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. *Corresponding author, †Shared first/last authorship. Also see PubMed.

Ten selected publications

Hsieh PH, Hsiao RX, Ferenc K, Mathelier A, Burkholz R, Chen CY, Sandve GK, Belova T†, Kuijjer ML†. CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. 2024 arXiv arXiv.2405.18655 [cs.LG] and presented at NeurIPS LMRL 2022
Meijer DM, Ruano D, Briaire-de Bruijn IH, Wijers-Koster PM, van de Sande MAJ, Gelderblom H, Cleton-Jansen AM, de Miranda N, Kuijjer ML†, Bovée JVGM†*. Genes Chr Cancer. 2024 Jul 18;63(7):e23253
Osorio D*, Capasso A, Eckhardt SG , Giri U, Somma A, Pitts TM, Lieu CH, Messersmith WA, Bagby SM, Singh H, Das J, Sahni N, Yi SS*, Kuijjer ML*. Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. Nat Comput Sci. 2024 Mar 4;(3):237-250
Hsieh PH, Lopes-Ramos CM, Zucknick M, Sandve GK, Glass K, Kuijjer ML*. Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics. 2023 Oct 6;btad610
Belova T, Biondi N, Hsieh PH, Lutsik P, Chudasama P, Kuijjer ML*. Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer. 2023 Jul 24;zcad037
Lopes-Ramos CM, Belova T, Brunner T, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML*. Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme. Cancer Res. 2021 Nov 1;81(21):5401-5412
Kuijjer ML*, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics. 2020 Jun 17;btaa571
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
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

Peer-reviewed original publications

Unal B, Kuzu OF, Jun Y, Osorio D, Kildal W, Pradhan M, Kung SHY, Oo HZ, Daugaard M, Vendelbo M, Patterson J, Thomsen MK, Kuijjer ML, Saatcioglu F. Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer. Nat Commun. 2024 Oct 15;15(1):8895
Meijer DM, Ruano D, Briaire-de Bruijn IH, Wijers-Koster PM, van de Sande MAJ, Gelderblom H, Cleton-Jansen AM, de Miranda N, Kuijjer ML†, Bovée JVGM†*. The Variable Genomic Landscape During Osteosarcoma Progression: Insights From a Longitudinal WGS Analysis. Genes Chr Cancer. 2024 Jul 18;63(7):e23253
Osorio D*, Capasso A, Eckhardt SG , Giri U, Somma A, Pitts TM, Lieu CH, Messersmith WA, Bagby SM, Singh H, Das J, Sahni N, Yi SS*, Kuijjer ML*. Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. Nat Comput Sci. 2024 Mar 4;(3):237-250
Struck E, Belova T, Hsieh PH, Odeberg J, Kuijjer ML, Dusart P, Butler L. Temporal transcriptome analysis of the endothelial response to tumour necrosis factor. J Immunol. 2024 Jan 1;212(1):117-129
Hsieh PH, Lopes-Ramos CM, Zucknick M, Sandve GK, Glass K, Kuijjer ML*. Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics. 2023 Oct 6;btad610
Belova T, Biondi N, Hsieh PH, Lutsik P, Chudasama P, Kuijjer ML*. Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer. 2023 Jul 24;zcad037
Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta K, Sonawane A, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, Marin A, Chen CY, Song A, Saha E, DeMea D, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J. The Network Zoo: a multilingual package for the inference and analysis of biological networks. Genome Biol. 2023 Mar 9;24(1):45
Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Laye JP, Haase K, Mell T, Iyer V, Robles-Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Engler SSM, Bishop DT, Newton-Bishop J†, Adams DJ†. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol. 2023 Jan;259(1):56-68
Stahlberg EA, Abdel-Rahman MH, Aguilar B, Asadpoure A, Beckman RA, Borkon L, Bryan JN, Cebulla CC, Chang YH, Chatterjee A, Deng J, Dolatshahi S, O Gevaert, EJ Greenspan, Hao W, Hernandez-Boussard T, Jackson P, Kuijjer ML, Lee AV, Macklin P, Madhavan S, McCoy MD, Mirzaei NM, Razzaghi T, Rocha H, Shahriyari L, Shmulevich I, Stover DG, Sun Y, Syeda-Mahmood T, Wang J, Wang Q, Zervantonakis I. Exploring Approaches for Predictive Cancer Patient Digital Twins: Opportunities for Collaboration and Innovation. Front Digit Health. 2022 Oct 6;4:1007784
Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. Cell Rep Meth. 2022 Aug 22;2(8)100269
Ben Guebila M, Weighill D, Lopes-Ramos CM, Burkholz R, Pop RT, Palepu K, Shapoval M, Fagny M, Schlauch D, Glass K, Altenbuchinger M, Kuijjer ML, Platig J, Quackenbush J. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Meth. 2022 Apr 22;19(5):511-513
Ben Guebila M, Morgan DC, Glass K, Kuijjer ML, DeMeo DL, Quackenbush J. gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR Genom Bioinf. 2022 Feb 8;4(1):lqac002
Pavlović M, Scheffer L, Motwani L, Kanduri C, Kompova R, Vazov N, Waagan K, Bernal FLM, Costa AA, Corrie B, Akbar R, Al Hajj GS, Balaban G, Brusko TM, Chernigovskaya M, Christley S, Cowell LG, Frank R, Grytten I, Gundersen S, Hobaek Haff I, Hovig E, Hsieh PH, Klambauer G, Kuijjer ML, Lund-Andersen C, Martini A, Minotto T, Pensar J, Rand K, Riccardi E, Robert PA, Rocha A, Slabodkin A, Snapkov I, Sollid LM, Titov D, Weber CR, Widrich M, Yaari G, Greiff V, Sandve GK. immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nat Mach Intell. 2021 Nov 16;3:6936-944
Ben Guebila M, Lopes-Ramos CM, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush J. GRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 2021 Sep 11;gkab778
Lopes-Ramos CM, Belova T, Brunner T, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML*. Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme. Cancer Res. 2021 Nov 1;81(21):5401-5412

Osorio D*, Kuijjer ML, Cai JJ. rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. Bioinformatics. 2021 Jul 28;btab549
Grad I, Hanes R, Ayuda-Durán P, Kuijjer ML, Enserink JM, Meza-Zepeda LA, Myklebost O. Discovery of novel candidates for anti-liposarcoma therapies by medium-scale high-throughput drug screening. PLoS ONE. 2021 Mar 10;16(3):e0248140
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. Front Genet. 2021 Jan 11;11:606285
Qiang J, Ding W, Kuijjer ML, Quackenbush J, Chen P. Clustering sparse data with feature correlation with application to discover subtypes in cancer. IEEE Access. 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

Peer-reviewed conference proceedings (papers)

Hsieh PH, Hsiao RX, Belova T, Ferenc K, Mathelier A, Burkholz R, Chen CY, Sandve GK, Kuijjer ML*. Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration. NeurIPS LMRL Workshop. 2022 Oct 9 (modified: 05 May 2023)
Andreeva O, Li W, Ding W, Kuijjer ML, Quackenbush J, Chen P. Catalysis clustering with GAN by incorporating domain knowledge. KDD '20: Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining. 2020 Aug;1344-1352
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). 2018

Pre-prints

Hovan L, Kuijjer ML*. SPONGE: Simple Prior Omics Network GEnerator. 2024 BioRxiv DOI: 10.1101/2024.10.24.619989
López-Sánchez P, Avila-Moreno F, Hernandez-Lemus E, Kuijjer ML, Espinal-Enriquez J. Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma. 2024 BioRxiv DOI: 10.1101/2024.08.06.606802v1
Hsieh PH, Hsiao RX, Ferenc K, Mathelier A, Burkholz R, Chen CY, Sandve GK, Belova T†, Kuijjer ML†. CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. 2024 arXiv arXiv.2405.18655 [cs.LG]
Osorio D†, Shahrouzi P†, Tekpli X, Kristensen V, Kuijjer ML*. Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures. BioRxiv. DOI: 10.1101/2022.03.31.486602
Kuijjer ML*, Glass K. Reconstructing sample-specific networks using LIONESS. BioRxiv. DOI: 10.1101/2021.09.27.461954

Peer-reviewed reviews and letters to the editor

Ferenc K, Rauluseviciute I, Hovan L, Kumar V, Kuijjer ML, Mathelier A. Improving bioinformatics software quality through teamwork. Letter to the editor. Bioinformatics. 2024 Oct 22;btae632
van Oost S†, Meijer DM†, Kuijjer ML, Bovée JVGM, de Miranda NFCC. Linking immunity with genomics in sarcomas: is genomic complexity an immunogenic trigger? Review. Biomedicines. 2021 Aug 19;9:1048
Calderer G, Kuijjer ML*. Community detection in large-scale bipartite biological networks. Mini review. Front Genet. 2021 Apr 21;12:649440

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

Osorio D*, Kuijjer ML*. Enabling comparative gene regulatory network analysis on single-cell data with SCORPION. Research Briefing in Nat Comput Sci. 2024 Mar 12 (online ahead of print)
DeMarzio M, Glass K*, Kuijjer ML*. Commentary: Single-sample network modeling on omics data. BMC Biology. 2023 Dec 29;21(1):296

Fagny M*, Glass K*, Kuijjer ML*. Editorial: Applications and Methods in Genomic Networks. Front Genet. 2022 Jun 8;13:936015
Kuijjer ML*. Predicting cancer evolution using cell state dynamics. Editorial Commentary in Cancer Res. 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

my resume

Modeling genome-wide regulatory network rewiring in healthy tissues and disease. Institute of Biotechnology, National Autonomous University of Mexico (UNAM). January 16, 2023
Modeling gene regulatory network rewiring in cancer. Program Frontiers in Genomics, National Autonomous University of Mexico (UNAM). November 21, 2021
Single-sample network modeling identifies regulation of PD1 signaling associated with glioblastoma survival. ISMB/ECCB. July 21–25, 2019, Basel, Switzerland
Big data integration-Inferring and using individual patient network models. LabRoots Genetics and Genomics virtual conference. May 11-12, 2016
Estimating sample-specific regulatory networks. Banff/BIRS conference: Statistical and Computational Challenges in Bridging Functional Genomics, Epigenomics, Molecular QTLs, and Disease Genetics (BIRS/Banff 15w5142). August 3-7, 2015, Banff, Canada

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

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