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  • Yu Shyr
2018

Design and conduct of clinical trials for breast cancer

Klimberg, V. S., Shyr, Y. & Wells, T., 2018 Jan 1, The Breast: Comprehensive Management of Benign and Malignant Diseases. Elsevier Inc., p. 362-376.e1

Research output: Chapter in Book/Report/Conference proceedingChapter

2017

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

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
2019

Income, costs, and health care utilization may influence surgical choice in early stage breast cancer

Sweeting, R. S., Du, L., Shyr, Y. & Hooks, M. A., 2019 Mar 1, In : Breast Journal. 25, 2, p. 334-337 4 p.

Research output: Contribution to journalComment/debate

2016

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)
2017

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

2016

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

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)

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)
2019

Erratum for the research article: Genomic proling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance (Science Translational Medicine DOI: 10.1126/scitranslmed.aai7993)

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., Gόmez, 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., 2019 Feb 13, In : Science translational medicine. 11, 479, eaaw7620.

Research output: Contribution to journalComment/debate

2017

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)

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, In : Oncotarget. 8, 1, p. 722-741 20 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)
2016

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)
2017

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)

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)
2020

Outcomes of acute cardiovascular events in rheumatoid arthritis and systemic lupus erythematosus: A population-based study

Lai, C. H., Lai, C. H., Lai, C. H., Hsieh, C. Y., Barnado, A., Huang, L. C., Huang, L. C., Chen, S. C., Chen, S. C., Tsai, L. M., Shyr, Y., Shyr, Y. & Li, C. Y., 2020 Jun 1, In : Rheumatology (United Kingdom). 59, 6, p. 1355-1363 9 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2017

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)

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)
2018

Treatment options in idiopathic subglottic stenosis: Protocol for a prospective international multicentre pragmatic trial

Gelbard, A., Shyr, Y., Berry, L., Hillel, A. T., Ekbom, D. C., Edell, E. S., Kasperbauer, J. L., Lott, D. G., Donovan, D. T., Garrett, C. G., Sandhu, G., Daniero, J. J., Netterville, J. L., Schindler, J. S., Smith, M. E., Bryson, P. C., Lorenz, R. R. & Francis, D. O., 2018 Apr 1, In : BMJ open. 8, 4, e022243.

Research output: Contribution to journalArticle

4 Citations (Scopus)
2019

Identification of targetable recurrent MAP3K8 rearrangements in melanomas lacking known driver mutations

Lehmann, B. D., Shaver, T. M., Johnson, D. B., Li, Z., Gonzalez-Ericsson, P. I., Sánchez, V., Shyr, Y., Sanders, M. E. & Pietenpol, J. A., 2019 Jan 1, In : Molecular Cancer Research. 17, 9, p. 1842-1853 12 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Establishing and Evaluating an ASCO Learning Cohort: a Longitudinal Project Assessing the Learning Needs and Behaviors of Oncology Professionals

Manochakian, R., George, T. J., Wood, M., Polansky, M., Baer, A., Grupe, A., Shyr, Y., Wang, C. & Horn, L., 2019, (Accepted/In press) In : Journal of Cancer Education.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2017

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)

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)
2019

HACER: An atlas of human active enhancers to interpret regulatory variants

Wang, J., Dai, X., Berry, L. D., Cogan, J. D., Liu, Q. & Shyr, Y., 2019 Jan 8, In : Nucleic acids research. 47, D1, p. D106-D112

Research output: Contribution to journalArticle

Open Access
6 Citations (Scopus)
2018

Strategies for processing and quality control of Illumina genotyping arrays

Zhao, S., Jing, W., Samuels, D. C., Sheng, Q., Shyr, Y. & Guo, Y., 2018 Sep 28, In : Briefings in bioinformatics. 19, 5, p. 765-775 11 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

Allen, R. M., Zhao, S., Ramirez Solano, M. A., Zhu, W., Michell, D. L., Wang, Y., Shyr, Y., Sethupathy, P., Linton, M. F., Graf, G. A., Sheng, Q. & Vickers, K. C., 2018 Jan 1, In : Journal of Extracellular Vesicles. 7, 1, 1506198.

Research output: Contribution to journalArticle

Open Access
12 Citations (Scopus)

Directed solutions to address differences in access to liver transplantation

Ye, F., Sheng, Q., Feurer, I. D., Zhao, Z., Fan, R., Teng, J., Ping, J., Rega, S. A., Hanto, D. W., Shyr, Y. & Karp, S. J., 2018 Nov, In : American Journal of Transplantation. 18, 11, p. 2670-2678 9 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)
2020

Mortality of Cardiovascular Events in Patients With COPD and Preceding Hospitalization for Acute Exacerbation

Wang, M., Lin, E. P. Y., Huang, L. C., Li, C. Y., Shyr, Y. & Lai, C. H., 2020, (Accepted/In press) In : Chest.

Research output: Contribution to journalArticle

Open Access

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Human Tumor Atlas Network, 2020 Apr 16, In : Cell. 181, 2, p. 236-249 14 p.

Research output: Contribution to journalReview article

Open Access
1 Citation (Scopus)

Quantitative analysis of oncology professional learning preferences

George, T. J., Manochakian, R., Wood, M., Polansky, M., Baer, A., Grupe, A., Shyr, Y., Wang, C., Williams, J. & Horn, L., 2020 Feb 1, In : JCO Oncology Practice. 16, 2, p. E155-E165

Research output: Contribution to journalArticle

2018

Proteome analysis implicates adaptive changes in metabolism and body wall musculature of Caenorhabditis elegans Dauer Larva

Zaidi, A. K., Vukoti, K., Sheng, Q., Shyr, Y. & Miyagi, M., 2018 Jun, In : Journal of Integrated OMICS. 8, 1, p. 46-53 8 p., 237.

Research output: Contribution to journalArticle

2016

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)

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)
2017

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)
2016

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)

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)
2018

Erratum to: Feasibility trial for primary stroke prevention in children with sickle cell anemia in Nigeria (SPIN trial) (American Journal of Hematology, (2017), 92, 8, (780-788), 10.1002/ajh.24770)

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., 2018 Mar, In : American Journal of Hematology. 93, 3, p. E83

Research output: Contribution to journalComment/debate

Open Access

First-line Chemotherapy Responsiveness and Patterns of Metastatic Spread Identify Clinical Syndromes Present Within Advanced KRAS Mutant Non–Small-cell Lung Cancer With Different Prognostic Significance

Iams, W. T., Yu, H., Shyr, Y., Patil, T., Horn, L., McCoach, C., Kelly, K., Doebele, R. C. & Camidge, D. R., 2018 Nov, In : Clinical Lung Cancer. 19, 6, p. 531-543 13 p.

Research output: Contribution to journalArticle

2016

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)
2017

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)
2016

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)

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

Genomic profiling of T-cell neoplasms reveals frequent JAK1 and JAK3 mutations with clonal evasion from targeted therapies

Greenplate, A., Wang, K., Tripathi, R. M., Palma, N., Ali, S. M., Stephens, P. J., Miller, V. A., Shyr, Y., Guo, Y., Reddy, N. M., Kozhaya, L., Unutmaz, D., Chen, X., Irish, J. M. & Davé, U. P., 2017, In : JCO Precision Oncology. 1

Research output: Contribution to journalArticle

Open Access
2016

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)

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)

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)

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)
2018

Dynamics of Zebrafish Heart Regeneration Using an HPLC-ESI-MS/MS Approach

Ma, D., Tu, C., Sheng, Q., Yang, Y., Kan, Z., Guo, Y., Shyr, Y., Scott, I. C. & Lou, X., 2018 Mar 2, In : Journal of Proteome Research. 17, 3, p. 1300-1308 9 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Longitudinal Cell-Free DNA Analysis in Patients with Small Cell Lung Cancer Reveals Dynamic Insights into Treatment Efficacy and Disease Relapse

Almodovar, K., Iams, W. T., Meador, C. B., Zhao, Z., York, S., Horn, L., Yan, Y., Hernandez, J., Chen, H., Shyr, Y., Lim, L. P., Raymond, C. K. & Lovly, C. M., 2018 Jan, In : Journal of Thoracic Oncology. 13, 1, p. 112-123 12 p.

Research output: Contribution to journalArticle

Open Access
26 Citations (Scopus)

Quantitative assessment of cell population diversity in single-cell landscapes

Liu, Q., Herring, C. A., Sheng, Q., Ping, J., Simmons, A. J., Chen, B., Banerjee, A., Li, W., Gu, G., Coffey, R. J., Shyr, Y. & Lau, K. S., 2018 Oct, In : PLoS biology. 16, 10, e2006687.

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)