Yu X - Search Results

1

How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S. Yu X, et al. BioData Min. 2012 Jun 18;5(1):6. doi: 10.1186/1756-0381-5-6. BioData Min. 2012. PMID: 22709551 Free PMC article.

2

Global mutational profiling of formalin-fixed human colon cancers from a pathology archive.

Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J. Adams MD, et al. Among authors: yu x. Mod Pathol. 2012 Dec;25(12):1599-608. doi: 10.1038/modpathol.2012.121. Epub 2012 Aug 10. Mod Pathol. 2012. PMID: 22878650 Free PMC article.

3

MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment.

Sun S, Noviski A, Yu X. Sun S, et al. Among authors: yu x. BMC Bioinformatics. 2013 Aug 23;14:259. doi: 10.1186/1471-2105-14-259. BMC Bioinformatics. 2013. PMID: 23968174 Free PMC article.

4

Comparing a few SNP calling algorithms using low-coverage sequencing data.

Yu X, Sun S. Yu X, et al. BMC Bioinformatics. 2013 Sep 17;14:274. doi: 10.1186/1471-2105-14-274. BMC Bioinformatics. 2013. PMID: 24044377 Free PMC article.

5

HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test.

Sun S, Yu X. Sun S, et al. Among authors: yu x. Stat Appl Genet Mol Biol. 2016 Mar;15(1):55-67. doi: 10.1515/sagmb-2015-0076. Stat Appl Genet Mol Biol. 2016. PMID: 26854292 Free article.

6

HMM-DM: identifying differentially methylated regions using a hidden Markov model.

Yu X, Sun S. Yu X, et al. Stat Appl Genet Mol Biol. 2016 Mar;15(1):69-81. doi: 10.1515/sagmb-2015-0077. Stat Appl Genet Mol Biol. 2016. PMID: 26887041

7

Comparing five statistical methods of differential methylation identification using bisulfite sequencing data.

Yu X, Sun S. Yu X, et al. Stat Appl Genet Mol Biol. 2016 Apr;15(2):173-91. doi: 10.1515/sagmb-2015-0078. Stat Appl Genet Mol Biol. 2016. PMID: 26910753

8

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.

Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J. Wang X, et al. Among authors: yu x. Bioinformatics. 2015 Jun 15;31(12):2040-2. doi: 10.1093/bioinformatics/btv089. Epub 2015 Feb 13. Bioinformatics. 2015. PMID: 25681254 Free PMC article.

9

Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow.

Eschrich SA, Yu X, Teer JK. Eschrich SA, et al. Among authors: yu x. BMC Bioinformatics. 2023 Apr 24;24(1):164. doi: 10.1186/s12859-023-05288-y. BMC Bioinformatics. 2023. PMID: 37095442 Free PMC article.

10

Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments.

Yu X, Abbas-Aghababazadeh F, Chen YA, Fridley BL. Yu X, et al. Methods Mol Biol. 2021;2194:143-175. doi: 10.1007/978-1-0716-0849-4_9. Methods Mol Biol. 2021. PMID: 32926366 Free PMC article. Review.

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