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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. Lopes-Ramos CM, et al. Among authors: kuijjer ml. BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x. BMC Genomics. 2017. PMID: 28899340 Free PMC article.
PyPanda: a Python package for gene regulatory network reconstruction.
van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. van IJzendoorn DG, et al. Among authors: kuijjer ml. Bioinformatics. 2016 Nov 1;32(21):3363-3365. doi: 10.1093/bioinformatics/btw422. Epub 2016 Jul 10. Bioinformatics. 2016. PMID: 27402905 Free PMC article.
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. Hill KE, et al. Among authors: kuijjer ml. J Hematol Oncol. 2017 May 15;10(1):107. doi: 10.1186/s13045-017-0465-4. J Hematol Oncol. 2017. PMID: 28506242 Free PMC article.
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. Fagny M, et al. Among authors: kuijjer ml. Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7841-E7850. doi: 10.1073/pnas.1707375114. Epub 2017 Aug 29. Proc Natl Acad Sci U S A. 2017. PMID: 28851834 Free PMC article.
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. Sonawane AR, et al. Among authors: kuijjer ml. Cell Rep. 2017 Oct 24;21(4):1077-1088. doi: 10.1016/j.celrep.2017.10.001. Cell Rep. 2017. PMID: 29069589 Free PMC article.
Cancer subtype identification using somatic mutation data.
Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Kuijjer ML, et al. Br J Cancer. 2018 May;118(11):1492-1501. doi: 10.1038/s41416-018-0109-7. Epub 2018 May 16. Br J Cancer. 2018. PMID: 29765148 Free PMC article.
Estimating Sample-Specific Regulatory Networks.
Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Kuijjer ML, et al. iScience. 2019 Apr 26;14:226-240. doi: 10.1016/j.isci.2019.03.021. Epub 2019 Mar 28. iScience. 2019. PMID: 30981959 Free PMC article.
55 results