Johnson WE - Search Results

1

Robustifying genomic classifiers to batch effects via ensemble learning.

Zhang Y, Patil P, Johnson WE, Parmigiani G. Zhang Y, et al. Among authors: johnson we. Bioinformatics. 2021 Jul 12;37(11):1521-1527. doi: 10.1093/bioinformatics/btaa986. Bioinformatics. 2021. PMID: 33245114 Free PMC article.

2

Adjusting batch effects in microarray expression data using empirical Bayes methods.

Johnson WE, Li C, Rabinovic A. Johnson WE, et al. Biostatistics. 2007 Jan;8(1):118-27. doi: 10.1093/biostatistics/kxj037. Epub 2006 Apr 21. Biostatistics. 2007. PMID: 16632515

3

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. Leek JT, et al. Among authors: johnson we. Bioinformatics. 2012 Mar 15;28(6):882-3. doi: 10.1093/bioinformatics/bts034. Epub 2012 Jan 17. Bioinformatics. 2012. PMID: 22257669 Free PMC article.

4

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.

Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. Shen Y, et al. Among authors: johnson we. Bioinformatics. 2015 Jun 1;31(11):1745-53. doi: 10.1093/bioinformatics/btv031. Epub 2015 Jan 22. Bioinformatics. 2015. PMID: 25617415 Free PMC article.

5

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.

Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR. Rahman M, et al. Among authors: johnson we. Bioinformatics. 2015 Nov 15;31(22):3666-72. doi: 10.1093/bioinformatics/btv377. Epub 2015 Jul 24. Bioinformatics. 2015. PMID: 26209429 Free PMC article.

6

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: johnson we. Bioinformatics. 2016 Dec 15;32(24):3836-3838. doi: 10.1093/bioinformatics/btw538. Epub 2016 Aug 18. Bioinformatics. 2016. PMID: 27540268 Free PMC article.

7

Detection of multiple perturbations in multi-omics biological networks.

Griffin PJ, Zhang Y, Johnson WE, Kolaczyk ED. Griffin PJ, et al. Among authors: johnson we. Biometrics. 2018 Dec;74(4):1351-1361. doi: 10.1111/biom.12893. Epub 2018 May 17. Biometrics. 2018. PMID: 29772079

8

Alternative empirical Bayes models for adjusting for batch effects in genomic studies.

Zhang Y, Jenkins DF, Manimaran S, Johnson WE. Zhang Y, et al. Among authors: johnson we. BMC Bioinformatics. 2018 Jul 13;19(1):262. doi: 10.1186/s12859-018-2263-6. BMC Bioinformatics. 2018. PMID: 30001694 Free PMC article.

9

Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes.

McQuerry JA, Jenkins DF, Yost SE, Zhang Y, Schmolze D, Johnson WE, Yuan Y, Bild AH. McQuerry JA, et al. Among authors: johnson we. BMC Cancer. 2019 Sep 5;19(1):881. doi: 10.1186/s12885-019-6052-z. BMC Cancer. 2019. PMID: 31488082 Free PMC article.

10

ComBat-seq: batch effect adjustment for RNA-seq count data.

Zhang Y, Parmigiani G, Johnson WE. Zhang Y, et al. Among authors: johnson we. NAR Genom Bioinform. 2020 Sep;2(3):lqaa078. doi: 10.1093/nargab/lqaa078. Epub 2020 Sep 21. NAR Genom Bioinform. 2020. PMID: 33015620 Free PMC article.

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