University of Groningen
Integration techniques for modern bioinformatics workflows
Kanterakis, Alexandros
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Publication date: 2018
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Kanterakis, A. (2018). Integration techniques for modern bioinformatics workflows. University of Groningen.
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List of publications
• Alexandros Kanterakis, Patrick Deelen, Freerk van Dijk, Heorhiy Byelas, Martijn Dijkstra and Morris A Swertz. Molgenis-impute: imputation pipeline in a box. BMC Res Notes. 2015; 8: 359.
• Elisabeth M van Leeuwen, Alexandros Kanterakis, Patrick Deelen, Mathijs V Kattenberg, The Genome of the Netherlands Consortium, P Eline Slagboom, Paul I W de Bakker, Cisca Wijmenga, Morris A Swertz, Dorret I Boomsma, Cornelia M van Duijn, Lennart C Karssen & Jouke Jan Hottenga. Population-specific genotype imputations using minimac or IMPUTE2. Nature Protocols 10, 1285–1296 (2015).
• Elisabeth M. van Leeuwen, Lennart C. Karssen, Joris Deelen, Aaron Isaacs, Car-olina Medina-Gomez, Hamdi Mbarek, Alexandros Kanterakis, Stella Trompet, Iris Postmus, Niek Verweij, David J. van Enckevort, Jennifer E. Huffman, Charles C. White, Mary F. Feitosa, Traci M. Bartz, Ani Manichaikul, Peter K. Joshi, Gina M. Peloso, Patrick Deelen, Freerk van Dijk, Gonneke Willemsen, Eco J. de Geus, Yuri Milaneschi, Brenda W.J.H. Penninx, Laurent C. Francioli, Androniki Menelaou, Sara L. Pulit, Fernando Rivadeneira, Albert Hofman, Ben A. Oostra, Oscar H. Franco, Irene Mateo Leach, Marian Beekman, Anton J.M. de Craen, Hae-Won Uh, Holly Trochet, Lynne J. Hocking, David J. Porteous, Naveed Sat-tar, Chris J. Packard, Brendan M. Buckley, Jennifer A. Brody, Joshua C. Bis, Jerome I. Rotter, Josyf C. Mychaleckyj, Harry Campbell, Qing Duan, Leslie A. Lange, James F. Wilson, Caroline Hayward, Ozren Polasek, Veronique Vitart, Igor Rudan, Alan F. Wright, Stephen S. Rich, Bruce M. Psaty, Ingrid B. Borecki, Patricia M. Kearney, David J. Stott, L. Adrienne Cupples, The Genome of the Netherlands Consortium, J. Wouter Jukema, Pim van der Harst, Eric J. Sijbrands, Jouke-Jan Hottenga, Andre G. Uitterlinden, Morris A. Swertz, Gert-Jan B. van Ommen, Paul I.W. de Bakker, P. Eline Slagboom, Dorret I. Boomsma, Cisca Wi-jmenga & Cornelia M. van Duijn. Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nature communications. 2015 Mar 9;6.
• Alexandros Kanterakis, Joël Kuiper, George Potamias and Morris A. Swertz. PyPedia: using the wiki paradigm as crowd sourcing environment for bioinfor-matics protocols. Source Code for Biology and Medicine 2015 10:14.
• Patrick Deelen, Androniki Menelaou, Elisabeth M van Leeuwen, Alexandros
Kanterakis, Freerk van Dijk, Carolina Medina-Gomez, Laurent C Francioli,
Jouke Jan Hottenga, Lennart C Karssen, Karol Estrada, Eskil Kreiner-Møller, Fernando Rivadeneira, Jessica van Setten, Javier Gutierrez-Achury, Harm-Jan Westra, Lude Franke, David van Enckevort, Martijn Dijkstra, Heorhiy Byelas, Cornelia M van Duijn, Genome of the Netherlands Consortium, Paul I W de Bakker, Cisca Wijmenga and Morris A Swertz. European Journal of Human Genetics (2014) 22, 1321–1326.
• Laurent C Francioli, Androniki Menelaou, Sara L Pulit, Freerk van Dijk, Pier Francesco Palamara, Clara C Elbers, Pieter B T Neerincx, Kai Ye, Victor Guryev, Wigard P Kloosterman, Patrick Deelen, Abdel Abdellaoui, Elisabeth M van Leeuwen, Mannis van Oven, Martijn Vermaat, Mingkun Li, Jeroen F J Laros, Lennart C Karssen, Alexandros Kanterakis, Najaf Amin, Jouke Jan Hottenga, Eric-Wubbo Lameijer, Mathijs Kattenberg, Martijn Dijkstra, Heorhiy Byelas, Jessica van Setten, Barbera D C van Schaik, Jan Bot, Isaäc J Nijman, Ivo Renkens, Tobias Marschall, Alexander Schönhuth, Jayne Y Hehir-Kwa, Robert E Handsaker, Paz Polak, Mashaal Sohail, Dana Vuzman, Fereydoun Hormozdiari, David van Enckevort, Hailiang Mei, Vyacheslav Koval, Matthijs H Moed, K Joeri van der Velde, Fernando Rivadeneira, Karol Estrada, Carolina Medina-Gomez, Aaron Isaacs, Steven A McCarroll, Marian Beekman, Anton J M de Craen, H Eka D Suchiman, Albert Hofman, Ben Oostra, André G Uitterlinden, Gonneke Willemsen, LifeLines Cohort Study, Mathieu Platteel, Jan H Veldink, Leonard H van den Berg, Steven J Pitts, Shobha Potluri, Purnima Sundar, David R Cox, Shamil R Sunyaev, Johan T den Dunnen, Mark Stoneking, Peter de Knijff, Manfred Kayser, Qibin Li, Yingrui Li, Yuanping Du, Ruoyan Chen, Hongzhi Cao, Ning Li, Sujie Cao, Jun Wang, Jasper A Bovenberg, Itsik Pe’er, P Eline Slagboom, Cornelia M van Duijn, Dorret I Boomsma, Gert-Jan B van Ommen, Paul I W de Bakker, Morris A Swertz & Cisca Wijmenga for The Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics 2014; 46, 818–25.
• Dorret I Boomsma, Cisca Wijmenga, Eline P Slagboom, Morris A Swertz, Lennart C Karssen, Abdel Abdellaoui, Kai Ye, Victor Guryev, Martijn Vermaat, Freerk
van Dijk, Laurent C Francioli, Jouke Jan Hottenga, Jeroen F J Laros, Qibin Li, Yingrui Li, Hongzhi Cao, Ruoyan Chen, Yuanping Du, Ning Li, Sujie Cao, Jessica van Setten, Androniki Menelaou, Sara L Pulit, Jayne Y Hehir-Kwa, Marian Beekman, Clara C Elbers, Heorhiy Byelas, Anton J M de Craen, Patrick Deelen, Martijn Dijkstra, Johan T den Dunnen, Peter de Knijff, Jeanine Houwing-Duistermaat, Vyacheslav Koval, Karol Estrada, Albert Hofman, Alexandros
Kanterakis, David van Enckevort, Hailiang Mai, Mathijs Kattenberg, Elisabeth
M van Leeuwen, Pieter B T Neerincx, Ben Oostra, Fernanodo Rivadeneira, Eka H D Suchiman, Andre G Uitterlinden, Gonneke Willemsen, Bruce H Wolffenbuttel, Jun Wang, Paul I W de Bakker, Gert-Jan van Ommen and Cornelia M van Duijn. The Genome of the Netherlands: design, and project goals. European Journal of Human Genetics (2014) 22, 221–227.
• Rodrigo Almeida, Isis Ricaño-Ponce, Vinod Kumar, Patrick Deelen, Agata Szperl, Gosia Trynka, Javier Gutierrez-Achury, Alexandros Kanterakis, Harm-Jan Westra, Lude Franke, Morris A. Swertz, Mathieu Platteel, Jose Ramon Bilbao, Donatella Barisani, Luigi Greco, Luisa Mearin, Victorien M. Wolters, Chris Mulder, Maria Cristina Mazzilli, Ajit Sood, Bozena Cukrowska, Concepción Núñez, Riccardo Pratesi, Sebo Withoff, Cisca Wijmenga. Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant. Human Molecular Genetics, 23(9), 2014, Pages 2481–2489.
• Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, Joeri K van der Velde,
Alexandros Kanterakis, Erik T Roos, Joris Lops, Gudmundur A Thorisson,
Danny Arends, George Byelas, Juha Muilu, Anthony J Brookes, Engbert O de Brock, Ritsert C Jansen and Helen Parkinson. The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC bioinformatics 11, no. 12 (2010): S12.
• Szperl AM, Ricaño-Ponce I, Li JK, Deelen P, Kanterakis A, Plagnol V, van Dijk F, Westra HJ, Trynka G, Mulder CJ, Swertz M. Exome sequencing in a family segregating for celiac disease. Clinical genetics. 2011 Aug 1;80(2):138-47.
Conference Presentations
• Alexandros Kanterakis, Tomasz Adamusiak, Juha Muilu, Helen Parkinson, Despoina Antonakaki, Morris A. Swertz. Towards a federated microarray gene expression repository using MOLGENIS and MAGE-TAB. 11th Annual Bioinfor-matics Open Source Conference (BOSC) 2010. Boston, Massachusetts, USA.
• Alexandros Kanterakis, George Potamias, Morris A Swertz. PyPedia: A python crowdsourcing development environment for bioinformatics and com-putational biology. 13th Annual Bioinformatics Open Source Conference (BOSC 2012) 2012, Long Beach, CA, USA.
• Alexandros Kanterakis, George Potamias, Morris A Swertz. Pypedia: a python development environment on a wiki. EuroPython 2012, Florence, Italy.
