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Applications of ultra-high-throughput sequencing.
Fox S, Filichkin S, Mockler TC. Fox S, et al. Methods Mol Biol. 2009;553:79-108. doi: 10.1007/978-1-60327-563-7_5. Methods Mol Biol. 2009. PMID: 19588102 Review.
The genome of black raspberry (Rubus occidentalis).
VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC. VanBuren R, et al. Plant J. 2016 Sep;87(6):535-47. doi: 10.1111/tpj.13215. Epub 2016 Jul 20. Plant J. 2016. PMID: 27228578
Exploring the switchgrass transcriptome using second-generation sequencing technology.
Wang Y, Zeng X, Iyer NJ, Bryant DW, Mockler TC, Mahalingam R. Wang Y, et al. PLoS One. 2012;7(3):e34225. doi: 10.1371/journal.pone.0034225. Epub 2012 Mar 29. PLoS One. 2012. PMID: 22479570 Free PMC article.
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.
Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH. Vining KJ, et al. BMC Genomics. 2012 Jan 17;13:27. doi: 10.1186/1471-2164-13-27. BMC Genomics. 2012. PMID: 22251412 Free PMC article.
GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.
Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH. Cumbie JS, et al. PLoS One. 2011;6(10):e25279. doi: 10.1371/journal.pone.0025279. Epub 2011 Oct 6. PLoS One. 2011. PMID: 21998647 Free PMC article.
Supersplat--spliced RNA-seq alignment.
Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC. Bryant DW Jr, et al. Bioinformatics. 2010 Jun 15;26(12):1500-5. doi: 10.1093/bioinformatics/btq206. Epub 2010 Apr 21. Bioinformatics. 2010. PMID: 20410051 Free PMC article.
Cis-regulatory elements in plant cell signaling.
Priest HD, Filichkin SA, Mockler TC. Priest HD, et al. Curr Opin Plant Biol. 2009 Oct;12(5):643-9. doi: 10.1016/j.pbi.2009.07.016. Epub 2009 Aug 28. Curr Opin Plant Biol. 2009. PMID: 19717332 Review.
QSRA: a quality-value guided de novo short read assembler.
Bryant DW Jr, Wong WK, Mockler TC. Bryant DW Jr, et al. BMC Bioinformatics. 2009 Feb 24;10:69. doi: 10.1186/1471-2105-10-69. BMC Bioinformatics. 2009. PMID: 19239711 Free PMC article.
The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J. Mockler TC, et al. Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006. Cold Spring Harb Symp Quant Biol. 2007. PMID: 18419293
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