Kuijjer Lab

Publications

List of peer-reviewed publications, pre-prints, book chapters, etc. Publications by Kuijjer Lab members are underlined. First/last Kuijjer Lab authors are in bold. Please check Dr. Kuijjer's publications on PubMed too.

Ten selected publications

  • Kuijjer ML*, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics. 2020 Jun 17;btaa571
  • Kuijjer ML*, Hsieh PH, Quackenbush J, Glass K. lionessR: single-sample network reconstruction in R. BMC Cancer. 2019 Oct 25;19(1):1003
  • Kuijjer ML†, Tung M†, Quackenbush J, Yuan GC, Glass K. Estimating sample-specific regulatory networks. iScience. 2019 Apr 26;14:226-240
  • van IJzendoorn DGP, Szuhai K, Briaire-de Bruijn IH, Kostine M, Kuijjer ML*†, Bovée JVMG*†. Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. PLoS Comput Biol. 2019 Feb 20;15(2):e1006826
  • Kuijjer ML*, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. Br J Cancer. 2018 May 16
  • Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, Quackenbush J, Glass K†*, Kuijjer ML†*. Understanding Tissue-Specific Gene Regulation. Cell Reports. 2017 Oct 24;21(4):1077-1088
  • van IJzendoorn DGP, Quackenbush J, Glass K, Kuijjer ML*. PyPanda: A Python package for gene regulatory network reconstruction. Bioinformatics. 2016 Nov 1;32(21):3363-3365
  • Kuijjer ML, Peterse EFP, van den Akker BEWM, Briaire-de Bruijn IH, Serra M, Meza-Zepeda LA, Myklebost O, Hassan AB, Hogendoorn PCW, Cleton-Jansen AM. IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma. BMC Cancer. 2013;20(13):245
  • Kuijjer ML, Rydbeck H, Kresse SH, Buddingh EP, Lid AB, Roelofs H, Bürger H, Myklebost O, Hogendoorn PC, Meza-Zepeda LA, Cleton-Jansen AM. Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data. Genes Chromosomes Cancer. 2012 Jul;51(7):696-706
  • Buddingh EP†, Kuijjer ML†, Duim RA, Bürger H, Agelopoulos K, Myklebost O, Serra M, Mertens F, Hogendoorn PC, Lankester AC, Cleton-Jansen AM. Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage activating agents. Clin Cancer Res. 2011 Apr 15;17(8):2110-9
    *Corresponding author, †Shared first/last authorship

Peer-reviewed original publications

  • Quang J, Ding W, Kuijjer ML, Quackenbush J, Chen P. Clustering sparse data with feature correlation with application to discover subtpes in cancer. IEEE Access (in press). 2020 Dec;8(1)67775-67789
  • Kuijjer ML*, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics. 2020 Jun 17;btaa571
  • Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports. 2020 Jun 23;31:107795
  • Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumor suppressor genes, and immune function. Br J Cancer. 2019 Dec 6
  • Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single-sample network reconstruction in R. BMC Cancer. 2019 Oct 25;19(1):1003
  • Barnett I, Malik N, Kuijjer ML, Mucha P, Onnela JP. Feature-based classification of networks. Network Science. 2019 Sep 23;7(3):438-444
  • Kuijjer ML†, Tung M†, Quackenbush J, Yuan GC, Glass K. Estimating sample-specific regulatory networks. iScience. 2019 Apr 26;14:226-240
  • van IJzendoorn DGP, Szuhai K, Briaire-de Bruijn IH, Kostine M, Kuijjer ML*†, Bovée JVMG*†. Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. PLoS Comput Biol. 2019 Feb 20;15(2):e1006826
  • 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. Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Nat Commun. 2019 Jan 21;10(1):353
  • Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs C, DeMeo DL, Glass K, Quackenbush J. Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism processes. Cancer Research. 2018 Oct 1;78(19)5538-5547
  • Kuijjer ML*, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. Br J Cancer. 2018 May 16
  • Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, Quackenbush J, Glass K†*, Kuijjer ML†*. Understanding Tissue-Specific Gene Regulation. Cell Reports. 2017 Oct 24;21(4):1077-1088
  • Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics. 2017 Oct 3;18(1):437
  • Lopes-Ramos CM†, Paulson JN†, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. 2017 Sep 12;18(1):723
  • Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7841-E7850
  • Hill K, Kelly A, Kuijjer ML, Barry W, Rattani A, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani M, Cote G, Hornicek F, Choy E, Duan Z, Quackenbush J, Haibe-Kains B, Spentzos D. An imprinted non-coding genomic region at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. J Hematol Oncol. 2017 May 15;10(1):107
  • van IJzendoorn DGP, Quackenbush J, Glass K, Kuijjer ML*. PyPanda: A Python package for gene regulatory network reconstruction. Bioinformatics. 2016 Nov 1;32(21):3363-3365
  • Baranski Z, Booij TH, Kuijjer ML, de Jong Y, Cleton-Jansen AM, Price LS, van de Water B, Bovée JVGM, Hogendoorn PCW, Danen EH. MEK inhibition induces apoptosis in osteosarcoma cells with constitutive ERK1/2 phosphorylation. Genes Cancer. 2015;6(11-12):503-512
  • Buddingh EP, Ruslan SEN, Reijnders CMA, Szuhai K, Kuijjer ML, Roelofs H, Hogendoorn PCW, Egeler RM, Cleton-Jansen AM, Lankester AC. Mesenchymal stromal cells of osteosarcoma patients do not show evidence of neoplastic changes during long-term culture. Clin Sarcoma Res. 2015 Jun 23;5:16
  • Wouters MC†, Dijkgraaf EM†, Kuijjer ML, Jordanova ES, Welters MJP, Nortier JWR, van der Hoeven JJM, Kroep JR, Deamen T, Nijman HW, van der Burg SH. IL-6, IL-6 receptor, pSTAT3 and myeloid cell populations in ovarian cancer. OncoImmunology. 2015 Jan 7;3(12):e962397
  • Pahl JHW, Santos SJ, Kuijjer ML, Boerman H, Sand L, Szuhai K, Cleton-Jansen AM, Egeler RM, Bovée JV, Schilham MW, Lankester AC. Expression of the immune regulation antigen CD70 in osteosarcoma. Cancer Cell Int. 2015 Mar 18;15:31
  • Pahl JHW, Kwappenberg KMC, Varypataki EM, Santos SJ, Kuijjer ML, Mohamed S, Wijnen JT, van Tol MJD, Cleton-Jansen AM, Egeler RM, Jiskoot W, Lankester AC, Schilham MW. Macrophages inhibit human osteosarcoma cell growth after activation with the bacterial cell wall derivative liposomal muramyl tripeptide in combination with interferon-gamma. JECCR. 2014 Mar 10;33(1):27
  • Kuijjer ML, van den Akker BEWM, Hilhorst R, Mommersteeg M, Buddingh EP, Serra M, Bürger H, Hogendoorn PCW, Cleton-Jansen AM. Kinome and mRNA expression profiling of high-grade osteosarcoma identifies genomic instability, and reveals Akt as potential target for treatment. BMC Med Genomics. 2014 Jan 21;7:4 Highly accessed
  • Kansara E, 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. Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation. J Clin Invest. 2013 Dec 2;123(12):5351-60
  • de Vos van Steenwijk PJ, Ramwadhdoebe TH, Goedemans R, Doorduijn E, van den Ham JJ, Gorter A, van Hall T, Kuijjer ML, van Poelgeest MIE, van der Burg SH, Jordanova ES. Tumor infiltrating CD14 positive myeloid cells work side by side with T cells to prolong the survival in patients with cervical carcinoma. Int J Cancer. 2013;133(12):2884-94
  • Kuijjer ML, Peterse EFP, van den Akker BEWM, Briaire-de Bruijn IH, Serra M, Meza-Zepeda LA, Myklebost O, Hassan AB, Hogendoorn PCW, Cleton-Jansen AM. IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma. BMC Cancer. 2013;20(13):245
  • Namløs HM, Meza-Zepeda LA, Barøy T, Østensen IHG, Kresse SH, Kuijjer ML, Serra M, Bürger H, Cleton-Jansen AM, Myklebost O. Modulation of the Osteosarcoma Expression Phenotype by MicroRNAs. PlosONE. 2012;7(10):e48086
  • Mohseny AB, Cai Y, Kuijjer ML, Xiao W, van den Akker B, de Andrea CE, Jacobs R, ten Dijke P, Hogendoorn PC, Cleton-Jansen AM. The activities of Smad and Gli mediated signalling pathways in high-grade conventional osteosarcoma. Eur J Cancer. 2012 Dec;48(18):3429-38
  • 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. Alternate splicing of the p53 inhibitor HDMX offers a superior prognostic biomarker than p53 mutation in human cancer. Cancer Res. 2012 Aug 15;72(16):4074-84
  • Kuijjer ML, Rydbeck H, Kresse SH, Buddingh EP, Lid AB, Roelofs H, Bürger H, Myklebost O, Hogendoorn PC, Meza-Zepeda LA, Cleton-Jansen AM. Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data. Genes Chromosomes Cancer. 2012 Jul;51(7):696-706
  • 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. Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome. Nat Genet. 2011 Nov 6;43(12):1256-61
  • 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. mRNA expression profiles of primary high-grade central osteosarcoma are preserved in cell lines and xenografts. BMC Med Genomics. 2011 Sep 20;4:66
  • Buddingh EP†, Kuijjer ML†, Duim RA, Bürger H, Agelopoulos K, Myklebost O, Serra M, Mertens F, Hogendoorn PC, Lankester AC, Cleton-Jansen AM. Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage activating agents. Clin Cancer Res. 2011 Apr 15;17(8):2110-9
    *Corresponding author, †Shared first/last authorship

Conference proceedings (papers)

  • Andreeva O, Li W, Ding W, Kuijjer ML, Quackenbush J, Chen P. Catalysis clustering with GAN by incorporating domain knowledge. KDD2020 Knowledge Discovery and Databases (in press)
  • Kang T, Zarringhalam K, Kuijjer ML, Quackenbush J, Ding W. Clustering on sparse data in non-overlapping feature space with applications to cancer subtyping. 2018 IEEE International Conference on Data Mining (ICDM'18)

Pre-prints

  • Fagny M, Kuijjer ML, Stam M, Joets J, Turc O, Roziere J, Pateyron S, Venon A, Vitte C. Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks. Pre-published on the bioRχiv
    *Corresponding author, †Shared first/last authorship

Reviews

  • Kuijjer ML, Hogendoorn PCW, Cleton-Jansen AM. Genome-wide analyses on high-grade osteosarcoma; making sense of a most genomically instable tumor Review. Int J Cancer. 2013;133(11): 2512-21

Editorial commentaries

  • Kuijjer ML. Predicting cancer evolution using cell state dynamics. Cancer Research. 2020 Aug 1;80(15):3072-3073

Book chapters

  • Kuijjer ML, Paulson JNP, Quackenbush J. Expression analysis. Book chapter in Bioinformatics: A practical guide to the analysis of genes and proteins, 4th edition. Editors: Braxevanis AD, Bader G, Wishart D. Feb 2020, ISBN: 978-1-119-33558-0

Online presentations

Conference proceedings (abstracts with DOIs)

  • Kuijjer ML, Glass K, Quackenbush J. Abstract B1-20: Gene regulation by transcription factors and microRNAs in ovarian cancer. AACR Special Conference: Computational and Systems Biology of Cancer. Cancer Research (2015) Nov; 75(22):Supplement 2.
  • Kuijjer ML, Rydbeck H, Kresse SH, Buddingh E, Roeloefs H, Bürger H, Myklebost O, Hogendoorn PCW, Meza-Zepeda LA, Cleton-Jansen AM. Abstract 5128: Indetification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data. AACR 103rd Annual Meeting. Cancer Research (2012) Apr; 72(8):Supplement.
  • Buddingh EP†, Kuijjer ML†, Duim RA, Bürger H, Agelopoulos K, Myklebost O, Serra M, Mertens F, Hogendoorn PC, Lankester AC, Cleton-Jansen AM. Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage activating agents. Lab Invest. 2011 Feb (91):8-24
    *Corresponding author, †Shared first/last authorship

Other

  • Kuijjer ML. A systems biology approach to study high-grade osteosarcoma. 2013 Jun 26. PhD thesis. Leiden University's version, or direct download. .tex files of my thesis are available on GitHub