Yu Shyr, Ph.D.

Yu Shyr, Ph.D.

Director, Center for Quantitative Sciences & Technologies for Advanced Genomics Analysis and Res Design, Chair, Vanderbilt Department of Biostatistics

571 Preston Research Building

Nashville, TN 37232
(615) 936-2572


Dr. Shyr’s research focuses on the field of data science, and specifically big data analytics in biomedical research. Dr. Shyr has developed biostatistical and bioinformatic methodologies for in vivo and in vitro cancer research, high-dimensional data preprocessing, and estimating relative potency in a parallel line bioassay.  

Research Description

Large Grant

U24 CA163056 (Shyr)                             09/01/11-02/28/2022
NCI                                                       Role: Principal Investigator
Barrett’s Esophagus Translational Research Network Coordinating Center (BETRNetCC)

The major goals of this project are to coordinate the functioning of the BETRNet; to facilitate data collection, management, analysis, and dissemination across the BETRNet; to develop a multi-institutional patient registry/virtual biorepository; and to develop and apply evaluation metrics for the BETRNet.

 

PUBLICATIONS

1.Arnold Egloff SA, Du L, Loomans HA, Starchenko A, Su PF, Ketova T, Knoll PB, Wang J, Haddad AQ, Fadare O, Cates JM, Lotan Y, Shyr Y, Clark PE, Zijlstra A.Shed urinary ALCAM is an independent prognostic biomarker of three-year overall survival after cystectomy in patients with bladder cancer. Oncotarget 2017; 8(1):722-741.

2.Chen Z, Soutto M, Rahman B, Fazili MW, Peng D, Piazuelo MB, Chen H, Washington MK, Shyr Y, El-Rifai W. Integrated expression analysis identifies transcription networks in mouse and human gastric neoplasia. Genes Chromosomes Cancer 2017; 56(7):535-547.

3.Galadanci N, Abdullahi SU, Vance LD, Tabari AM, Ali S, Belonwu R, Salihu A, Galadanci AA, Jibir BW, Bello-Manga H, Neville K, Kirkham FJ, Shyr Y, Phillips S, Covert BV, Kassim AA, Jordan LC, Aliyu MH, DeBaun MR. Feasibility Trial for Primary Stroke Prevention in Children with Sickle Cell Anemia in Nigeria (SPIN Trial). Am J Hematol 2017; 92(8):780-788.

4.Guise NB, Koonce TY, Kusnoor SV, Prather AA, Gottlieb LM, Huang LC, Phillips SE, Shyr Y, Adler NE, Stead WW. Institute of Medicine Measures of Social and Behavorial Determinants of Health: A Feasbility Study. Am J Prev Med 2017; 52(2):199-206.

5.Guo YDai YYu HZhao SSamuels DCShyr Y Genomics 2017; 109(2):83-90.

6.Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y. Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control. Biomed Res Int.PMC5540237

7.Jovanovic B, Mayer IA, Mayer EL, Abramson VG, Bardia A, Sanders M, Kuba MG, Estrada MV, Beeler JS, Shaver TM, Johnson KN, Sanchez V, Rosenbluth JM, Dillon PM, Forrero-Torres A, Chang JC, Meszoely I, Grau A, Lehmann BD, Shyr Y, Sheng Q, Chen SC, Arteaga CL, Pietenpol JA. A randomized phase II neoadjuvant study of cisplatin, paclitaxel with or without everolimus in patients with stage II/III triple-negative breast cancer (TNBC). Clin Cancer Res 2017. PMCID: PMC5540799

8. Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y. Power and sample size calculations for high-throughput sequencing-based experiments. Brief Bioinformatics 2017; [E-pub ahead of print]

9. 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; 45: 13. PMID: 28460090.

10.Peng D, Guo Y, Chen H, Zhao S, Washington K, Hu T, Shyr Y, El-Rifai W. Integrated molecular analysis reveals complex interactions between genomic and epigenomic alterations in esophageal adenocarcinomas. Scientific Reports 2017; 7:40729.

11.Schulte ML, Hight MR, Ayers GD, Liu Q, Shyr Y, Washington MK, Manning HC. Non-Invasive Glutamine PET Reflects Pharmacological Inhibition of BRAFV600E In Vivo. Mol Imaging Biol 2017; 19(3):421-428. PMID:

12.Esbenshade AJ, Zhao Z, Aftandilian C, Saab R, Wattier RL, Beauchemin M, Miller TP, Wilkes JJ, Kelly MJ, Fernbach A, Jeng M, Schwartz CL, Dvorak CC, Shyr Y, Moons KGM, Sulis ML, Friedman DL. Multisite external validation of a risk prediction model for the diagnosis of blood stream infection in febrile pediatric oncology patients without severe neutropenia. Cancer 2017; [E-pub ahead of print]

13. Su PF, Mau YL, Guo Y, Li CI, Liu Q, Boice JD, Shyr Y. Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset. Stat Appl Genet Mol Biol 2017; 16(1):47-58.

14. Thomas, CR Jr, Shyr Y. Determining Penetration of Prostate-Specific Antigen Screening Recommendations. Jama Oncology 2017; 3(5):707.

15. Tu C, Shen S, Sheng Q, Shyr Y, Qu J. A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification. J Proteomics 2017; 152:276-282.

16.Vlacich G, Stavas MJ, Pendyala P, Chen SC, Shyr Y, Cmelak AJ. A comparative analysis between sequential boost and integrated boost intensity-modulated radiation therapy with concurrent chemotherapy for locally-advanced head and neck cancer. Radiation Oncology 2017; PMCID: PMC5237132.

17.Wang J, Samuels DC, Shyr Y, Guo Y. StrandScript: Evaluation of Illumina Genotyping Array Design and Strand Correction. Bioinformatics 2017; Aug 1;33(15):2399-2401. PMID: 28402386.

18.Wang YA, Sun Y, Palmer JD, Solomides C, Huang LC, Shyr Y, Dicker AP, Lu B. IGFBP3 Modulates Lung Tumorigenesis and Cell Growth through IGF1 Signaling. Mol Cancer Res 2017; 15(7):896-904.

19.Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao YY, Shyr Y, Guo Y. Estimating relative mitochondrial DNA copy number using high throughput sequencing data. Genomics 2017; [E-pub ahead of print].

20.Zhang P, Lehmann BD, Shyr Y, Guo Y. The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. PMCID: PMC5299160.

21.Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y. Strategies for processing and quality control of Illumina genotyping arrays. Brief Bioinform 2017; [E-pub ahead of print]