Johnson WE - Search Results

1

Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Leek JT, et al. Among authors: johnson we. Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14. Nat Rev Genet. 2010. PMID: 20838408 Free PMC article. Review.

2

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.

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

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.

5

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

6

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

7

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.

8

Overcoming the impacts of two-step batch effect correction on gene expression estimation and inference.

Li T, Zhang Y, Patil P, Johnson WE. Li T, et al. Among authors: johnson we. Biostatistics. 2023 Jul 14;24(3):635-652. doi: 10.1093/biostatistics/kxab039. Biostatistics. 2023. PMID: 34893807 Free PMC article.

9

Concordance and discordance of sequence survey methods for molecular epidemiology.

Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA. Castro-Nallar E, et al. Among authors: johnson we. PeerJ. 2015 Feb 17;3:e761. doi: 10.7717/peerj.761. eCollection 2015. PeerJ. 2015. PMID: 25737810 Free PMC article.

10

A Parsimonious Host Inflammatory Biomarker Signature Predicts Incident Tuberculosis and Mortality in Advanced Human Immunodeficiency Virus.

Manabe YC, Andrade BB, Gupte N, Leong S, Kintali M, Matoga M, Riviere C, Samaneka W, Lama JR, Naidoo K, Zhao Y, Johnson WE, Ellner JJ, Hosseinipour MC, Bisson GP, Salgame P, Gupta A. Manabe YC, et al. Among authors: johnson we. Clin Infect Dis. 2020 Dec 17;71(10):2645-2654. doi: 10.1093/cid/ciz1147. Clin Infect Dis. 2020. PMID: 31761933 Free PMC article. Clinical Trial.

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