Marieke Kuijjer

Image of Marieke Kuijjer
Norwegian version of this page
Phone +47 22840528
Visiting address Forskningsparken E3 Gaustadalléen 21 0349 Oslo
Postal address Postboks 1137 Blindern 0318 Blindern

Current Position

  • October 2018 - present: Group Leader, Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo

Academic Interests

  • Gene regulatory networks
  • Cancer genomics
  • Data integration
  • Computational Biology
  • Method development
  • Systems Medicine
  • Bioinformatics
  • Sarcomas



  • Dana-Farber Cancer Insitute, Boston, MA, USA
  • Harvard Chan School of Public Health, Boston, MA, USA
  • 07/2013-08/2018: Postdoctoral Fellow
  • 05/2013-07/2013: Visiting Scientist


  • 12/2008-06/2013: Doctor of Philosophy (PhD), Leiden University Medical Center, Leiden, the Netherlands
  • 09/2006-12/2008: Master of Science (MSc) in Biomedical Sciences, Leiden University Medical Center, Leiden, the Netherlands
  • 09/2003-07/2007: Bachelor of Science (BSc) in Biomedical Sciences, Leiden University Medical Center, Leiden, the Netherlands

Awards and Grants:

  • 2016-2018: Charles A. King Postdoctoral Fellowship, Sara Elizabeth O’Brien and Bank of America, co-Trustees
  • 2016-2017: National Cancer Institute Brain Cancer Specialized Program of Research Excellence Career Enhancement Program Award


Tags: Cancer Genomics, Systems medicine, Bioinformatics, Computational Biology, Genomics, Sarcomas, Cancer, Statistikk sannsynlighetsregning og forsikring


  • Grad, Iwona; Hanes, Robert; Ayuda-Durán, Pilar; Kuijjer, Marieke Lydia; Enserink, Jorrit; Meza-Zepeda, Leonardo A & Myklebost, Ola (2021). Discovery of novel candidates for anti- liposarcoma therapies by medium-scale high-throughput drug screening. PLOS ONE.  ISSN 1932-6203.  16(3) . doi: 10.1371/journal.pone.0248140 Full text in Research Archive.
  • Andreeva, Olga; Li, Wei; Ding, Wei; Kuijjer, Marieke Lydia; Quackenbush, John & Chen, Ping (2020). Catalysis Clustering with GAN by Incorporating Domain Knowledge, In Rajesh Gupta & Yan Liu (ed.),  KDD '20: Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining.  Association for Computing Machinery (ACM).  ISBN 978-1-4503-7998-4.  Proceeding.  s 1344 - 1352
  • Fagny, Maud; Kuijjer, Marieke Lydia; Stam, Maike; Joets, Johann; Turc, Olivier; Rozière, Julien; Pateyron, Stéphanie; Venon, Anthony & Vitte, Clémentine (2020). Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Frontiers in Genetics.  ISSN 1664-8021.  11 . doi: 10.3389/fgene.2020.606285 Full text in Research Archive.
  • Kuijjer, Marieke Lydia (2020). Predicting Cancer Evolution Using Cell State Dynamics. Cancer Research.  ISSN 0008-5472.  80(15) . doi: 10.1158/0008-5472.CAN-20-1878
  • Kuijjer, Marieke Lydia; Fagny, Maud; Marin, Alessandro; Quackenbush, John & Glass, Kimberly (2020). PUMA: PANDA Using MicroRNA Associations. Bioinformatics.  ISSN 1367-4803. . doi: 10.1093/bioinformatics/btaa571 Full text in Research Archive.
  • Lopes-ramos, Camila; Chen, Cho-Yi; Kuijjer, Marieke Lydia; Paulson, Joseph N.; Sonawane, Abhijeet; Fagny, Maud; Platig, John; Glass, Kimberly; Quackenbush, John & DeMeo, Dawn L. (2020). Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell reports.  ISSN 2211-1247.  31(12) . doi: 10.1016/j.celrep.2020.107795 Full text in Research Archive.
  • Qiang, Jipeng; Ding, Wei; Kuijjer, Marieke Lydia; Quackenbush, John & Chen, Ping (2020). Clustering Sparse Data with Feature Correlation with Application to Discover Subtypes in Cancer. IEEE Access.  ISSN 2169-3536.  8, s 67775- 67789 Full text in Research Archive.
  • Barnett, Ian; Nishant, Malik; Kuijjer, Marieke Lydia; Mucha, Peter & Onnela, Jukka-Pekka (2019). Feature-based classification of networks. Network Science.  ISSN 2050-1242.  7(3), s 438- 444 . doi:
  • Fagny, Maud; Platig, John; Kuijjer, Marieke Lydia; Lin, Xihong & Quackenbush, John (2019). Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. British Journal of Cancer.  ISSN 0007-0920. . doi: 10.1038/s41416-019-0614-3 Full text in Research Archive.
  • Kuijjer, Marieke Lydia; Hsieh, Ping-Han; Quackenbush, John & Glass, Kimberly (2019). lionessR: single sample network inference in R. BMC Cancer.  ISSN 1471-2407.  19(1003) . doi: 10.1186/s12885-019-6235-7 Full text in Research Archive.
  • Kuijjer, Marieke Lydia; Tung, Matthew George; Yuan, GuoCheng; Quackenbush, John & Glass, Kimberly (2019). Estimating Sample-Specific Regulatory Networks. iScience.  ISSN 2589-0042.  14, s 226- 240 . doi: 10.1016/j.isci.2019.03.021 Full text in Research Archive.
  • van IJzendoorn, David G.P.; Szuhai, Karoly; Briaire-De Bruijn, Inge H; Kostine, Marie; Kuijjer, Marieke Lydia & Bovée, Judith V.M.G. (2019). Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. PLoS Computational Biology.  ISSN 1553-734X.  15(2), s 1- 19 . doi: 10.1371/journal.pcbi.1006826 Full text in Research Archive.
  • Wong, Kim; van der Weyden, Louise; Schott, Courtney R.; Foote, Alastair; Constantino-Casas, Fernando; Smith, Sionagh; Dobson, Jane M.; Murchison, Elizabeth P.; Wu, Hong; Yeh, Iwei; Fullen, Douglas R.; Joseph, Nancy; Bastian, Boris C.; Patel, Rajiv M.; Martincorena, Inigo; Robles-Espinoza, Carla Daniela; Iyer, Vivek; Kuijjer, Marieke Lydia; Arends, Mark J.; Brenn, Thomas; Harms, Paul W.; Wood, Geoffrey A. & Adams, David J. (2019). Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Nature Communications.  ISSN 2041-1723.  10(353), s 1- 14 . doi: 10.1038/s41467-018-08081-1 Full text in Research Archive.
  • Kang, Tianyu; Zarringhalam, Kourosh; Kuijjer, Marieke Lydia; Chen, Ping; Quackenbush, John & Ding, Wei (2018). Clustering on Sparse Data in Non-Overlapping Feature Space with Applications toCancer Subtyping. IEEE International Conference on Data Mining. Proceedings.  ISSN 1550-4786. . doi: 10.1109/ICDM.2018.00138
  • Kuijjer, Marieke; Paulson, Joseph N.; Salzman, Peter; Ding, Wei & Quackenbush, John (2018). Cancer subtype identification using somatic mutation data. British Journal of Cancer.  ISSN 0007-0920.  118(11), s 1492- 1501 . doi: 10.1038/s41416-018-0109-7
  • Lopes-Ramos, Camila; Kuijjer, Marieke; Ogino, Shuji; Fuchs, Charles; DeMeo, Dawn L; Glass, Kimberly & Quackenbush, John (2018). Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research.  ISSN 0008-5472.  78(19), s 5538- 5547 . doi: 10.1158/0008-5472.CAN-18-0454
  • Fagny, Maud; Paulson, Joseph N.; Kuijjer, Marieke; Sonawane, Abhijeet; Chen, Cho-Yi; Lopes-ramos, Camila; Glass, Kimberly; Quackenbush, John & Platig, John (2017). Exploring regulation in tissues with eQTL networks. Proceedings of the National Academy of Sciences of the United States of America.  ISSN 0027-8424. . doi: 10.1073/pnas.1707375114
  • Hill, Katherine; Kelly, Andrew; Kuijjer, Marieke; Barry, William; Rattani, Ahmed; Garbutt, Cassandra; Kissick, Haydn; Janeway, Katherine A.; Perez-Atayde, Antonio R.; Goldsmith, Jeffrey; Gebhardt, Mark C.; Arredouani, Mohamed; Cote, Greg; Hornicek, Francis John; Choy, Edwin; Duan, Zhenfeng; Quackenbush, John; Haibe-Kains, Benjamin & Spentzos, Dimitrios (2017). An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. Journal of Hematology & Oncology.  ISSN 1756-8722. . doi: 10.1186/s13045-017-0465-4
  • Lopes-ramos, Camila; Paulson, Joseph N.; Chen, Cho-Yi; Kuijjer, Marieke; Fagny, Maud; Platig, John; Sonawane, Abhijeet; DeMeo, Dawn L.; Quackenbush, John & Glass, Kimberly (2017). Regulatory network changes between cell lines and their tissues of origin. BMC Genomics.  ISSN 1471-2164. . doi: 10.1186/s12864-017-4111-x
  • Paulson, Joseph N.; Chen, Cho-Yi; Lopes-Ramos, Camila; Kuijjer, Marieke; Platig, John; Sonawane, Abhijeet; Fagny, Maud; Glass, Kimberly & Quackenbush, John (2017). Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics.  ISSN 1471-2105. . doi: 10.1186/s12859-017-1847-x
  • Sonawane, Abhijeet; Platig, John; Fagny, Maud; Chen, Cho-Yi; Paulson, Joseph N.; DeMeo, Dawn L; Quackenbush, John; Glass, Kimberly & Kuijjer, Marieke (2017). Understanding Tissue-Specific Gene Regulation. Cell reports.  ISSN 2211-1247.  21(4) . doi: 10.1016/j.celrep.2017.10.001
  • van IJzendoorn, David G.P.; Glass, Kimberly; Quackenbush, John & Kuijjer, Marieke (2016). PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics.  ISSN 1367-4803. . doi: 10.1093/bioinformatics/btw422
  • Baranski, Zuzanna; Booij, Tijmen H.; Kuijjer, Marieke; de Jong, Yvonne; Cleton-Jansen, Anne-Marie; Price, Leo S.; van de Water, Bob; Bovée, Judith; Hogendoorn, Pancras C.W. & Danen, Erik H.J. (2015). MEK inhibition induces apoptosis in osteosarcoma cells with constitutive ERK1/2 phosphorylation. Genes & cancer.  ISSN 1947-6019.  6
  • Buddingh, Emmeline P.; Ruslan, S. Eriaty N.; Reijnders, Christianne M.A.; Szuhai, Karoly; Kuijjer, Marieke; Roelofs, Helene; Hogendoorn, Pancras C.W.; Egeler, Maarten; Cleton-Jansen, Anne-Marie & Lankester, Arjan C. (2015). Mesenchymal stromal cells of osteosarcoma patients do not show evidence of neoplastic changes during long‑term culture. Clinical Sarcoma Research.  ISSN 2045-3329. . doi: 10.1186/s13569-015-0031-1
  • Pahl, Jens H.W.; Santos, Susy J.; Kuijjer, Marieke; Boerman, Gerharda H.; Sand, Laurens G.L.; Szuhai, Karoly; Cleton-Jansen, Anne-Marie; Egeler, R. Maarten; Bovée, Judith V.M.G.; Schilham, Marco W. & Lankester, Arjan C. (2015). Expression of the immune regulation antigen CD70 in osteosarcoma. Cancer Cell International.  ISSN 1475-2867. . doi: 10.1186/s12935-015-0181-5
  • Wouters, Maartje C.A.; Dijkgraaf, Eveline M.; Kuijjer, Marieke; Jordanova, Ekaterina S.; Hollema, H.; Welters, M.J.P.; van der Hoeven, J.J.M.; Daemen, T.; Kroep, J.R.; Nijman, H.W. & van der Burg, Sjoerd H. (2015). Interleukin-6 receptor and its ligand interleukin-6 are opposite markers for survival and infiltration with mature myeloid cells in ovarian cancer. Oncoimmunology.  ISSN 2162-4011. . doi: 10.4161/21624011.2014.962397
  • Kuijjer, Marieke; van den Akker, Brendy E.W.M.; Hilhorst, Riet; Mommersteeg, Monique; Buddingh, Emilie P.; Serra, Massimo; Bürger, Horst; Hogendoorn, Pancras C.W. & Cleton-Jansen, Anne-Marie (2014). Kinome and mRNA expression profiling of high-grade osteosarcoma cell lines implies Akt signaling as possible target for therapy. BMC Medical Genomics.  ISSN 1755-8794. . doi: 10.1186/1755-8794-7-4
  • Pahl, Jens H.W.; Kwappenberg, Kitty M.C.; Varypataki, Eleni M.; Santos, Susy J.; Kuijjer, Marieke; Mohamed, Susan; Wijnen, Juul T.; van Tol, Maarten J.D.; Cleton-Jansen, Anne-Marie; Egeler, R. Maarten; Jiskoot, Wim; Lankester, Arjan C. & Schilham, Marco W. (2014). Macrophages inhibit human osteosarcoma cell growth after activation with the bacterial cell wall derivative liposomal muramyl tripeptide in combination with interferon-γ. Journal of Experimental and Clinical Cancer Research.  ISSN 0392-9078. . doi: 10.1186/1756-9966-33-27
  • de Vos van Steenwijk, Peggy J.; Ramwadhdoebe, T.H.; Goedemans, R.; Doorduijn, E.M.; van Ham, J.J.; Gorter, A.; van Hall, Thorbald; Kuijjer, Marieke; van Poelgeest, M.I.E.; van der Burg, Sjoerd H. & Jordanova, Ekaterina S. (2013). Tumor-infiltrating CD14-positive myeloid cells and CD8- positive T-cells prolong survival in patients with cervical carcinoma. International Journal of Cancer.  ISSN 0020-7136. . doi: 10.1002/ijc.28309
  • Kansara, Maya; Leong, Huei San; Lin, Dan Mei; Popkiss, Sophie; Pang, Puiyi; Garsed, Dale W.; Walkley, Carl R.; Cullinane, Carleen; Ellul, Jason; Haynes, Nicole M.; Hicks, Rod; Kuijjer, Marieke; Cleton-Jansen, Anne-Marie; Hinds, Philip W.; Smyth, Mark J. & Thomas, David M. (2013). Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation. Journal of Clinical Investigation.  ISSN 0021-9738. . doi: 10.1172/JCI70559
  • Kuijjer, Marieke; Hogendoorn, Pancras C.W. & Cleton-Jansen, Anne-Marie (2013). Genome-wide analyses on high-grade osteosarcoma: making sense of a genomically most unstable tumor. International Journal of Cancer.  ISSN 0020-7136. . doi: 10.1002/ijc.28124
  • Lenos, Kristiaan; Grawenda, Anna M.; Lodder, Kirsten; Kuijjer, Marieke; Teunisse, Amina F.A.S.; Repapi, Emmanouela; Grochola, Lukasz F.; Bartel, Frank; Hogendoorn, Pancras C.W.; Wuerl, Peter; Taubert, Helge; Cleton-Jansen, Anne-Marie; Bond, Gareth L. & Jochemsen, Aart G. (2012). Alternate Splicing of the p53 Inhibitor HDMX Offers a Superior Prognostic Biomarker than p53 Mutation in Human Cancer. Cancer Research.  ISSN 0008-5472. . doi: 10.1158/0008-5472.CAN-12-0215
  • Mohseny, Alexander B.; Cai, Yongping; Kuijjer, Marieke; Xiao, Wei; van den Akker, Brendy E.W.M.; de Andrea, Carlos E.; Jacobs, Rutger; ten Dijke, Peter; Hogendoorn, Pancras C.W. & Cleton-Jansen, Anne-Marie (2012). The activities of Smad and Gli mediated signalling pathways in high-grade conventional osteosarcoma. European Journal of Cancer.  ISSN 0959-8049. . doi: 10.1016/j.ejca.2012.06.018
  • Pansuriya, Twinkal C.; van Eijk, Ronald; D'Adamo, Pio; van Ruler, Maayke A.J.H.; Kuijjer, Marieke; Oosting, Jan; Cleton-Jansen, Anne-Marie; van Oosterwijk, Jolieke G.; Verbeke, Sofie L.J.; Meijer, Daniëlle; van Wezel, Tom; Nord, Karolin; Sangiorgi, Luca; Toker, Berkin; Liegl-Atzwanger, Bernadette; San-Julian, Mikel; Sciot, Raf; Limaye, Nisha; Kindblom, Lars-Gunnar; Daugaard, Soeren; Godfraind, Catherine; Boon, Laurence M.; Vikkula, Miika; Kurek, Kyle C.; Szuhai, Karoly; French, Pim J. & Bovée, Judith V.M.G. (2011). Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome. Nature Genetics.  ISSN 1061-4036. . doi: 10.1038/ng.1004

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  • Kuijjer, Marieke Lydia; Paulson, Joseph N. & Quackenbush, John (2020). Expression analysis, In Andreas D. Baxevanis; Gary D. Bader & David S. Wishart (ed.),  Bioinformatics.  John Wiley & Sons.  ISBN 978-1-119-33558-0.  Chapter 10.  s 279 - 314
  • Lopes-ramos, Camila; Kuijjer, Marieke Lydia; Ogino, Shuji; Fuchs, Charles S.; DeMeo, Dawn L.; Glass, Kimberly & Quackenbush, John (2019). Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research.  ISSN 0008-5472.

View all works in Cristin

Published Oct. 11, 2018 11:50 AM - Last modified Jan. 7, 2021 8:34 PM

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