Kocher JP - Search Results

1

Concordance of changes in metabolic pathways based on plasma metabolomics and skeletal muscle transcriptomics in type 1 diabetes.

Dutta T, Chai HS, Ward LE, Ghosh A, Persson XM, Ford GC, Kudva YC, Sun Z, Asmann YW, Kocher JP, Nair KS. Dutta T, et al. Among authors: kocher jp. Diabetes. 2012 May;61(5):1004-16. doi: 10.2337/db11-0874. Epub 2012 Mar 13. Diabetes. 2012. PMID: 22415876 Free PMC article.

2

Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.

Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Sun Z, et al. Among authors: kocher jp. PLoS One. 2013 Aug 19;8(8):e71745. doi: 10.1371/journal.pone.0071745. eCollection 2013. PLoS One. 2013. PMID: 23977132 Free PMC article.

3

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays.

Chai HS, Therneau TM, Bailey KR, Kocher JP. Chai HS, et al. Among authors: kocher jp. BMC Bioinformatics. 2010 Jun 29;11:356. doi: 10.1186/1471-2105-11-356. BMC Bioinformatics. 2010. PMID: 20587065 Free PMC article.

4

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP. Asmann YW, et al. Among authors: kocher jp. BMC Genomics. 2009 Nov 16;10:531. doi: 10.1186/1471-2164-10-531. BMC Genomics. 2009. PMID: 19917133 Free PMC article.

5

Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling.

Sun Z, Prodduturi N, Sun SY, Thompson EA, Kocher JP. Sun Z, et al. Among authors: kocher jp. Epigenomics. 2015 Oct;7(7):1099-110. doi: 10.2217/epi.15.43. Epub 2015 May 18. Epigenomics. 2015. PMID: 26039248 Free article.

6

Batch effect correction for genome-wide methylation data with Illumina Infinium platform.

Sun Z, Chai HS, Wu Y, White WM, Donkena KV, Klein CJ, Garovic VD, Therneau TM, Kocher JP. Sun Z, et al. Among authors: kocher jp. BMC Med Genomics. 2011 Dec 16;4:84. doi: 10.1186/1755-8794-4-84. BMC Med Genomics. 2011. PMID: 22171553 Free PMC article.

7

GLOSSI: a method to assess the association of genetic loci-sets with complex diseases.

Chai HS, Sicotte H, Bailey KR, Turner ST, Asmann YW, Kocher JP. Chai HS, et al. Among authors: kocher jp. BMC Bioinformatics. 2009 Apr 3;10:102. doi: 10.1186/1471-2105-10-102. BMC Bioinformatics. 2009. PMID: 19344520 Free PMC article.

8

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA. Asmann YW, et al. Among authors: kocher jp. Nucleic Acids Res. 2011 Aug;39(15):e100. doi: 10.1093/nar/gkr362. Epub 2011 May 27. Nucleic Acids Res. 2011. PMID: 21622959 Free PMC article.

9

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.

Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. Asmann YW, et al. Among authors: kocher jp. Bioinformatics. 2012 Jan 15;28(2):277-8. doi: 10.1093/bioinformatics/btr612. Epub 2011 Nov 15. Bioinformatics. 2012. PMID: 22088845 Free PMC article.

10

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. Sun Z, et al. Among authors: kocher jp. Bioinformatics. 2012 Aug 15;28(16):2180-1. doi: 10.1093/bioinformatics/bts337. Epub 2012 Jun 10. Bioinformatics. 2012. PMID: 22689387 Free PMC article.

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