| Year |
Citation |
Score |
| 2024 |
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. Nature Computational Science. PMID 38438786 DOI: 10.1038/s43588-024-00597-5 |
0.325 |
|
| 2023 |
Belova T, Biondi N, Hsieh PH, Lutsik P, Chudasama P, Kuijjer ML. Heterogeneity in the gene regulatory landscape of leiomyosarcoma. Nar Cancer. 5: zcad037. PMID 37492373 DOI: 10.1093/narcan/zcad037 |
0.346 |
|
| 2023 |
Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, ... ... Kuijjer ML, et al. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology. 24: 45. PMID 36894939 DOI: 10.1186/s13059-023-02877-1 |
0.491 |
|
| 2022 |
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. Nature Methods. PMID 35459940 DOI: 10.1038/s41592-022-01479-2 |
0.473 |
|
| 2022 |
Guebila MB, Morgan DC, Glass K, Kuijjer ML, DeMeo DL, Quackenbush J. gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. Nar Genomics and Bioinformatics. 4: lqac002. PMID 35156023 DOI: 10.1093/nargab/lqac002 |
0.479 |
|
| 2021 |
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 Research. PMID 34508353 DOI: 10.1093/nar/gkab778 |
0.53 |
|
| 2021 |
Lopes-Ramos CM, Belova T, Brunner TH, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML. Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme. Cancer Research. PMID 34493595 DOI: 10.1158/0008-5472.CAN-21-0730 |
0.534 |
|
| 2020 |
Qiang J, Ding W, Kuijjer M, Quackenbush J, Chen P. Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. Ieee Access : Practical Innovations, Open Solutions. 8: 67775-67789. PMID 36329870 DOI: 10.1109/access.2020.2982569 |
0.486 |
|
| 2020 |
Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics (Oxford, England). PMID 32860050 DOI: 10.1093/Bioinformatics/Btaa571 |
0.513 |
|
| 2020 |
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. 31: 107795. PMID 32579922 DOI: 10.1016/J.Celrep.2020.107795 |
0.552 |
|
| 2020 |
Lopes-Ramos CM, Kuijjer M, Glass K, DeMeo D, Quackenbush J. Abstract 6569: Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation Cancer Research. 80: 6569-6569. DOI: 10.1158/1538-7445.Am2020-6569 |
0.549 |
|
| 2020 |
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. 8: 67775-67789. DOI: 10.1109/Access.2020.2982569 |
0.463 |
|
| 2019 |
Barnett I, Malik N, Kuijjer ML, Mucha PJ, Onnela JP. EndNote: Feature-based classification of networks. Network Science (Cambridge University Press). 7: 438-444. PMID 31984135 DOI: 10.1017/Nws.2019.21 |
0.314 |
|
| 2019 |
Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. British Journal of Cancer. PMID 31806877 DOI: 10.1038/S41416-019-0614-3 |
0.484 |
|
| 2019 |
Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single sample network inference in R. Bmc Cancer. 19: 1003. PMID 31653243 DOI: 10.1186/S12885-019-6235-7 |
0.511 |
|
| 2019 |
Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 79: 2084. PMID 30987980 DOI: 10.1158/0008-5472.Can-19-0678 |
0.521 |
|
| 2019 |
Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. Iscience. 14: 226-240. PMID 30981959 DOI: 10.1016/J.Isci.2019.03.021 |
0.543 |
|
| 2019 |
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 Computational Biology. 15: e1006826. PMID 30785874 DOI: 10.1371/Journal.Pcbi.1006826 |
0.386 |
|
| 2019 |
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, ... ... Kuijjer ML, et al. Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Nature Communications. 10: 353. PMID 30664638 DOI: 10.1038/S41467-018-08081-1 |
0.335 |
|
| 2018 |
Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 78: 5538-5547. PMID 30275053 DOI: 10.1158/0008-5472.Can-18-0454 |
0.559 |
|
| 2018 |
Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. British Journal of Cancer. PMID 29765148 DOI: 10.1038/S41416-018-0109-7 |
0.498 |
|
| 2017 |
Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Reports. 21: 1077-1088. PMID 29069589 DOI: 10.1016/J.Celrep.2017.10.001 |
0.54 |
|
| 2017 |
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. 18: 437. PMID 28974199 DOI: 10.1186/S12859-017-1847-X |
0.476 |
|
| 2017 |
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. 18: 723. PMID 28899340 DOI: 10.1186/S12864-017-4111-X |
0.529 |
|
| 2017 |
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. Proceedings of the National Academy of Sciences of the United States of America. PMID 28851834 DOI: 10.1073/Pnas.1707375114 |
0.53 |
|
| 2017 |
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, et al. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. Journal of Hematology & Oncology. 10: 107. PMID 28506242 DOI: 10.1186/S13045-017-0465-4 |
0.46 |
|
| 2016 |
van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics (Oxford, England). PMID 27402905 DOI: 10.1093/Bioinformatics/Btw422 |
0.536 |
|
| 2015 |
Baranski Z, Booij TH, Kuijjer ML, de Jong Y, Cleton-Jansen AM, Price LS, van de Water B, Bovée JV, Hogendoorn PC, Danen EH. MEK inhibition induces apoptosis in osteosarcoma cells with constitutive ERK1/2 phosphorylation. Genes & Cancer. 6: 503-12. PMID 26807203 DOI: 10.18632/Genesandcancer.91 |
0.583 |
|
| 2015 |
Buddingh EP, Ruslan SEN, Reijnders CMA, Szuhai K, Kuijjer ML, Roelofs H, Hogendoorn PCW, Maarten Egeler R, Cleton-Jansen AM, Lankester AC. Mesenchymal stromal cells of osteosarcoma patients do not show evidence of neoplastic changes during long-term culture. Clinical Sarcoma Research. 5: 16. PMID 26106474 DOI: 10.1186/S13569-015-0031-1 |
0.571 |
|
| 2015 |
Pahl JH, Santos SJ, Kuijjer ML, Boerman GH, Sand LG, Szuhai K, Cleton-Jansen A, Egeler RM, Boveé JV, Schilham MW, Lankester AC. Expression of the immune regulation antigen CD70 in osteosarcoma. Cancer Cell International. 15: 31. PMID 25792975 DOI: 10.1186/S12935-015-0181-5 |
0.559 |
|
| 2015 |
Kuijjer ML, Glass K, Quackenbush J. Abstract B1-20: Gene regulation by transcription factors and microRNAs in ovarian cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-20 |
0.57 |
|
| 2014 |
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. Interleukin-6 receptor and its ligand interleukin-6 are opposite markers for survival and infiltration with mature myeloid cells in ovarian cancer. Oncoimmunology. 3: e962397. PMID 25964862 DOI: 10.4161/21624011.2014.962397 |
0.32 |
|
| 2014 |
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. 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 & Clinical Cancer Research : Cr. 33: 27. PMID 24612598 DOI: 10.1186/1756-9966-33-27 |
0.576 |
|
| 2014 |
Kuijjer ML, van den Akker BE, Hilhorst R, Mommersteeg M, Buddingh EP, Serra M, Bürger H, Hogendoorn PC, Cleton-Jansen AM. Kinome and mRNA expression profiling of high-grade osteosarcoma cell lines implies Akt signaling as possible target for therapy. Bmc Medical Genomics. 7: 4. PMID 24447333 DOI: 10.1186/1755-8794-7-4 |
0.615 |
|
| 2013 |
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, et al. Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation. The Journal of Clinical Investigation. 123: 5351-60. PMID 24231354 DOI: 10.1172/Jci70559 |
0.586 |
|
| 2013 |
Steenwijk PJdVv, Ramwadhdoebe TH, Goedemans R, Doorduijn EM, Ham JJv, Gorter A, Hall Tv, Kuijjer ML, Poelgeest MIEv, Burg SHvd, Jordanova ES. Tumor-infiltrating CD14-positive myeloid cells and CD8-positive T-cells prolong survival in patients with cervical carcinoma. International Journal of Cancer. 133: 2884-2894. PMID 23740735 DOI: 10.1002/Ijc.28309 |
0.325 |
|
| 2013 |
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. IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma. Bmc Cancer. 13: 245. PMID 23688189 DOI: 10.1186/1471-2407-13-245 |
0.575 |
|
| 2013 |
Kuijjer ML, Hogendoorn PC, Cleton-Jansen AM. Genome-wide analyses on high-grade osteosarcoma: making sense of a genomically most unstable tumor. International Journal of Cancer. 133: 2512-21. PMID 23436697 DOI: 10.1002/Ijc.28124 |
0.599 |
|
| 2012 |
Namløs HM, Meza-Zepeda LA, Barøy T, Østensen IH, Kresse SH, Kuijjer ML, Serra M, Bürger H, Cleton-Jansen AM, Myklebost O. Modulation of the osteosarcoma expression phenotype by microRNAs. Plos One. 7: e48086. PMID 23133552 DOI: 10.1371/Journal.Pone.0048086 |
0.514 |
|
| 2012 |
Mohseny AB, Cai Y, Kuijjer M, 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. European Journal of Cancer (Oxford, England : 1990). 48: 3429-38. PMID 22868198 DOI: 10.1016/J.Ejca.2012.06.018 |
0.59 |
|
| 2012 |
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 Research. 72: 4074-84. PMID 22700878 DOI: 10.1158/0008-5472.Can-12-0215 |
0.603 |
|
| 2012 |
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. 51: 696-706. PMID 22454324 DOI: 10.1002/Gcc.21956 |
0.618 |
|
| 2012 |
Kuijjer ML, Rydbeck H, Kresse SH, Buddingh EP, Roelofs H, Bürger H, Myklebost O, Hogendoorn PC, Meza-Zepeda LA, Cleton-Jansen A. Abstract 5128: Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data Cancer Research. 72: 5128-5128. DOI: 10.1158/1538-7445.Am2012-5128 |
0.62 |
|
| 2011 |
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, et al. Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome. Nature Genetics. 43: 1256-61. PMID 22057234 DOI: 10.1038/Ng.1004 |
0.571 |
|
| 2011 |
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 Medical Genomics. 4: 66. PMID 21933437 DOI: 10.1186/1755-8794-4-66 |
0.616 |
|
| 2011 |
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. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 17: 2110-9. PMID 21372215 DOI: 10.1158/1078-0432.Ccr-10-2047 |
0.598 |
|
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