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  • Yu Shyr
2016

A Distinct Lung-Interstitium-Resident Memory CD8+ T Cell Subset Confers Enhanced Protection to Lower Respiratory Tract Infection

Gilchuk, P., Hill, T. M., Guy, C., McMaster, S. R., Boyd, K. L., Rabacal, W. A., Lu, P., Shyr, Y., Kohlmeier, J. E., Sebzda, E., Green, D. R. & Joyce, S., 2016 Aug 16, In : Cell Reports. 16, 7, p. 1800-1809 10 p.

Research output: Contribution to journalArticle

Open Access
31 Citations (Scopus)

A novel resistance mutation in eccC5 of the ESX-5 secretion system confers ofloxacin resistance in Mycobacterium tuberculosis

Eilertson, B., Maruri, F., Blackman, A., Guo, Y., Herrera, M., van der Heijden, Y., Shyr, Y. & Sterling, T. R., 2016 Sep 1, In : The Journal of antimicrobial chemotherapy. 71, 9, p. 2419-2427 9 p.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)

Clinical and Biological Insights Into Combined Post- and Pre-Capillary Pulmonary Hypertension

Assad, T. R., Hemnes, A. R., Larkin, E. K., Glazer, A. M., Xu, M., Wells, Q. S., Farber-Eger, E. H., Sheng, Q., Shyr, Y., Harrell, F. E., Newman, J. H. & Brittain, E. L., 2016 Dec 13, In : Journal of the American College of Cardiology. 68, 23, p. 2525-2536 12 p.

Research output: Contribution to journalArticle

Open Access
67 Citations (Scopus)

Connecting the Dots: Therapy-Induced Senescence and a Tumor-Suppressive Immune Microenvironment

Vilgelm, A. E., Johnson, C. A., Prasad, N., Yang, J., Chen, S. C., Ayers, G. D., Pawlikowski, J. S., Raman, D., Sosman, J. A., Kelley, M., Ecsedy, J. A., Shyr, Y., Levy, S. E. & Richmond, A., 2016 Jun 1, In : Journal of the National Cancer Institute. 108, 6, djv406.

Research output: Contribution to journalArticle

Open Access
23 Citations (Scopus)

Disrupted cooperation between transcription factors across diverse cancer types

Wang, J., Liu, Q., Sun, J. & Shyr, Y., 2016 Aug 5, In : BMC genomics. 17, 1, 560.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Diverse, biologically relevant, and targetable gene rearrangements in triple-negative breast cancer and other malignancies

Shaver, T. M., Lehmann, B. D., Beeler, J. S., Li, C. I., Li, Z., Jin, H., Stricker, T. P., Shyr, Y. & Pietenpol, J. A., 2016 Aug 15, In : Cancer Research. 76, 16, p. 4850-4860 11 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Effects of combination PPARγ agonist and angiotensin receptor blocker on glomerulosclerosis

Matsushita, K., Yang, H. C., Mysore, M. M., Zhong, J., Shyr, Y., Ma, L. J. & Fogo, A. B., 2016 Jun 1, In : Laboratory Investigation. 96, 6, p. 602-609 8 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Evidence Combination from an Evolutionary Game Theory Perspective

Deng, X., Han, D., Dezert, J., Deng, Y. & Shyr, Y., 2016 Sep, In : IEEE Transactions on Cybernetics. 46, 9, p. 2070-2082 13 p., 7194765.

Research output: Contribution to journalArticle

97 Citations (Scopus)

Heterozygosity ratio, a robust global genomic measure of autozygosity and its association with height and disease risk

Samuels, D. C., Wang, J., Ye, F., He, J., Levinson, R. T., Sheng, Q., Zhao, S., Capra, J. A., Shyr, Y., Zheng, W. & Guo, Y., 2016 Nov, In : Genetics. 204, 3, p. 893-904 12 p.

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy

Johnson, D. B., Estrada, M. V., Salgado, R., Sanchez, V., Doxie, D. B., Opalenik, S. R., Vilgelm, A. E., Feld, E., Johnson, A. S., Greenplate, A. R., Sanders, M. E., Lovly, C. M., Frederick, D. T., Kelley, M. C., Richmond, A., Irish, J. M., Shyr, Y., Sullivan, R. J., Puzanov, I., Sosman, J. A. & 1 others, Balko, J. M., 2016 Jan 29, In : Nature communications. 7, 10582.

Research output: Contribution to journalArticle

Open Access
152 Citations (Scopus)

Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data

Zhang, P., Samuels, D. C., Lehmann, B., Stricker, T., Pietenpol, J., Shyr, Y. & Guo, Y., 2016 Mar 1, In : Briefings in bioinformatics. 17, 2, p. 224-232 9 p.

Research output: Contribution to journalArticle

Open Access
10 Citations (Scopus)

Mitochondria single nucleotide variation across six blood cell types

Zhang, P., Samuels, D. C., Wang, J., Zhao, S., Shyr, Y. & Guo, Y., 2016 May 1, In : Mitochondrion. 28, p. 16-22 7 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Non-invasive imaging of oxygen extraction fraction in adults with sickle cell anaemia

Jordan, L. C., Gindville, M. C., Scott, A. O., Juttukonda, M. R., Strother, M. K., Kassim, A. A., Chen, S. C., Lu, H., Pruthi, S., Shyr, Y. & Donahue, M. J., 2016 Mar 1, In : Brain. 139, 3, p. 738-750 13 p.

Research output: Contribution to journalArticle

Open Access
52 Citations (Scopus)

P73 Is Required for Multiciliogenesis and Regulates the Foxj1-Associated Gene Network

Marshall, C. B., Mays, D. J., Beeler, J. S., Rosenbluth, J. M., Boyd, K. L., Santos Guasch, G. L., Shaver, T. M., Tang, L. J., Liu, Q., Shyr, Y., Venters, B. J., Magnuson, M. A. & Pietenpol, J. A., 2016 Mar 15, In : Cell Reports. 14, 10, p. 2289-2300 12 p.

Research output: Contribution to journalArticle

Open Access
48 Citations (Scopus)

Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument

Tu, C., Li, J., Shen, S., Sheng, Q., Shyr, Y. & Qu, J., 2016 Jan 1, In : PloS one. 11, 7, p. e0160160

Research output: Contribution to journalArticle

Open Access
10 Citations (Scopus)

Practicability of detecting somatic point mutation from RNA high throughput sequencing data

Sheng, Q., Zhao, S., Li, C. I., Shyr, Y. & Guo, Y., 2016 May 1, In : Genomics. 107, 5, p. 163-169 7 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array

Zhang, P., Samuels, D. C., Zhao, S., Wang, J., Shyr, Y. & Guo, Y., 2016 Nov 1, In : Mitochondrion. 31, p. 75-78 4 p.

Research output: Contribution to journalArticle

Refinement of triple-negative breast cancer molecular subtypes: Implications for neoadjuvant chemotherapy selection

Lehmann, B. D., Jovanović, B., Chen, X., Estrada, M. V., Johnson, K. N., Shyr, Y., Moses, H. L., Sanders, M. E. & Pietenpol, J. A., 2016 Jun, In : PloS one. 11, 6, e0157368.

Research output: Contribution to journalArticle

Open Access
272 Citations (Scopus)

RNA sequencing identifies transcriptionally viable gene fusions in esophageal adenocarcinomas

Blum, A. E., Venkitachalam, S., Guo, Y., Kieber-Emmons, A. M., Ravi, L., Chandar, A. K., Iyer, P. G., Canto, M. I., Wang, J. S., Shaheen, N. J., Barnholtz-Sloan, J. S., Markowitz, S. D., Willis, J. E., Shyr, Y., Chak, A., Varadan, V. & Guda, K., 2016 Oct 1, In : Cancer Research. 76, 19, p. 5628-5633 6 p.

Research output: Contribution to journalArticle

Open Access
12 Citations (Scopus)
2 Citations (Scopus)

Targeted next generation sequencing identifies markers of response to PD-1 blockade

Johnson, D. B., Frampton, G. M., Rioth, M. J., Yusko, E., Xu, Y., Guo, X., Ennis, R. C., Fabrizio, D., Chalmers, Z. R., Greenbowe, J., Ali, S. M., Balasubramanian, S., Sun, J. X., He, Y., Frederick, D. T., Puzanov, I., Balko, J. M., Cates, J. M., Ross, J. S., Sanders, C. & 7 others, Robins, H., Shyr, Y., Miller, V. A., Stephens, P. J., Sullivan, R. J., Sosman, J. A. & Lovly, C. M., 2016 Nov, In : Cancer Immunology Research. 4, 11, p. 959-967 9 p.

Research output: Contribution to journalArticle

Open Access
189 Citations (Scopus)

Utility of [18F]FSPG PET to Image Hepatocellular Carcinoma: First Clinical Evaluation in a US Population

Kavanaugh, G., Williams, J., Morris, A. S., Nickels, M. L., Walker, R., Koglin, N., Stephens, A. W., Washington, M. K., Geevarghese, S. K., Liu, Q., Ayers, D., Shyr, Y. & Manning, H. C., 2016 Dec 1, In : Molecular Imaging and Biology. 18, 6, p. 924-934 11 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)
2017

A comparative analysis between sequential boost and integrated boost intensity-modulated radiation therapy with concurrent chemotherapy for locally-advanced head and neck cancer

Vlacich, G., Stavas, M. J., Pendyala, P., Chen, S. C., Shyr, Y. & Cmelak, A. J., 2017 Jan 13, In : Radiation Oncology. 12, 1, 13.

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification

Tu, C., Shen, S., Sheng, Q., Shyr, Y. & Qu, J., 2017 Jan 30, In : Journal of Proteomics. 152, p. 276-282 7 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

A randomized phase II neoadjuvant study of cisplatin, paclitaxel with or without everolimus in patients with stage II/III triple-negative breast cancer (TNBC): Responses and long-term outcome correlated with increased frequency of DNA damage response gene mutations, TNBC subtype, AR status, and Ki67

Jovanovic, B., Mayer, I. A., Mayer, E. L., Abramson, V. G., Bardia, A., Sanders, M. E., Kuba, M. G., Estrada, M. V., Beeler, J. S., Shaver, T. M., Johnson, K. C., Sanchez, V., Rosenbluth, J. M., Dillon, P. M., Forero-Torres, A., Chang, J. C., Meszoely, I. M., Grau, A. M., Lehmann, B. D., Shyr, Y. & 4 others, Sheng, Q., Chen, S. C., Arteaga, C. L. & Pietenpol, J. A., 2017 Aug 1, In : Clinical Cancer Research. 23, 15, p. 4035-4045 11 p.

Research output: Contribution to journalArticle

Open Access
32 Citations (Scopus)

Bivariate Poisson models with varying offsets: An application to the paired mitochondrial DNA dataset

Su, P. F., Mau, Y. L., Guo, Y., Li, C. I., Liu, Q., Boice, J. D. & Shyr, Y., 2017 Mar 1, In : Statistical Applications in Genetics and Molecular Biology. 16, 1, p. 47-58 12 p.

Research output: Contribution to journalArticle

Corrigendum to "Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control"

Guo, Y., Sheng, Q., Samuels, D. C., Lehmann, B., Bauer, J. A., Pietenpol, J. & Shyr, Y., 2017 Jan 1, In : BioMed research international. 2017, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Determining penetration of prostate-specific antigen screening recommendations

Thomas, C. R. & Shyr, Y., 2017 Jan 1, In : JAMA Oncology. 3, 5, 1 p.

Research output: Contribution to journalEditorial

Open Access
3 Citations (Scopus)

Estimating relative mitochondrial DNA copy number using high throughput sequencing data

Zhang, P., Lehmann, B. D., Samuels, D. C., Zhao, S., Zhao, Y. Y., Shyr, Y. & Guo, Y., 2017 Oct, In : Genomics. 109, 5-6, p. 457-462 6 p.

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

Etoposide and cisplatin versus paclitaxel and carboplatin with concurrent thoracic radiotherapy in unresectable stage III non-small cell lung cancer: A multicenter randomized phase III trial

Liang, J., Bi, N., Wu, S., Chen, M., Lv, C., Zhao, L., Shi, A., Jiang, W., Xu, Y., Zhou, Z., Wang, W., Chen, D., Hui, Z., Lv, J., Zhang, H., Feng, Q., Xiao, Z., Wang, X., Liu, L., Zhang, T. & 7 others, Du, L., Chen, W., Shyr, Y., Yin, W., Li, J., He, J. & Wang, L., 2017 Apr 1, In : Annals of Oncology. 28, 4, p. 777-783 7 p., mdx009.

Research output: Contribution to journalArticle

Open Access
43 Citations (Scopus)

Feasibility trial for primary stroke prevention in children with sickle cell anemia in Nigeria (SPIN trial)

Galadanci, N. A., Umar Abdullahi, S., Vance, L. D., Musa Tabari, A., Ali, S., Belonwu, R., Salihu, A., Amal Galadanci, A., Wudil Jibir, B., Bello-Manga, H., Neville, K., Kirkham, F. J., Shyr, Y., Phillips, S., Covert, B. V., Kassim, A. A., Jordan, L. C., Aliyu, M. H. & DeBaun, M. R., 2017 Aug, In : American Journal of Hematology. 92, 8, p. 780-788 9 p.

Research output: Contribution to journalArticle

Open Access
19 Citations (Scopus)

Functional data classification using covariate-adjusted subspace projection

Li, P. L., Chiou, J. M. & Shyr, Y., 2017 Nov, In : Computational Statistics and Data Analysis. 115, p. 21-34 14 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance

Giltnane, J. M., Hutchinson, K. E., Stricker, T. P., Formisano, L., Young, C. D., Estrada, M. V., Nixon, M. J., Du, L., Sanchez, V., Ericsson, P. G., Kuba, M. G., Sanders, M. E., Mu, X. J., Van Allen, E. M., Wagle, N., Mayer, I. A., Abramson, V., Gómez, H., Rizzo, M., Toy, W. & 15 others, Chandarlapaty, S., Mayer, E. L., Christiansen, J., Murphy, D., Fitzgerald, K., Wang, K., Ross, J. S., Miller, V. A., Stephens, P. J., Yelensky, R., Garraway, L., Shyr, Y., Meszoely, I., Balko, J. M. & Arteaga, C. L., 2017 Aug 9, In : Science Translational Medicine. 9, 402, aai7993.

Research output: Contribution to journalArticle

Open Access
29 Citations (Scopus)

Identification of active miRNA promoters from nuclear run-on RNA sequencing

Liu, Q., Wang, J., Zhao, Y., Li, C. I., Stengel, K. R., Acharya, P., Johnston, G., Hiebert, S. W. & Shyr, Y., 2017 Jul 1, In : Nucleic acids research. 45, 13, e121.

Research output: Contribution to journalArticle

9 Citations (Scopus)

IGFBP3 modulates lung tumorigenesis and cell growth through IGF1 signaling

Wang, Y. A., Sun, Y., Palmer, J., Solomides, C., Huang, L. C., Shyr, Y., Dicker, A. P. & Lu, B., 2017 Jul, In : Molecular Cancer Research. 15, 7, p. 896-904 9 p.

Research output: Contribution to journalArticle

Open Access
14 Citations (Scopus)

Implementing a standard-of-care clinic for stroke prevention in children with sickle cell disease in Nigeria: A feasible strategy outside a clinical trial setting

Galadanci, N. A., Abdullahi, S. U., Vance, L. D., Tabari, M. A., Abubakar, S., Belonwu, R., Salihu, A., Galadanci, A. A., Jibir, B. W., Gambo, S., Suwaid, S., Bello-Manga, H., Neville, K., Kirkham, F., Shyr, Y., Phillips, S., Covert, B. V., Kassim, A. A., Trevathan, E., Jordan, L. C. & 2 others, Aliyu, M. H. & DeBaun, M. R., 2017 Dec 8, In : Blood Advances. 1, p. 23-25 3 p.

Research output: Contribution to journalShort survey

Open Access

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis

Guo, Y., Dai, Y., Yu, H., Zhao, S., Samuels, D. C. & Shyr, Y., 2017 Mar 1, In : Genomics. 109, 2, p. 83-90 8 p.

Research output: Contribution to journalArticle

Open Access
24 Citations (Scopus)

Institute of Medicine Measures of Social and Behavioral Determinants of Health: A Feasibility Study

Giuse, N. B., Koonce, T. Y., Kusnoor, S. V., Prather, A. A., Gottlieb, L. M., Huang, L. C., Phillips, S. E., Shyr, Y., Adler, N. E. & Stead, W. W., 2017 Feb 1, In : American Journal of Preventive Medicine. 52, 2, p. 199-206 8 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Integrated expression analysis identifies transcription networks in mouse and human gastric neoplasia

Chen, Z., Soutto, M., Rahman, B., Fazili, M. W., Peng, D. F., Blanca Piazuelo, M., Chen, H., Kay Washington, M., Shyr, Y. & El-Rifai, W., 2017 Jul, In : Genes Chromosomes and Cancer. 56, 7, p. 535-547 13 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Integrated molecular analysis reveals complex interactions between genomic and epigenomic alterations in esophageal adenocarcinomas

Peng, D., Guo, Y., Chen, H., Zhao, S., Washington, K., Hu, T., Shyr, Y. & El-Rifai, W., 2017 Jan 19, In : Scientific reports. 7, 40729.

Research output: Contribution to journalArticle

Open Access
8 Citations (Scopus)

Multi-perspective quality control of Illumina RNA sequencing data analysis

Sheng, Q., Vickers, K., Zhao, S., Wang, J., Samuels, D. C., Koues, O., Shyr, Y. & Guo, Y., 2017 Jan 1, In : Briefings in functional genomics. 16, 4, p. 194-204 11 p.

Research output: Contribution to journalArticle

Open Access
16 Citations (Scopus)

Multisite external validation of a risk prediction model for the diagnosis of blood stream infections in febrile pediatric oncology patients without severe neutropenia

Esbenshade, A. J., Zhao, Z., Aftandilian, C., Saab, R., Wattier, R. L., Beauchemin, M., Miller, T. P., Wilkes, J. J., Kelly, M. J., Fernbach, A., Jeng, M., Schwartz, C. L., Dvorak, C. C., Shyr, Y., Moons, K. G. M., Sulis, M. L. & Friedman, D. L., 2017 Oct 1, In : Cancer. 123, 19, p. 3781-3790 10 p.

Research output: Contribution to journalArticle

Open Access
4 Citations (Scopus)

Non-Invasive Glutamine PET Reflects Pharmacological Inhibition of BRAFV600E In Vivo

Schulte, M. L., Hight, M. R., Ayers, G. D., Liu, Q., Shyr, Y., Washington, M. K. & Manning, H. C., 2017 Jun 1, In : Molecular Imaging and Biology. 19, 3, p. 421-428 8 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Power and sample size calculations for high-throughput sequencing-based experiments

Li, C-I., Samuels, D. C., Zhao, Y. Y., Shyr, Y. & Guo, Y., 2017 May 30, In : Briefings in bioinformatics. 19, 6, p. 1247-1255 9 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Sample size calculation for differential expression analysis of RNA-seq data

Hoskins, S. P., Shyr, D. & Shyr, Y., 2017 Oct 3, Frontiers of Biostatistical Methods and Applications in Clinical Oncology. Springer Singapore, p. 359-379 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Shanghai score: A prognostic and adjuvant treatment-evaluating system constructed for Chinese patients with hepatocellular carcinoma after curative resection

Sun, H. C., Xie, L., Yang, X. R., Li, W., Yu, J., Zhu, X. D., Xia, Y., Zhang, T., Xu, Y., Hu, B., Du, L. P., Zeng, L. Y., Ouyang, J., Zhang, W., Song, T. Q., Li, Q., Shi, Y. H., Zhou, J., Qiu, S. J., Liu, Q. & 5 others, Li, Y. X., Tang, Z. Y., Shyr, Y., Shen, F. & Fan, J., 2017 Nov 20, In : Chinese Medical Journal. 130, 22, p. 2650-2660 11 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Shed urinary ALCAM is an independent prognostic biomarker of three-year overall survival after cystectomy in patients with bladder cancer

Egloff, S. A. A., Du, L., Loomans, H. A., Starchenko, A., Su, P. F., Ketova, T., Knoll, P. B., Wang, J., Haddad, A. Q., Fadare, O., Cates, J. M., Lotan, Y., Shyr, Y., Clark, P. E. & Zijlstra, A., 2017 Jan 1, In : Oncotarget. 8, 1, p. 722-741 20 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

StrandScript: Evaluation of Illumina genotyping array design and strand correction

Wang, J., Samuels, D. C., Shyr, Y. & Guo, Y., 2017 Aug 1, In : Bioinformatics. 33, 15, p. 2399-2401 3 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data

Guo, Y., Zhao, S., Sheng, Q., Samuels, D. C. & Shyr, Y., 2017 Oct 3, In : BMC genomics. 18, 690.

Research output: Contribution to journalArticle

Open Access
8 Citations (Scopus)

The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies

Zhang, P., Lehmann, B. D., Shyr, Y. & Guo, Y., 2017 Jan 1, In : International Journal of Genomics. 2017, 1926304.

Research output: Contribution to journalReview article

Open Access
29 Citations (Scopus)