in American journal of human genetics (02.05.2019)
Published in American journal of human genetics (02.05.2019)
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PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs
Vochteloo, Martijn, Deelen, Patrick, Vink, Britt, Tsai, Ellen A, Runz, Heiko, Andreu-Sánchez, Sergio, Fu, Jingyuan, Zhernakova, Alexandra, Westra, Harm-Jan, Franke, Lude
Published in Genome Biology (22.01.2024)
Published in Genome Biology (22.01.2024)
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Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease
Hu, Shixian, Uniken Venema, Werna T, Westra, Harm-Jan, Vich Vila, Arnau, Barbieri, Ruggero, Voskuil, Michiel D, Blokzijl, Tjasso, Jansen, Bernadien H, Li, Yanni, Daly, Mark J, Xavier, Ramnik J, Dijkstra, Gerard, Festen, Eleonora A, Weersma, Rinse K
Published in Nature communications (18.02.2021)
Published in Nature communications (18.02.2021)
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Human disease-associated genetic variation impacts large intergenic non-coding RNA expression
Kumar, Vinod, Westra, Harm-Jan, Karjalainen, Juha, Zhernakova, Daria V, Esko, Tõnu, Hrdlickova, Barbara, Almeida, Rodrigo, Zhernakova, Alexandra, Reinmaa, Eva, Võsa, Urmo, Hofker, Marten H, Fehrmann, Rudolf S N, Fu, Jingyuan, Withoff, Sebo, Metspalu, Andres, Franke, Lude, Wijmenga, Cisca
Published in PLoS genetics (01.01.2013)
Published in PLoS genetics (01.01.2013)
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Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci
Trynka, Gosia, Westra, Harm-Jan, Slowikowski, Kamil, Hu, Xinli, Xu, Han, Stranger, Barbara E., Klein, Robert J., Han, Buhm, Raychaudhuri, Soumya
Published in American journal of human genetics (02.07.2015)
Published in American journal of human genetics (02.07.2015)
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An integrative approach for building personalized gene regulatory networks for precision medicine
van der Wijst, Monique G P, de Vries, Dylan H, Brugge, Harm, Westra, Harm-Jan, Franke, Lude
Published in Genome medicine (19.12.2018)
Published in Genome medicine (19.12.2018)
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Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data
Li, Shuang, Schmid, Katharina T, de Vries, Dylan H, Korshevniuk, Maryna, Losert, Corinna, Oelen, Roy, van Blokland, Irene V, Groot, Hilde E, Swertz, Morris A, van der Harst, Pim, Westra, Harm-Jan, van der Wijst, Monique G P, Heinig, Matthias, Franke, Lude
Published in Genome Biology (18.04.2023)
Published in Genome Biology (18.04.2023)
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Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development
Kim, Taehyeung, Martínez-Bonet, Marta, Wang, Qiang, Hackert, Nicolaj, Sparks, Jeffrey A, Baglaenko, Yuriy, Koh, Byunghee, Darbousset, Roxane, Laza-Briviesca, Raquel, Chen, Xiaoting, Aguiar, Vitor R C, Chiu, Darren J, Westra, Harm-Jan, Gutierrez-Arcelus, Maria, Weirauch, Matthew T, Raychaudhuri, Soumya, Rao, Deepak A, Nigrovic, Peter A
Published in Nature communications (09.03.2024)
Published in Nature communications (09.03.2024)
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Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians
Pierce, Brandon L, Tong, Lin, Chen, Lin S, Rahaman, Ronald, Argos, Maria, Jasmine, Farzana, Roy, Shantanu, Paul-Brutus, Rachelle, Westra, Harm-Jan, Franke, Lude, Esko, Tonu, Zaman, Rakibuz, Islam, Tariqul, Rahman, Mahfuzar, Baron, John A, Kibriya, Muhammad G, Ahsan, Habibul
Published in PLoS genetics (01.12.2014)
Published in PLoS genetics (01.12.2014)
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An epigenome-wide association study identifies multiple DNA methylation markers of exposure to endocrine disruptors
Lu, Xueling, Fraszczyk, Eliza, van der Meer, Thomas P., van Faassen, Martijn, Bloks, Vincent W., Kema, Ido P., van Beek, André P., Li, Shuang, Franke, Lude, Westra, Harm-Jan, Xu, Xijin, Huo, Xia, Snieder, Harold, Wolffenbuttel, Bruce H.R., van Vliet-Ostaptchouk, Jana V.
Published in Environment international (01.11.2020)
Published in Environment international (01.11.2020)
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Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial
Davenport, Emma E, Amariuta, Tiffany, Gutierrez-Arcelus, Maria, Slowikowski, Kamil, Westra, Harm-Jan, Luo, Yang, Shen, Ciyue, Rao, Deepak A, Zhang, Ying, Pearson, Stephen, von Schack, David, Beebe, Jean S, Bing, Nan, John, Sally, Vincent, Michael S, Zhang, Baohong, Raychaudhuri, Soumya
Published in Genome Biology (19.10.2018)
Published in Genome Biology (19.10.2018)
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Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression
Fu, Jingyuan, Wolfs, Marcel G M, Deelen, Patrick, Westra, Harm-Jan, Fehrmann, Rudolf S N, Te Meerman, Gerard J, Buurman, Wim A, Rensen, Sander S M, Groen, Harry J M, Weersma, Rinse K, van den Berg, Leonard H, Veldink, Jan, Ophoff, Roel A, Snieder, Harold, van Heel, David, Jansen, Ritsert C, Hofker, Marten H, Wijmenga, Cisca, Franke, Lude
Published in PLoS genetics (01.01.2012)
Published in PLoS genetics (01.01.2012)
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Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response
de Vries, Dylan H, Matzaraki, Vasiliki, Bakker, Olivier B, Brugge, Harm, Westra, Harm-Jan, Netea, Mihai G, Franke, Lude, Kumar, Vinod, van der Wijst, Monique G P
Published in PLoS pathogens (01.04.2020)
Published in PLoS pathogens (01.04.2020)
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Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'
Deelen, Patrick, Menelaou, Androniki, van Leeuwen, Elisabeth M, Kanterakis, Alexandros, van Dijk, Freerk, Medina-Gomez, Carolina, Francioli, Laurent C, Hottenga, Jouke Jan, Karssen, Lennart C, Estrada, Karol, Kreiner-Møller, Eskil, Rivadeneira, Fernando, van Setten, Jessica, Gutierrez-Achury, Javier, Westra, Harm-Jan, Franke, Lude, van Enckevort, David, Dijkstra, Martijn, Byelas, Heorhiy, van Duijn, Cornelia M, de Bakker, Paul I W, Wijmenga, Cisca, Swertz, Morris A
Published in European journal of human genetics : EJHG (01.11.2014)
Published in European journal of human genetics : EJHG (01.11.2014)
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Correction for both common and rare cell types in blood is important to identify genes that correlate with age
Pellegrino-Coppola, Damiano, Claringbould, Annique, Stutvoet, Maartje, Boomsma, Dorret I, Ikram, M Arfan, Slagboom, P Eline, Westra, Harm-Jan, Franke, Lude
Published in BMC genomics (15.03.2021)
Published in BMC genomics (15.03.2021)
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