Marieke Kuijjer

Head of Group - Marieke Kuijjer Group - Computational Biology and Systems Medicine

Norwegian version of this page

Email marieke.kuijjer@ncmm.uio.no

Phone +47 22840528

Username

Visiting address Forskningsparken E3 Gaustadalléen 21 0349 Oslo

Postal address ,Postboks 1137 Blindern 0318 Oslo

Download business card

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

Background

Research:

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

Education:

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

Osorio, Daniel; Capasso, Anna; Eckhardt, S. Gail; Giri, Uma; Somma, Alexander & Pitts, Todd M. [Show all 14 contributors for this article] (2024). Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. Nature Computational Science. ISSN 2662-8457. doi: 10.1038/s43588-024-00597-5. Full text in Research Archive
Hsieh, Ping-Han; Lopes-Ramos, Camila Miranda; Zucknick, Manuela; Sandve, Geir Kjetil Ferkingstad; Glass, Kimberly & Kuijjer, Marieke (2023). Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics. ISSN 1367-4803. 39(10). doi: 10.1093/bioinformatics/btad610. Full text in Research Archive
Belova, Tatiana; Biondi, Nicola; Hsieh, Ping-Han; Lutsik, Pavlo; Chudasama, Priya & Kuijjer, Marieke (2023). Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer. ISSN 2632-8674. 5(3). doi: 10.1093/narcan/zcad037. Full text in Research Archive
Ben Guebila, Marouen; Wang, Tian; Lopes-Ramos, Camila M.; Fanfani, Viola; Weighill, Des & Burkholz, Rebekka [Show all 25 contributors for this article] (2023). The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology. ISSN 1465-6906. 24(1). doi: 10.1186/s13059-023-02877-1. Full text in Research Archive
Stahlberg, Eric A; Abdel-Rahman, Mohamed; Aguilar, Boris; Asadpoure, Alireza; Beckman, Robert A & Borkon, Lynn L [Show all 33 contributors for this article] (2022). Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. Frontiers in Digital Health. 4. doi: 10.3389/fdgth.2022.1007784. Full text in Research Archive
Birkeälv, Sofia; Harland, Mark; Matsuyama, Larissa Satiko Alcantara Sekim; Rashid, Mamun; Mehta, Ishan & Laye, Jonathan P [Show all 18 contributors for this article] (2022). Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. Journal of Pathology. ISSN 0022-3417. doi: 10.1002/path.6019. Full text in Research Archive
Weber, Cédric R.; Rubio, Teresa; Wang, Longlong; Zhang, Wei; Robert, Philippe Paul Auguste & Akbar, Rahmad [Show all 15 contributors for this article] (2022). Reference-based comparison of adaptive immune receptor repertoires. Cell Reports Methods. 2(8). doi: 10.1016/j.crmeth.2022.100269. Full text in Research Archive
Guebila, Marouen Ben; Morgan, Daniel C.; Glass, Kimberly; Kuijjer, Marieke; Demeo, Dawn L. & Quackenbush, John (2022). gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR Genomics and Bioinformatics. ISSN 2631-9268. 4(1). doi: 10.1093/nargab/lqac002. Full text in Research Archive
Ben Guebila, Marouen; Lopes-Ramos, Camila; Weighill, Deborah; Sonawane, Abhijeet; Burkholz, Rebekka & Shamsaei, Behrouz [Show all 10 contributors for this article] (2022). GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Research (NAR). ISSN 0305-1048. 50, p. D610–D621. doi: 10.1093/nar/gkab778. Full text in Research Archive
Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Kanduri, Chakravarthi; Kompova, Radmila & Vazov, Nikolay Aleksandrov [Show all 41 contributors for this article] (2021). The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nature Machine Intelligence. 3(11), p. 936–944. doi: 10.1038/s42256-021-00413-z.
van Oost, Siddh; Meijer, Debora; Kuijjer, Marieke; Bovée, Judith V.M.G. & de Miranda, Noel F.C.C. (2021). Linking Immunity with Genomics in Sarcomas: Is Genomic Complexity an Immunogenic Trigger? Biomedicines. doi: 10.3390/biomedicines9081048. Full text in Research Archive
Osorio, Daniel; Kuijjer, Marieke & Cai, James (2021). rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btab549. Full text in Research Archive
Calderer i Garcia, Genís & Kuijjer, Marieke (2021). Community Detection in Large-Scale Bipartite Biological Networks. Frontiers in Genetics. ISSN 1664-8021. doi: 10.3389/fgene.2021.649440. Full text in Research Archive
Lopes-Ramos, Camila; Belova, Tatiana; Brunner, Tess; Ben Guebila, Marouen; Osorio, Daniel & Quackenbush, John [Show all 7 contributors for this article] (2021). Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme. Cancer Research. ISSN 0008-5472. 81(21), p. 5401–5412. doi: 10.1158/0008-5472.CAN-21-0730. Full text in Research Archive
Grad, Iwona; Hanes, Robert; Ayuda-Duran, Maria del Pilar; Kuijjer, Marieke Lydia; Enserink, Jorrit & Meza, Leonardo Zepeda [Show all 7 contributors for this article] (2021). Discovery of novel candidates for anti-liposarcoma therapies by medium-scale high-throughput drug screening. PLOS ONE. ISSN 1932-6203. 16(3), p. 1–23. doi: 10.1371/journal.pone.0248140. Full text in Research Archive
Fagny, Maud; Kuijjer, Marieke Lydia; Stam, Maike; Joets, Johann; Turc, Olivier & Rozière, Julien [Show all 9 contributors for this article] (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
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, p. 67775 –67789. doi: 10.1109/ACCESS.2020.2982569. 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 Gupta, Rajesh & Liu, Yan (Ed.), KDD '20: Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining. Association for Computing Machinery (ACM). ISSN 978-1-4503-7998-4. p. 1344–1352. doi: https:/doi.org/10.1145/3394486.3403187.
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
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.
Lopes-ramos, Camila; Chen, Cho-Yi; Kuijjer, Marieke Lydia; Paulson, Joseph N.; Sonawane, Abhijeet & Fagny, Maud [Show all 10 contributors for this article] (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
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), p. 438–444. doi: 10.1017/nws.2019.21.
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, p. 226–240. doi: 10.1016/j.isci.2019.03.021. Full text in Research Archive
Wong, Kim; van der Weyden, Louise; Schott, Courtney R.; Foote, Alastair; Constantino-Casas, Fernando & Smith, Sionagh [Show all 23 contributors for this article] (2019). Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Nature Communications. ISSN 2041-1723. 10(353), p. 1–14. doi: 10.1038/s41467-018-08081-1. 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), p. 1–19. doi: 10.1371/journal.pcbi.1006826. 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.
Lopes-Ramos, Camila; Kuijjer, Marieke; Ogino, Shuji; Fuchs, Charles; DeMeo, Dawn L & Glass, Kimberly [Show all 7 contributors for this article] (2018). Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. ISSN 0008-5472. 78(19), p. 5538–5547. doi: 10.1158/0008-5472.CAN-18-0454.
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), p. 1492–1501. doi: 10.1038/s41416-018-0109-7.
Hill, Katherine; Kelly, Andrew; Kuijjer, Marieke; Barry, William; Rattani, Ahmed & Garbutt, Cassandra [Show all 19 contributors for this article] (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.
Fagny, Maud; Paulson, Joseph N.; Kuijjer, Marieke; Sonawane, Abhijeet; Chen, Cho-Yi & Lopes-ramos, Camila [Show all 9 contributors for this article] (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.
Lopes-ramos, Camila; Paulson, Joseph N.; Chen, Cho-Yi; Kuijjer, Marieke; Fagny, Maud & Platig, John [Show all 10 contributors for this article] (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 [Show all 9 contributors for this article] (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 [Show all 9 contributors for this article] (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.
Pahl, Jens H.W.; Santos, Susy J.; Kuijjer, Marieke; Boerman, Gerharda H.; Sand, Laurens G.L. & Szuhai, Karoly [Show all 11 contributors for this article] (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. [Show all 11 contributors for this article] (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.
Buddingh, Emmeline P.; Ruslan, S. Eriaty N.; Reijnders, Christianne M.A.; Szuhai, Karoly; Kuijjer, Marieke & Roelofs, Helene [Show all 10 contributors for this article] (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.
Baranski, Zuzanna; Booij, Tijmen H.; Kuijjer, Marieke; de Jong, Yvonne; Cleton-Jansen, Anne-Marie & Price, Leo S. [Show all 10 contributors for this article] (2015). MEK inhibition induces apoptosis in osteosarcoma cells with constitutive ERK1/2 phosphorylation. Genes & cancer. ISSN 1947-6019. 6.
Kuijjer, Marieke; van den Akker, Brendy E.W.M.; Hilhorst, Riet; Mommersteeg, Monique; Buddingh, Emilie P. & Serra, Massimo [Show all 9 contributors for this article] (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 [Show all 13 contributors for this article] (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.
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.
de Vos van Steenwijk, Peggy J.; Ramwadhdoebe, T.H.; Goedemans, R.; Doorduijn, E.M.; van Ham, J.J. & Gorter, A. [Show all 11 contributors for this article] (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. [Show all 16 contributors for this article] (2013). Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation. Journal of Clinical Investigation. ISSN 0021-9738. doi: 10.1172/JCI70559.
Lenos, Kristiaan; Grawenda, Anna M.; Lodder, Kirsten; Kuijjer, Marieke; Teunisse, Amina F.A.S. & Repapi, Emmanouela [Show all 14 contributors for this article] (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. [Show all 10 contributors for this article] (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 [Show all 27 contributors for this article] (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.

View all works in Cristin

DeMarzio, Margherita; Glass, Kimberly & Kuijjer, Marieke (2023). Single-sample network modeling on omics data. BMC Biology. ISSN 1741-7007. doi: 10.1186/s12915-023-01783-z.
Sajib, Saikat Das; Florholmen-Kjær, Åse; Brun, Vegard; Mortensen, Elin Synnøve; Hovd, Aud-Malin Karlsson & Tekpli, Xavier [Show all 10 contributors for this article] (2023). Epithelial-to-mesenchymal transition (EMT) is a major contributor to intratumor heterogeneity in lymph node metastasis in breast cancer.
Kuijjer, Marieke (2022). Gene regulatory networks in precision medicine.
Kuijjer, Marieke (2022). A network approach to personalized medicine.
Kuijjer, Marieke (2022). Modeling genome-wide regulatory network rewiring in healthy tissues and cancer.
Kuijjer, Marieke (2022). Modeling regulatory network rewiring in cancer.
Fagny, Maud; Glass, Kimberly & Kuijjer, Marieke (2022). Editorial: Applications and Methods in Genomic Networks. Frontiers in Genetics. ISSN 1664-8021. 13. doi: 10.3389/fgene.2022.936015.
Ben Guebila, Marouen; Weighill, Deborah; Lopes-Ramos, Camila M.; Burkholz, Rebekka; Pop, Romana-Tabita & Palepu, Kalyan [Show all 14 contributors for this article] (2022). An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods. ISSN 1548-7091. 19, p. 511–513. doi: 10.1038/s41592-022-01479-2.
Kuijjer, Marieke (2021). Modeling gene regulatory network rewiring in healthy tissues and cancer.
Kuijjer, Marieke Lydia; Paulson, Joseph N. & Quackenbush, John (2020). Expression analysis. In Baxevanis, Andreas D.; Bader, Gary D. & Wishart, David S. (Ed.), Bioinformatics. John Wiley & Sons. ISSN 978-1-119-33558-0. p. 279–314.
Lopes-ramos, Camila; Kuijjer, Marieke Lydia; Ogino, Shuji; Fuchs, Charles S.; DeMeo, Dawn L. & Glass, Kimberly [Show all 7 contributors for this article] (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

Research groups

The Kuijjer Group