Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD) is a research service core with administrative oversight from the Office of Research as well as scientific and technical direction provided by the Vanderbilt Center for Quantitative Sciences. The mission of the core is to consolidate the genomics data pipeline across the university and allow investigators to leverage the opportunities provided by next-generation sequencing and other genomics technologies.
We have many years' experience on developing novel methods for next-generation sequencing analysis and also collaborating with inside and outside researchers for data interpretation1-12. VANGARD provides standard analysis for RNA-seq, DNA-seq, ChIP-seq, and GRO/PRO-seq, which implements "best practices" pipeline for the sequencing data provided.
We care your data as much as you. Good experimental design will let your data talk, but torturing data will not. Keep in mind that thinking hard and defining your hypothesis well before you start the experiment will not only save your time and money but also promise reliable and meaningful results.
1. Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y: Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics 2012, 13:S8.
2. Shyr D, Liu Q: Next generation sequencing in cancer research and clinical application. Biol Proced Online 2013, 15(4).
3. Madison BB, Liu Q, Zhong X, Hahn CM, Lin N, Emmett MJ, Stanger BZ, Lee J-S, Rustgi AK: LIN28B promotes growth and tumorigenesis of the intestinal epithelium via Let-7. Genes Dev 2013, 27(20): 2233-2245.
4. Liu Q, Zhao S, Su P-F, Shyr Y: Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma. BMC Systems Biology 2013, 7(Suppl 5): S7.
5. Liu Q, Zhong X, Madison BB, Rustgi AK, Shyr Y: Assessing computational steps for CLIP-Seq data analysis. Biomed Research International. 2015, 11: 196082.
6. Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R: Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data. Mol Cell Proteomics 2015, 14(2):405-417.
7. Zhao Y, Liu Q, Acharya P, Stengel KR, Sheng Q, Zhou X, Kwak H, Fischer MA, Bradner JE, Strickland SA, Mohan SR, Savona MR, Venters BJ, Zhou MM, Lis JT, Hiebert SW. High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML. Cell Rep. 2016, 16(7):2003-16.
8. Sheng Q, Vickers K, Zhao S, Wang J, Samuels DC, Koues O, Shyr Y, Guo Y: Multi-perspective quality control of Illumina RNA sequencing data analysis. Brief Funct Genomics 2016.
9. Sheng Q, Zhao S, Li CI, Shyr Y, Guo Y: Practicability of detecting somatic point mutation from RNA high throughput sequencing data. Genomics 2016, 107(5):163-169.
10. Liu Q, Wang J, Zhao Y, Li CI, Stengel KR, Acharya P, Johnston G, Hiebert SW, Shyr Y. Identification of active miRNA promoters from nuclear run-on RNA sequencing. Nucleic Acids Res. 2017 Apr 28; 45(13): e121.
11. Stengel KR, Barnett KR, Wang J, Liu Q, Hodges E, Hiebert SW, Bhaskara S. Deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B-cell development. Proc Natl Acad Sci U S A. 2017 ; 114(32):8608-8613.
12. Lu Y, Zhao X, Liu Q, Li C, Graves-Deal R, Cao Z, Singh B, Franklin JL, Wang J, Hu H, Wei T, Yang M, Yeatman TJ, Lee E, Saito-Diaz K, Hinger S, Patton JG, Chung CH, Emmrich S, Klusmann JH, Fan D, Coffey RJ.. lncRNA MIR100HG-derived miR-100 and miR-125b mediate cetuximab resistance via Wnt/β-catenin signaling. Nature Medicine. 2017 Oct 16. doi: 10.1038/nm.4424.