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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: paulson jn. Genome Biol. 2023 Mar 9;24(1):45. doi: 10.1186/s13059-023-02877-1. Genome Biol. 2023. PMID: 36894939 Free PMC article.
Estimating gene regulatory networks with pandaR.
Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Schlauch D, et al. Among authors: paulson jn. Bioinformatics. 2017 Jul 15;33(14):2232-2234. doi: 10.1093/bioinformatics/btx139. Bioinformatics. 2017. PMID: 28334344 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: paulson jn. 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.
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: paulson jn. BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x. BMC Genomics. 2017. PMID: 28899340 Free PMC article.
Smooth quantile normalization.
Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Hicks SC, et al. Among authors: paulson jn. Biostatistics. 2018 Apr 1;19(2):185-198. doi: 10.1093/biostatistics/kxx028. Biostatistics. 2018. PMID: 29036413 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: paulson jn. 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.
Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface.
Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN. Carette X, et al. Among authors: paulson jn. mBio. 2018 Mar 6;9(2):e02333-17. doi: 10.1128/mBio.02333-17. mBio. 2018. PMID: 29511081 Free PMC article.
Cancer subtype identification using somatic mutation data.
Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Kuijjer ML, et al. Among authors: paulson jn. 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.
72 results