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Items: 28


Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.

Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J.

Cancer Res. 2019 Apr 15;79(8):2084. doi: 10.1158/0008-5472.CAN-19-0678. No abstract available.


Estimating Sample-Specific Regulatory Networks.

Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K.

iScience. 2019 Apr 26;14:226-240. doi: 10.1016/j.isci.2019.03.021. Epub 2019 Mar 28.


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

van IJzendoorn DGP, Szuhai K, Briaire-de Bruijn IH, Kostine M, Kuijjer ML, Bovée JVMG.

PLoS Comput Biol. 2019 Feb 20;15(2):e1006826. doi: 10.1371/journal.pcbi.1006826. eCollection 2019 Feb.


Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma.

Wong K, van der Weyden L, Schott CR, Foote A, Constantino-Casas F, Smith S, Dobson JM, Murchison EP, Wu H, Yeh I, Fullen DR, Joseph N, Bastian BC, Patel RM, Martincorena I, Robles-Espinoza CD, Iyer V, Kuijjer ML, Arends MJ, Brenn T, Harms PW, Wood GA, Adams DJ.

Nat Commun. 2019 Jan 21;10(1):353. doi: 10.1038/s41467-018-08081-1.


Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.

Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J.

Cancer Res. 2018 Oct 1;78(19):5538-5547. doi: 10.1158/0008-5472.CAN-18-0454. Erratum in: Cancer Res. 2019 Apr 15;79(8):2084.


Cancer subtype identification using somatic mutation data.

Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J.

Br J Cancer. 2018 May;118(11):1492-1501. doi: 10.1038/s41416-018-0109-7. Epub 2018 May 16.


Understanding Tissue-Specific Gene Regulation.

Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML.

Cell Rep. 2017 Oct 24;21(4):1077-1088. doi: 10.1016/j.celrep.2017.10.001.


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

Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J.

BMC Bioinformatics. 2017 Oct 3;18(1):437. doi: 10.1186/s12859-017-1847-x.


Regulatory network changes between cell lines and their tissues of origin.

Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K.

BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x.


Exploring regulation in tissues with eQTL networks.

Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7841-E7850. doi: 10.1073/pnas.1707375114. Epub 2017 Aug 29.


An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets.

Hill KE, Kelly AD, Kuijjer ML, Barry W, Rattani A, Garbutt CC, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani MS, Cote G, Hornicek F, Choy E, Duan Z, Quackenbush J, Haibe-Kains B, Spentzos D.

J Hematol Oncol. 2017 May 15;10(1):107. doi: 10.1186/s13045-017-0465-4.


PyPanda: a Python package for gene regulatory network reconstruction.

van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML.

Bioinformatics. 2016 Nov 1;32(21):3363-3365. Epub 2016 Jul 10.


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

Baranski Z, Booij TH, Kuijjer ML, de Jong Y, Cleton-Jansen AM, Price LS, van de Water B, Bovée JV, Hogendoorn PC, Danen EH.

Genes Cancer. 2015 Nov;6(11-12):503-12.


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

Buddingh EP, Ruslan SEN, Reijnders CMA, Szuhai K, Kuijjer ML, Roelofs H, Hogendoorn PCW, Maarten Egeler R, Cleton-Jansen AM, Lankester AC.

Clin Sarcoma Res. 2015 Jun 23;5:16. doi: 10.1186/s13569-015-0031-1. eCollection 2015.


Interleukin-6 receptor and its ligand interleukin-6 are opposite markers for survival and infiltration with mature myeloid cells in ovarian cancer.

Wouters M, Dijkgraaf EM, Kuijjer ML, Jordanova ES, Hollema H, Welters M, van der Hoeven J, Daemen T, Kroep JR, Nijman HW, van der Burg SH.

Oncoimmunology. 2015 Jan 7;3(12):e962397. eCollection 2014 Dec.


Expression of the immune regulation antigen CD70 in osteosarcoma.

Pahl JH, Santos SJ, Kuijjer ML, Boerman GH, Sand LG, Szuhai K, Cleton-Jansen A, Egeler RM, Boveé JV, Schilham MW, Lankester AC.

Cancer Cell Int. 2015 Mar 18;15:31. doi: 10.1186/s12935-015-0181-5. eCollection 2015.


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

Pahl JH, Kwappenberg KM, Varypataki EM, Santos SJ, Kuijjer ML, Mohamed S, Wijnen JT, van Tol MJ, Cleton-Jansen AM, Egeler RM, Jiskoot W, Lankester AC, Schilham MW.

J Exp Clin Cancer Res. 2014 Mar 10;33:27. doi: 10.1186/1756-9966-33-27.


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

Kuijjer ML, van den Akker BE, Hilhorst R, Mommersteeg M, Buddingh EP, Serra M, Bürger H, Hogendoorn PC, Cleton-Jansen AM.

BMC Med Genomics. 2014 Jan 21;7:4. doi: 10.1186/1755-8794-7-4.


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

Kansara M, Leong HS, Lin DM, Popkiss S, Pang P, Garsed DW, Walkley CR, Cullinane C, Ellul J, Haynes NM, Hicks R, Kuijjer ML, Cleton-Jansen AM, Hinds PW, Smyth MJ, Thomas DM.

J Clin Invest. 2013 Dec;123(12):5351-60. doi: 10.1172/JCI70559. Epub 2013 Nov 15.


Tumor-infiltrating CD14-positive myeloid cells and CD8-positive T-cells prolong survival in patients with cervical carcinoma.

de Vos van Steenwijk PJ, Ramwadhdoebe TH, Goedemans R, Doorduijn EM, van Ham JJ, Gorter A, van Hall T, Kuijjer ML, van Poelgeest MI, van der Burg SH, Jordanova ES.

Int J Cancer. 2013 Dec 15;133(12):2884-94. doi: 10.1002/ijc.28309. Epub 2013 Jul 5.


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

Kuijjer ML, Peterse EF, van den Akker BE, Briaire-de Bruijn IH, Serra M, Meza-Zepeda LA, Myklebost O, Hassan AB, Hogendoorn PC, Cleton-Jansen AM.

BMC Cancer. 2013 May 20;13:245. doi: 10.1186/1471-2407-13-245.


Genome-wide analyses on high-grade osteosarcoma: making sense of a genomically most unstable tumor.

Kuijjer ML, Hogendoorn PC, Cleton-Jansen AM.

Int J Cancer. 2013 Dec 1;133(11):2512-21. doi: 10.1002/ijc.28124. Epub 2013 Mar 16. Review.


Modulation of the osteosarcoma expression phenotype by microRNAs.

Namløs HM, Meza-Zepeda LA, Barøy T, Østensen IH, Kresse SH, Kuijjer ML, Serra M, Bürger H, Cleton-Jansen AM, Myklebost O.

PLoS One. 2012;7(10):e48086. doi: 10.1371/journal.pone.0048086. Epub 2012 Oct 25.


Alternate splicing of the p53 inhibitor HDMX offers a superior prognostic biomarker than p53 mutation in human cancer.

Lenos K, Grawenda AM, Lodder K, Kuijjer ML, Teunisse AF, Repapi E, Grochola LF, Bartel F, Hogendoorn PC, Wuerl P, Taubert H, Cleton-Jansen AM, Bond GL, Jochemsen AG.

Cancer Res. 2012 Aug 15;72(16):4074-84. Epub 2012 Jun 14.


Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data.

Kuijjer ML, Rydbeck H, Kresse SH, Buddingh EP, Lid AB, Roelofs H, Bürger H, Myklebost O, Hogendoorn PC, Meza-Zepeda LA, Cleton-Jansen AM.

Genes Chromosomes Cancer. 2012 Jul;51(7):696-706. doi: 10.1002/gcc.21956. Epub 2012 Mar 27.


Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome.

Pansuriya TC, van Eijk R, d'Adamo P, van Ruler MA, Kuijjer ML, Oosting J, Cleton-Jansen AM, van Oosterwijk JG, Verbeke SL, Meijer D, van Wezel T, Nord KH, Sangiorgi L, Toker B, Liegl-Atzwanger B, San-Julian M, Sciot R, Limaye N, Kindblom LG, Daugaard S, Godfraind C, Boon LM, Vikkula M, Kurek KC, Szuhai K, French PJ, Bovée JV.

Nat Genet. 2011 Nov 6;43(12):1256-61. doi: 10.1038/ng.1004.


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

Kuijjer ML, Namløs HM, Hauben EI, Machado I, Kresse SH, Serra M, Llombart-Bosch A, Hogendoorn PC, Meza-Zepeda LA, Myklebost O, Cleton-Jansen AM.

BMC Med Genomics. 2011 Sep 20;4:66. doi: 10.1186/1755-8794-4-66.


Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage activating agents.

Buddingh EP, Kuijjer ML, Duim RA, Bürger H, Agelopoulos K, Myklebost O, Serra M, Mertens F, Hogendoorn PC, Lankester AC, Cleton-Jansen AM.

Clin Cancer Res. 2011 Apr 15;17(8):2110-9. doi: 10.1158/1078-0432.CCR-10-2047. Epub 2011 Mar 3.

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