An integrative approach for building personalized gene regulatory networks for precision medicine

by Monique G. P. van der Wijst, Dylan H. de Vries, Harm Brugge, Harm-Jan Westra, Lude Franke
Published 2018-12-01

Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids

by Adriaan van der Graaf, Annique Claringbould, Antoine Rimbert, BIOS Consortium, Harm-Jan Westra, Yang Li, Cisca Wijmenga, Serena Sanna
Published 2020-10-01

Correction for both common and rare cell types in blood is important to identify genes that correlate with age

by Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, BIOS Consortium, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra, Lude Franke
Published 2021-03-01

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response.

by Dylan H de Vries, Vasiliki Matzaraki, Olivier B Bakker, Harm Brugge, Harm-Jan Westra, Mihai G Netea, Lude Franke, Vinod Kumar, Monique G P van der Wijst
Published 2020-04-01

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells.

by Silva Kasela, Kai Kisand, Liina Tserel, Epp Kaleviste, Anu Remm, Krista Fischer, Tõnu Esko, Harm-Jan Westra, Benjamin P Fairfax, Seiko Makino, Julian C Knight, Lude Franke, Andres Metspalu, Pärt Peterson, Lili Milani
Published 2017-03-01

reGenotyper: Detecting mislabeled samples in genetic data.

by Konrad Zych, Basten L Snoek, Mark Elvin, Miriam Rodriguez, K Joeri Van der Velde, Danny Arends, Harm-Jan Westra, Morris A Swertz, Gino Poulin, Jan E Kammenga, Rainer Breitling, Ritsert C Jansen, Yang Li
Published 2017-01-01

A genome-wide association study of circulating galectin-3.

by Rudolf A de Boer, Niek Verweij, Dirk J van Veldhuisen, Harm-Jan Westra, Stephan J L Bakker, Ron T Gansevoort, Anneke C Muller Kobold, Wiek H van Gilst, Lude Franke, Irene Mateo Leach, Pim van der Harst
Published 2012-01-01

Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease

by Shixian Hu, Werna T. Uniken Venema, Harm-Jan Westra, Arnau Vich Vila, Ruggero Barbieri, Michiel D. Voskuil, Tjasso Blokzijl, Bernadien H. Jansen, Yanni Li, Mark J. Daly, Ramnik J. Xavier, Gerard Dijkstra, Eleonora A. Festen, Rinse K. Weersma
Published 2021-02-01

Human disease-associated genetic variation impacts large intergenic non-coding RNA expression.

by Vinod Kumar, Harm-Jan Westra, Juha Karjalainen, Daria V Zhernakova, Tõnu Esko, Barbara Hrdlickova, Rodrigo Almeida, Alexandra Zhernakova, Eva Reinmaa, Urmo Võsa, Marten H Hofker, Rudolf S N Fehrmann, Jingyuan Fu, Sebo Withoff, Andres Metspalu, Lude Franke, Cisca Wijmenga
Published 2013-01-01

Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians.

by Brandon L Pierce, Lin Tong, Lin S Chen, Ronald Rahaman, Maria Argos, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Harm-Jan Westra, Lude Franke, Tonu Esko, Rakibuz Zaman, Tariqul Islam, Mahfuzar Rahman, John A Baron, Muhammad G Kibriya, Habibul Ahsan
Published 2014-12-01

Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial

by Emma E. Davenport, Tiffany Amariuta, Maria Gutierrez-Arcelus, Kamil Slowikowski, Harm-Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang, Soumya Raychaudhuri
Published 2018-10-01

An epigenome-wide association study identifies multiple DNA methylation markers of exposure to endocrine disruptors

by Xueling Lu, Eliza Fraszczyk, Thomas P. van der Meer, Martijn van Faassen, Vincent W. Bloks, Ido P. Kema, André P. van Beek, Shuang Li, Lude Franke, Harm-Jan Westra, Xijin Xu, Xia Huo, Harold Snieder, Bruce H.R. Wolffenbuttel, Jana V. van Vliet-Ostaptchouk
Published 2020-11-01

Correction: DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts

by Daria V. Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyurek, Rick Jansen, Brenda W. Penninx, Jouke J. Hottenga, Gonneke Willemsen, Eco J. de Geus, Dorret I. Boomsma, Jan H. Veldink, Leonard H. van den Berg, Cisca Wijmenga, Johan T. den Dunnen, Gert-Jan B. van Ommen, Peter A. C. 't Hoen, Lude Franke
Published 2013-09-01

Correction: DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts.

by Daria V. Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyurek, Rick Jansen, Brenda W. Penninx, Jouke J. Hottenga, Gonneke Willemsen, Eco J. de Geus, Dorret I. Boomsma, Jan H. Veldink, Leonard H. van den Berg, Cisca Wijmenga, Johan T. den Dunnen, Gert-Jan B. van Ommen, Peter A. C. 't Hoen, Lude Franke
Published 2013-09-01

Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

by Jingyuan Fu, Marcel G M Wolfs, Patrick Deelen, Harm-Jan Westra, Rudolf S N Fehrmann, Gerard J Te Meerman, Wim A Buurman, Sander S M Rensen, Harry J M Groen, Rinse K Weersma, Leonard H van den Berg, Jan Veldink, Roel A Ophoff, Harold Snieder, David van Heel, Ritsert C Jansen, Marten H Hofker, Cisca Wijmenga, Lude Franke
Published 2012-01-01

DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts.

by Daria V Zhernakova, Eleonora de Klerk, Harm-Jan Westra, Anastasios Mastrokolias, Shoaib Amini, Yavuz Ariyurek, Rick Jansen, Brenda W Penninx, Jouke J Hottenga, Gonneke Willemsen, Eco J de Geus, Dorret I Boomsma, Jan H Veldink, Leonard H van den Berg, Cisca Wijmenga, Johan T den Dunnen, Gert-Jan B van Ommen, Peter A C 't Hoen, Lude Franke
Published 2013-06-01

Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.

by Rudolf S N Fehrmann, Ritsert C Jansen, Jan H Veldink, Harm-Jan Westra, Danny Arends, Marc Jan Bonder, Jingyuan Fu, Patrick Deelen, Harry J M Groen, Asia Smolonska, Rinse K Weersma, Robert M W Hofstra, Wim A Buurman, Sander Rensen, Marcel G M Wolfs, Mathieu Platteel, Alexandra Zhernakova, Clara C Elbers, Eleanora M Festen, Gosia Trynka, Marten H Hofker, Christiaan G J Saris, Roel A Ophoff, Leonard H van den Berg, David A van Heel, Cisca Wijmenga, Gerard J Te Meerman, Lude Franke
Published 2011-08-01

Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.

by Alexandra Zhernakova, Eli A Stahl, Gosia Trynka, Soumya Raychaudhuri, Eleanora A Festen, Lude Franke, Harm-Jan Westra, Rudolf S N Fehrmann, Fina A S Kurreeman, Brian Thomson, Namrata Gupta, Jihane Romanos, Ross McManus, Anthony W Ryan, Graham Turner, Elisabeth Brouwer, Marcel D Posthumus, Elaine F Remmers, Francesca Tucci, Rene Toes, Elvira Grandone, Maria Cristina Mazzilli, Anna Rybak, Bozena Cukrowska, Marieke J H Coenen, Timothy R D J Radstake, Piet L C M van Riel, Yonghong Li, Paul I W de Bakker, Peter K Gregersen, Jane Worthington, Katherine A Siminovitch, Lars Klareskog, Tom W J Huizinga, Cisca Wijmenga, Robert M Plenge
Published 2011-02-01

Cell Specific eQTL Analysis without Sorting Cells.

by Harm-Jan Westra, Danny Arends, Tõnu Esko, Marjolein J Peters, Claudia Schurmann, Katharina Schramm, Johannes Kettunen, Hanieh Yaghootkar, Benjamin P Fairfax, Anand Kumar Andiappan, Yang Li, Jingyuan Fu, Juha Karjalainen, Mathieu Platteel, Marijn Visschedijk, Rinse K Weersma, Silva Kasela, Lili Milani, Liina Tserel, Pärt Peterson, Eva Reinmaa, Albert Hofman, André G Uitterlinden, Fernando Rivadeneira, Georg Homuth, Astrid Petersmann, Roberto Lorbeer, Holger Prokisch, Thomas Meitinger, Christian Herder, Michael Roden, Harald Grallert, Samuli Ripatti, Markus Perola, Andrew R Wood, David Melzer, Luigi Ferrucci, Andrew B Singleton, Dena G Hernandez, Julian C Knight, Rossella Melchiotti, Bernett Lee, Michael Poidinger, Francesca Zolezzi, Anis Larbi, De Yun Wang, Leonard H van den Berg, Jan H Veldink, Olaf Rotzschke, Seiko Makino, Veikko Salomaa, Konstantin Strauch, Uwe Völker, Joyce B J van Meurs, Andres Metspalu, Cisca Wijmenga, Ritsert C Jansen, Lude Franke
Published 2015-05-01

PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity

by Jessica van Setten, Jennifer A. Brody, Yalda Jamshidi, Brenton R. Swenson, Anne M. Butler, Harry Campbell, Fabiola M. Del Greco, Daniel S. Evans, Quince Gibson, Daniel F. Gudbjartsson, Kathleen F. Kerr, Bouwe P. Krijthe, Leo-Pekka Lyytikäinen, Christian Müller, Martina Müller-Nurasyid, Ilja M. Nolte, Sandosh Padmanabhan, Marylyn D. Ritchie, Antonietta Robino, Albert V. Smith, Maristella Steri, Toshiko Tanaka, Alexander Teumer, Stella Trompet, Sheila Ulivi, Niek Verweij, Xiaoyan Yin, David O. Arnar, Folkert W. Asselbergs, Joel S. Bader, John Barnard, Josh Bis, Stefan Blankenberg, Eric Boerwinkle, Yuki Bradford, Brendan M. Buckley, Mina K. Chung, Dana Crawford, Marcel den Hoed, Josh C. Denny, Anna F. Dominiczak, Georg B. Ehret, Mark Eijgelsheim, Patrick T. Ellinor, Stephan B. Felix, Oscar H. Franco, Lude Franke, Tamara B. Harris, Hilma Holm, Gandin Ilaria, Annamaria Iorio, Mika Kähönen, Ivana Kolcic, Jan A. Kors, Edward G. Lakatta, Lenore J. Launer, Honghuang Lin, Henry J. Lin, Ruth J. F. Loos, Steven A. Lubitz, Peter W. Macfarlane, Jared W. Magnani, Irene Mateo Leach, Thomas Meitinger, Braxton D. Mitchell, Thomas Munzel, George J. Papanicolaou, Annette Peters, Arne Pfeufer, Peter P. Pramstaller, Olli T. Raitakari, Jerome I. Rotter, Igor Rudan, Nilesh J. Samani, David Schlessinger, Claudia T. Silva Aldana, Moritz F. Sinner, Jonathan D. Smith, Harold Snieder, Elsayed Z. Soliman, Timothy D. Spector, David J. Stott, Konstantin Strauch, Kirill V. Tarasov, Unnur Thorsteinsdottir, Andre G. Uitterlinden, David R. Van Wagoner, Uwe Völker, Henry Völzke, Melanie Waldenberger, Harm Jan Westra, Philipp S. Wild, Tanja Zeller, Alvaro Alonso, Christy L. Avery, Stefania Bandinelli, Emelia J. Benjamin, Francesco Cucca, Marcus Dörr, Luigi Ferrucci, Paolo Gasparini, Vilmundur Gudnason, Caroline Hayward, Susan R. Heckbert, Andrew A. Hicks, J. Wouter Jukema, Stefan Kääb, Terho Lehtimäki, Yongmei Liu, Patricia B. Munroe, Afshin Parsa, Ozren Polasek, Bruce M. Psaty, Dan M. Roden, Renate B. Schnabel, Gianfranco Sinagra, Kari Stefansson, Bruno H. Stricker, Pim van der Harst, Cornelia M. van Duijn, James F. Wilson, Sina A. Gharib, Paul I. W. de Bakker, Aaron Isaacs, Dan E. Arking, Nona Sotoodehnia
Published 2018-07-01