Marieke Kuijjer
English version of this page
E-post
marieke.kuijjer@ncmm.uio.no
Telefon
+47 22840528
Brukernavn
Besøksadresse
Forskningsparken
E3
Gaustadalléen 21
0349 Oslo
Postadresse
,Postboks 1137 Blindern
0318 Oslo
Publikasjoner
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Osorio, Daniel; Capasso, Anna; Eckhardt, S. Gail; Giri, Uma; Somma, Alexander & Pitts, Todd M. [Vis alle 14 forfattere av denne artikkelen] (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.
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Struck, Eike Christopher; Belova, Tatiana; Hsieh, Ping-Han; Odeberg, Jacob Olof; Kuijjer, Marieke & Dusart, PJ [Vis alle 7 forfattere av denne artikkelen] (2023). Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF. . Journal of Immunology. ISSN 0022-1767. doi: 10.4049/jimmunol.2300419.
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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. Fulltekst i vitenarkiv
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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.
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Ben Guebila, Marouen; Wang, Tian; Lopes-Ramos, Camila M.; Fanfani, Viola; Weighill, Des & Burkholz, Rebekka [Vis alle 25 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
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Stahlberg, Eric A; Abdel-Rahman, Mohamed; Aguilar, Boris; Asadpoure, Alireza; Beckman, Robert A & Borkon, Lynn L [Vis alle 33 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
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Birkeälv, Sofia; Harland, Mark; Matsuyama, Larissa Satiko Alcantara Sekim; Rashid, Mamun; Mehta, Ishan & Laye, Jonathan P [Vis alle 18 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
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Weber, Cédric R.; Rubio, Teresa; Wang, Longlong; Zhang, Wei; Robert, Philippe Paul Auguste & Akbar, Rahmad [Vis alle 15 forfattere av denne artikkelen] (2022). Reference-based comparison of adaptive immune receptor repertoires. Cell Reports Methods. 2(8). doi: 10.1016/j.crmeth.2022.100269. Fulltekst i vitenarkiv
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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. Fulltekst i vitenarkiv
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Ben Guebila, Marouen; Lopes-Ramos, Camila; Weighill, Deborah; Sonawane, Abhijeet; Burkholz, Rebekka & Shamsaei, Behrouz [Vis alle 10 forfattere av denne artikkelen] (2022). GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Research (NAR). ISSN 0305-1048. 50, s. D610–D621. doi: 10.1093/nar/gkab778. Fulltekst i vitenarkiv
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Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Kanduri, Chakravarthi; Kompova, Radmila & Vazov, Nikolay Aleksandrov [Vis alle 41 forfattere av denne artikkelen] (2021). The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nature Machine Intelligence. 3(11), s. 936–944. doi: 10.1038/s42256-021-00413-z.
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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. Fulltekst i vitenarkiv
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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. Fulltekst i vitenarkiv
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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. Fulltekst i vitenarkiv
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Lopes-Ramos, Camila; Belova, Tatiana; Brunner, Tess; Ben Guebila, Marouen; Osorio, Daniel & Quackenbush, John [Vis alle 7 forfattere av denne artikkelen] (2021). Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme. Cancer Research. ISSN 0008-5472. 81(21), s. 5401–5412. doi: 10.1158/0008-5472.CAN-21-0730. Fulltekst i vitenarkiv
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Grad, Iwona; Hanes, Robert; Ayuda-Duran, Maria del Pilar; Kuijjer, Marieke Lydia; Enserink, Jorrit & Meza, Leonardo Zepeda [Vis alle 7 forfattere av denne artikkelen] (2021). Discovery of novel candidates for anti-liposarcoma therapies by medium-scale high-throughput drug screening. PLOS ONE. ISSN 1932-6203. 16(3), s. 1–23. doi: 10.1371/journal.pone.0248140. Fulltekst i vitenarkiv
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Fagny, Maud; Kuijjer, Marieke Lydia; Stam, Maike; Joets, Johann; Turc, Olivier & Rozière, Julien [Vis alle 9 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
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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. doi: 10.1109/ACCESS.2020.2982569. Fulltekst i vitenarkiv
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Andreeva, Olga; Li, Wei; Ding, Wei; Kuijjer, Marieke Lydia; Quackenbush, John & Chen, Ping (2020). Catalysis Clustering with GAN by Incorporating Domain Knowledge. I Gupta, Rajesh & Liu, Yan (Red.), 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. s. 1344–1352. doi: https:/doi.org/10.1145/3394486.3403187.
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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. Fulltekst i vitenarkiv
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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.
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Lopes-ramos, Camila; Chen, Cho-Yi; Kuijjer, Marieke Lydia; Paulson, Joseph N.; Sonawane, Abhijeet & Fagny, Maud [Vis alle 10 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
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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: 10.1017/nws.2019.21.
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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. Fulltekst i vitenarkiv
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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. Fulltekst i vitenarkiv
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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. Fulltekst i vitenarkiv
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Wong, Kim; van der Weyden, Louise; Schott, Courtney R.; Foote, Alastair; Constantino-Casas, Fernando & Smith, Sionagh [Vis alle 23 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
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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. Fulltekst i vitenarkiv
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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.
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Lopes-Ramos, Camila; Kuijjer, Marieke; Ogino, Shuji; Fuchs, Charles; DeMeo, Dawn L & Glass, Kimberly [Vis alle 7 forfattere av denne artikkelen] (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.
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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.
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Hill, Katherine; Kelly, Andrew; Kuijjer, Marieke; Barry, William; Rattani, Ahmed & Garbutt, Cassandra [Vis alle 19 forfattere av denne artikkelen] (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.
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Fagny, Maud; Paulson, Joseph N.; Kuijjer, Marieke; Sonawane, Abhijeet; Chen, Cho-Yi & Lopes-ramos, Camila [Vis alle 9 forfattere av denne artikkelen] (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.
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Lopes-ramos, Camila; Paulson, Joseph N.; Chen, Cho-Yi; Kuijjer, Marieke; Fagny, Maud & Platig, John [Vis alle 10 forfattere av denne artikkelen] (2017). Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. ISSN 1471-2164. doi: 10.1186/s12864-017-4111-x.
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Paulson, Joseph N.; Chen, Cho-Yi; Lopes-Ramos, Camila; Kuijjer, Marieke; Platig, John & Sonawane, Abhijeet [Vis alle 9 forfattere av denne artikkelen] (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.
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Sonawane, Abhijeet; Platig, John; Fagny, Maud; Chen, Cho-Yi; Paulson, Joseph N. & DeMeo, Dawn L [Vis alle 9 forfattere av denne artikkelen] (2017). Understanding Tissue-Specific Gene Regulation. Cell reports. ISSN 2211-1247. 21(4). doi: 10.1016/j.celrep.2017.10.001.
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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.
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Pahl, Jens H.W.; Santos, Susy J.; Kuijjer, Marieke; Boerman, Gerharda H.; Sand, Laurens G.L. & Szuhai, Karoly [Vis alle 11 forfattere av denne artikkelen] (2015). Expression of the immune regulation antigen CD70 in osteosarcoma. Cancer Cell International. ISSN 1475-2867. doi: 10.1186/s12935-015-0181-5.
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Wouters, Maartje C.A.; Dijkgraaf, Eveline M.; Kuijjer, Marieke; Jordanova, Ekaterina S.; Hollema, H. & Welters, M.J.P. [Vis alle 11 forfattere av denne artikkelen] (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.
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Buddingh, Emmeline P.; Ruslan, S. Eriaty N.; Reijnders, Christianne M.A.; Szuhai, Karoly; Kuijjer, Marieke & Roelofs, Helene [Vis alle 10 forfattere av denne artikkelen] (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.
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Baranski, Zuzanna; Booij, Tijmen H.; Kuijjer, Marieke; de Jong, Yvonne; Cleton-Jansen, Anne-Marie & Price, Leo S. [Vis alle 10 forfattere av denne artikkelen] (2015). MEK inhibition induces apoptosis in osteosarcoma cells with constitutive ERK1/2 phosphorylation. Genes & cancer. ISSN 1947-6019. 6.
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Kuijjer, Marieke; van den Akker, Brendy E.W.M.; Hilhorst, Riet; Mommersteeg, Monique; Buddingh, Emilie P. & Serra, Massimo [Vis alle 9 forfattere av denne artikkelen] (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.
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Pahl, Jens H.W.; Kwappenberg, Kitty M.C.; Varypataki, Eleni M.; Santos, Susy J.; Kuijjer, Marieke & Mohamed, Susan [Vis alle 13 forfattere av denne artikkelen] (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.
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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.
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de Vos van Steenwijk, Peggy J.; Ramwadhdoebe, T.H.; Goedemans, R.; Doorduijn, E.M.; van Ham, J.J. & Gorter, A. [Vis alle 11 forfattere av denne artikkelen] (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.
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Kansara, Maya; Leong, Huei San; Lin, Dan Mei; Popkiss, Sophie; Pang, Puiyi & Garsed, Dale W. [Vis alle 16 forfattere av denne artikkelen] (2013). Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation. Journal of Clinical Investigation. ISSN 0021-9738. doi: 10.1172/JCI70559.
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Lenos, Kristiaan; Grawenda, Anna M.; Lodder, Kirsten; Kuijjer, Marieke; Teunisse, Amina F.A.S. & Repapi, Emmanouela [Vis alle 14 forfattere av denne artikkelen] (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.
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Mohseny, Alexander B.; Cai, Yongping; Kuijjer, Marieke; Xiao, Wei; van den Akker, Brendy E.W.M. & de Andrea, Carlos E. [Vis alle 10 forfattere av denne artikkelen] (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.
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Pansuriya, Twinkal C.; van Eijk, Ronald; D'Adamo, Pio; van Ruler, Maayke A.J.H.; Kuijjer, Marieke & Oosting, Jan [Vis alle 27 forfattere av denne artikkelen] (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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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.
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Sajib, Saikat Das; Florholmen-Kjær, Åse; Brun, Vegard; Mortensen, Elin Synnøve; Hovd, Aud-Malin Karlsson & Tekpli, Xavier [Vis alle 10 forfattere av denne artikkelen] (2023). Epithelial-to-mesenchymal transition (EMT) is a major contributor to intratumor heterogeneity in lymph node metastasis in breast cancer.
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Kuijjer, Marieke (2022). Gene regulatory networks in precision medicine.
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Kuijjer, Marieke (2022). A network approach to personalized medicine.
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Kuijjer, Marieke (2022). Modeling genome-wide regulatory network rewiring in healthy tissues and cancer.
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Kuijjer, Marieke (2022). Modeling regulatory network rewiring in cancer.
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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.
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Ben Guebila, Marouen; Weighill, Deborah; Lopes-Ramos, Camila M.; Burkholz, Rebekka; Pop, Romana-Tabita & Palepu, Kalyan [Vis alle 14 forfattere av denne artikkelen] (2022). An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods. ISSN 1548-7091. 19, s. 511–513. doi: 10.1038/s41592-022-01479-2.
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Kuijjer, Marieke (2021). Modeling gene regulatory network rewiring in healthy tissues and cancer.
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Kuijjer, Marieke Lydia; Paulson, Joseph N. & Quackenbush, John (2020). Expression analysis. I Baxevanis, Andreas D.; Bader, Gary D. & Wishart, David S. (Red.), Bioinformatics. John Wiley & Sons. ISSN 978-1-119-33558-0. s. 279–314.
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Lopes-ramos, Camila; Kuijjer, Marieke Lydia; Ogino, Shuji; Fuchs, Charles S.; DeMeo, Dawn L. & Glass, Kimberly [Vis alle 7 forfattere av denne artikkelen] (2019). Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. ISSN 0008-5472.
Publisert
11. okt. 2018 11:50
- Sist endret
7. jan. 2021 20:35