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Kemmeren Group

Patrick Kemmeren

Patrick Kemmeren obtained his PhD in 2005 from Utrecht University for his work on analyzing and integrating genome-scale data. A postdoctoral fellowship obtained through EMBO and the Netherlands Genomics Initiative (NGI) allowed him to work at the University of California, San Francisco. Under the supervision of Nevan Krogan, he worked on the definition of an accurate and comprehensive map of stable protein-protein interactions. After returning to University Medical Center Utrecht (UMC Utrecht), he obtained a VENI grant from the Dutch Science Foundation (NWO) in 2007. After starting his own research group, Patrick received an NWO VIDI award in 2012 to investigate further the molecular mechanisms underlying genetic interactions. In 2013, Patrick became an Assistant Professor at the Center for Molecular Medicine, UMC Utrecht. In addition to these research activities, Patrick has been the coordinator of the High-Performance Computing facility for Life Sciences at Utrecht Science Park since 2012 and executive committee member of the Utrecht Bioinformatics Center since 2014. Patrick joined the Princess Máxima Center for Pediatric Oncology in 2016.

Research

The Kemmeren group uses bioinformatics and systems biology to understand the molecular mechanisms underlying genetic interactions in relation to cellular processes and complex human diseases. We have developed a unique combination of expertise in bioinformatics, gene expression profiling and molecular-genetic interactions. While our focus is on the computational aspects, we have a strong collaboration with the Holstege group, thus enabling a truly multidisciplinary approach with biochemistry, molecular biology and genetics, with bioinformatics, systems biology and functional genomics also being part of our expertise. We also have extensive experience with setting up and coordinating bioinformatics infrastructures such as High-Performance Computing, workflow management systems and data sharing and collaboration facilities.

Key publications

  • A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. Sameith K, Amini S, Groot Koerkamp MJ, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FC, Kemmeren P. BMC Biology. 2015 Dec 23;13(1):112. 
  • Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.
    Kemmeren P, Sameith K, Pasch LA van de, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, Wageningen S van, Ko CW, Heesch S van, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, Hooff SR van, Bakel H van, Sluiters E, Bakker LV, Snel B, Lijnzaad P, Leenen D van, Groot Koerkamp MJ, Holstege FC Cell. 2014 Apr 24;157(3):740-52. 
  • Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.
    Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P. BMC Genomics. 2012 Jun 14;13:239. 
  • Functional overlap and regulatory links shape genetic interactions between signaling pathways.
    Wageningen S van, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, Castro IJ de, Leenen D van, Groot Koerkamp MJ, Ko C, Miles AJ, Brabers NAC, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, Pasch LAL van de, Hooff SR van, Bakker LV, Krogan NJ, Snel B, Holstege FCP Cell. 2010 Dec 10;143(6):991-1004
  • A consensus of core protein complex compositions for Saccharomyces cerevisiae.Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HW, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FC, Kemmeren P.
    Molecular Cell. 2010 Jun 25;38(6):916-28. 

Group members

  • Patrick Kemmeren, PI
  • Hinri Kerstens, Postdoc/bioinformatician
  • Saman Amini, PhD student
  • Wim de Jonge, PhD student (shared with Holstege)
  • Jayne Hehir-Kwa, post-doc/bioinformatician (shared with diagnostics lab)
  • Tineka Blake, bioinformatician
  • Josephine Daub, post-doc/bioinformatician
  • Ellen de Jong bachelor student

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