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  • Yu Shyr
Article

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, In : Briefings in functional genomics. 16, 4, p. 194-204 11 p.

Research output: Contribution to journalArticle

Open Access
23 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
5 Citations (Scopus)

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

Wang, J., Zhao, Y., Zhou, X., Hiebert, S. W., Liu, Q. & Shyr, Y., 2018 Aug 23, In : BMC genomics. 19, 1, 633.

Research output: Contribution to journalArticle

Open Access
8 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)

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
54 Citations (Scopus)

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)

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
51 Citations (Scopus)

Palliative Care Referrals for Advanced Non–small-cell Lung Cancer (NSCLC): Patient and Provider Attitudes and Practices

Feld, E., Singhi, E. K., Phillips, S., Huang, L. C., Shyr, Y. & Horn, L., 2019 May, In : Clinical Lung Cancer. 20, 3, p. e291-e298

Research output: Contribution to journalArticle

2 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 Jul, In : PloS one. 11, 7, e0160160.

Research output: Contribution to journalArticle

Open Access
12 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

12 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

15 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

2 Citations (Scopus)

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

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

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
12 Citations (Scopus)

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
310 Citations (Scopus)

RnaSeqSampleSize: Real data based sample size estimation for RNA sequencing

Zhao, S., Li, C. I., Guo, Y., Sheng, Q. & Shyr, Y., 2018 May 30, In : BMC Bioinformatics. 19, 1, 191.

Research output: Contribution to journalArticle

11 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
14 Citations (Scopus)
2 Citations (Scopus)

ScRNABatchQC: Multi-samples quality control for single cell RNA-seq data

Liu, Q., Sheng, Q., Ping, J., Ramirez, M. A., Lau, K. S., Coffey, R. J. & Shyr, Y., 2019 Dec 15, In : Bioinformatics. 35, 24, p. 5306-5308 3 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

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

7 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)

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
2 Citations (Scopus)

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

7 Citations (Scopus)

Systems Biology Analyses Show Hyperactivation of Transforming Growth Factor-β and JNK Signaling Pathways in Esophageal Cancer

Blum, A. E., Venkitachalam, S., Ravillah, D., Chelluboyina, A. K., Kieber-Emmons, A. M., Ravi, L., Kresak, A., Chandar, A. K., Markowitz, S. D., Canto, M. I., Wang, J. S., Shaheen, N. J., Guo, Y., Shyr, Y., Willis, J. E., Chak, A., Varadan, V. & Guda, K., 2019 May, In : Gastroenterology. 156, 6, p. 1761-1774 14 p.

Research output: Contribution to journalArticle

8 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
205 Citations (Scopus)

Targeting MYCN-expressing triple-negative breast cancer with BET and MEK inhibitors

Schafer, J. M., Lehmann, B. D., Gonzalez-Ericsson, P. I., Marshall, C. B., Beeler, J. S., Redman, L. N., Jin, H., Sanchez, V., Stubbs, M. C., Scherle, P., Johnson, K. N., Sheng, Q., Roland, J. T., Bauer, J. A., Shyr, Y., Chakravarthy, B., Mobley, B. C., Hiebert, S. W., Balko, J. M., Sanders, M. E. & 2 others, Liu, P. C. C. & Pietenpol, J. A., 2020 Mar 11, In : Science translational medicine. 12, 534

Research output: Contribution to journalArticle

2 Citations (Scopus)

TBCRC 032 IB/II Multicenter Study: Molecular Insights to AR Antagonist and PI3K Inhibitor Efficacy in Patients with AR+ Metastatic Triple-Negative Breast Cancer

Translational Breast Cancer Research Consortium, 2020 May 1, In : Clinical Cancer Research. 26, 9, p. 2111-2123 13 p.

Research output: Contribution to journalArticle

4 Citations (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
10 Citations (Scopus)

The impact of smoking and tp53 mutations in lung adenocarcinoma patients with targetable mutations—the lung cancer mutation consortium (LCMC2)

Aisner, D. L., Sholl, L. M., Berry, L. D., Rossi, M. R., Chen, H., Fujimoto, J., Moreira, A. L., Ramalingam, S. S., Villaruz, L. C., Otterson, G. A., Haura, E., Politi, K., Glisson, B., Cetnar, J., Garon, E. B., Schiller, J., Waqar, S. N., Sequist, L. V., Brahmer, J., Shyr, Y. & 7 others, Kugler, K., Wistuba, I. I., Johnson, B. E., Minna, J. D., Kris, M. G., Bunn, P. A. & Kwiatkowski, D. J., 2018 Mar 1, In : Clinical Cancer Research. 24, 5, p. 1038-1047 10 p.

Research output: Contribution to journalArticle

65 Citations (Scopus)

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

6 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

20 Citations (Scopus)
Chapter

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

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

Comment/debate

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, p. 7409598 1 p.

Research output: Contribution to journalComment/debate

Open Access

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

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

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

Editorial

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)

What Constitutes a Valid Surrogate End Point in Cancer Clinical Trials?

Shyr, Y. & Shyr, D., 2020 Sep, In : JAMA Oncology. 6, 9, p. 1334-1335 2 p.

Research output: Contribution to journalEditorial

Review article

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
4 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, In : International Journal of Genomics. 2017, 1926304.

Research output: Contribution to journalReview article

Open Access
31 Citations (Scopus)
Short survey

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