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Smooth quantile normalization.
Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Hicks SC, et al. Among authors: quackenbush j. Biostatistics. 2018 Apr 1;19(2):185-198. doi: 10.1093/biostatistics/kxx028. Biostatistics. 2018. PMID: 29036413 Free PMC article.
RNA-Seq analysis in MeV.
Howe EA, Sinha R, Schlauch D, Quackenbush J. Howe EA, et al. Among authors: quackenbush j. Bioinformatics. 2011 Nov 15;27(22):3209-10. doi: 10.1093/bioinformatics/btr490. Epub 2011 Oct 5. Bioinformatics. 2011. PMID: 21976420 Free PMC article.
BatchQC: interactive software for evaluating sample and batch effects in genomic data.
Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE. Manimaran S, et al. Among authors: quackenbush j. Bioinformatics. 2016 Dec 15;32(24):3836-3838. doi: 10.1093/bioinformatics/btw538. Epub 2016 Aug 18. Bioinformatics. 2016. PMID: 27540268 Free PMC article.
Proceedings of the third international molecular pathological epidemiology (MPE) meeting.
Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. Campbell PT, et al. Among authors: quackenbush j. Cancer Causes Control. 2017 Feb;28(2):167-176. doi: 10.1007/s10552-016-0845-z. Epub 2017 Jan 17. Cancer Causes Control. 2017. PMID: 28097472 Free PMC article. Review.
Estimating gene regulatory networks with pandaR.
Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Schlauch D, et al. Among authors: quackenbush j. Bioinformatics. 2017 Jul 15;33(14):2232-2234. doi: 10.1093/bioinformatics/btx139. Bioinformatics. 2017. PMID: 28334344 Free PMC article.
Challenges and emerging directions in single-cell analysis.
Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Yuan GC, et al. Among authors: quackenbush j. Genome Biol. 2017 May 8;18(1):84. doi: 10.1186/s13059-017-1218-y. Genome Biol. 2017. PMID: 28482897 Free PMC article. Review.
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: quackenbush j. 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: quackenbush j. BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x. BMC Genomics. 2017. PMID: 28899340 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: quackenbush j. 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.
354 results