Community Detection in Large-Scale Bipartite Biological Networks

by Calderer, Genís, Kuijjer, Marieke L.
Published in Front Genet (2021)

lionessR: single sample network inference in R

by Kuijjer, Marieke L, Hsieh, Ping-Han, Quackenbush, John, Glass, Kimberly
Published in BMC Cancer (2019)

PUMA: PANDA Using MicroRNA Associations

by Kuijjer, Marieke L, Fagny, Maud, Marin, Alessandro, Quackenbush, John, Glass, Kimberly
Published in Bioinformatics (2020)

PyPanda: a Python package for gene regulatory network reconstruction

by van IJzendoorn, David G.P., Glass, Kimberly, Quackenbush, John, Kuijjer, Marieke L.
Published in Bioinformatics (2016)

EndNote: Feature-based classification of networks

by Barnett, Ian, Malik, Nishant, Kuijjer, Marieke L., Mucha, Peter J., Onnela, Jukka-Pekka
Published in Netw Sci (Camb Univ Press) (2019)

Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism

by Lopes-Ramos, Camila M., Kuijjer, Marieke L., Ogino, Shuji, Fuchs, Charles S., DeMeo, Dawn L., Glass, Kimberly, Quackenbush, John
Published in Cancer Res (2018)

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas

by van IJzendoorn, David G. P., Szuhai, Karoly, Briaire-de Bruijn, Inge H., Kostine, Marie, Kuijjer, Marieke L., Bovée, Judith V. M. G.
Published in PLoS Comput Biol (2019)

Exploring regulation in tissues with eQTL networks

by Fagny, Maud, Paulson, Joseph N., Kuijjer, Marieke L., Sonawane, Abhijeet R., Chen, Cho-Yi, Lopes-Ramos, Camila M., Glass, Kimberly, Quackenbush, John, Platig, John
Published in Proc Natl Acad Sci U S A (2017)

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

by Paulson, Joseph N., Chen, Cho-Yi, Lopes-Ramos, Camila M., Kuijjer, Marieke L., Platig, John, Sonawane, Abhijeet R., Fagny, Maud, Glass, Kimberly, Quackenbush, John
Published in BMC Bioinformatics (2017)

Kinome and mRNA expression profiling of high-grade osteosarcoma cell lines implies Akt signaling as possible target for therapy

by Kuijjer, Marieke L, van den Akker, Brendy EWM, Hilhorst, Riet, Mommersteeg, Monique, Buddingh, Emilie P, Serra, Massimo, Bürger, Horst, Hogendoorn, Pancras CW, Cleton-Jansen, Anne-Marie
Published 2014

Regulatory network changes between cell lines and their tissues of origin

by Lopes-Ramos, Camila M., Paulson, Joseph N., Chen, Cho-Yi, Kuijjer, Marieke L., Fagny, Maud, Platig, John, Sonawane, Abhijeet R., DeMeo, Dawn L., Quackenbush, John, Glass, Kimberly
Published in BMC Genomics (2017)

Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues

by Lopes-Ramos, Camila M., Chen, Cho-Yi, Kuijjer, Marieke L., Paulson, Joseph N., Sonawane, Abhijeet R., Fagny, Maud, Platig, John, Glass, Kimberly, Quackenbush, John, DeMeo, Dawn L.
Published in Cell Rep (2020)

Modulation of the Osteosarcoma Expression Phenotype by MicroRNAs

by Namløs, Heidi M., Meza-Zepeda, Leonardo A., Barøy, Tale, Østensen, Ingrid H. G., Kresse, Stine H., Kuijjer, Marieke L., Serra, Massimo, Bürger, Horst, Cleton-Jansen, Anne-Marie, Myklebost, Ola
Published 2012

Mesenchymal stromal cells of osteosarcoma patients do not show evidence of neoplastic changes during long-term culture

by Buddingh, Emilie P, Ruslan, S Eriaty N, Reijnders, Christianne M A, Szuhai, Karoly, Kuijjer, Marieke L, Roelofs, Helene, Hogendoorn, Pancras C W, Maarten Egeler, R, Cleton-Jansen, Anne-Marie, Lankester, Arjan C
Published in Clin Sarcoma Res (2015)

mRNA expression profiles of primary high-grade central osteosarcoma are preserved in cell lines and xenografts

by Kuijjer, Marieke L, Namløs, Heidi M, Hauben, Esther I, Machado, Isidro, Kresse, Stine H, Serra, Massimo, Llombart-Bosch, Antonio, Hogendoorn, Pancras CW, Meza-Zepeda, Leonardo A, Myklebost, Ola, Cleton-Jansen, Anne-Marie
Published 2011

Expression of the immune regulation antigen CD70 in osteosarcoma

by Pahl, Jens HW, Santos, Susy J, Kuijjer, Marieke L, Boerman, Gerharda H, Sand, Laurens GL, Szuhai, Karoly, Cleton-Jansen, Annemarie, Egeler, R Maarten, Boveé, Judith VMG, Schilham, Marco W, Lankester, Arjan C
Published in Cancer Cell Int (2015)

IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma

by Kuijjer, Marieke L, Peterse, Elisabeth FP, van den Akker, Brendy EWM, Briaire-de Bruijn, Inge H, Serra, Massimo, Meza-Zepeda, Leonardo A, Myklebost, Ola, Hassan, A Bassim, Hogendoorn, Pancras CW, Cleton-Jansen, Anne-Marie
Published 2013

MEK inhibition induces apoptosis in osteosarcoma cells with constitutive ERK1/2 phosphorylation

by Baranski, Zuzanna, Booij, Tijmen H., Kuijjer, Marieke L., de Jong, Yvonne, Cleton-Jansen, Anne-Marie, Price, Leo S., van de Water, Bob, Bovée, Judith V. M. G., Hogendoorn, Pancras C.W., Danen, Erik H.J.
Published in Genes Cancer (2015)

Macrophages inhibit human osteosarcoma cell growth after activation with the bacterial cell wall derivative liposomal muramyl tripeptide in combination with interferon-γ

by Pahl, Jens HW, Kwappenberg, Kitty MC, Varypataki, Eleni M, Santos, Susy J, Kuijjer, Marieke L, Mohamed, Susan, Wijnen, Juul T, van Tol, Maarten JD, Cleton-Jansen, Anne-Marie, Egeler, R Maarten, Jiskoot, Wim, Lankester, Arjan C, Schilham, Marco W
Published 2014

Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation

by 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 L., Cleton-Jansen, Anne-Marie, Hinds, Philip W., Smyth, Mark J., Thomas, David M.
Published 2013