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EndNote: Feature-based classification of networks.
Barnett I, Malik N, Kuijjer ML, Mucha PJ, Onnela JP. Barnett I, et al. Among authors: kuijjer ml. Netw Sci (Camb Univ Press). 2019 Sep;7(3):438-444. doi: 10.1017/nws.2019.21. Epub 2019 Sep 23. Netw Sci (Camb Univ Press). 2019. PMID: 31984135 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.
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.
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.
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, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J. Ben Guebila M, et al. Among authors: kuijjer ml. Genome Biol. 2023 Mar 9;24(1):45. doi: 10.1186/s13059-023-02877-1. Genome Biol. 2023. PMID: 36894939 Free PMC article.
An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.
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. Ben Guebila M, et al. Among authors: kuijjer ml. Nat Methods. 2022 May;19(5):511-513. doi: 10.1038/s41592-022-01479-2. Nat Methods. 2022. PMID: 35459940 Free PMC article. No abstract available.
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.
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.
55 results