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  • Yu Shyr
2017

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)
2018

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
14 Citations (Scopus)

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

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)

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

6 Citations (Scopus)

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

Forecasting Construction Cost Index based on visibility graph: A network approach

Zhang, R., Ashuri, B., Shyr, Y. & Deng, Y., 2018 Mar 1, In : Physica A: Statistical Mechanics and its Applications. 493, p. 239-252 14 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Interplay between miRNAs and host genes and their role in cancer

Liu, B., Shyr, Y., Cai, J. & Liu, Q., 2018, In : Briefings in functional genomics. 18, 4, p. 255-266 12 p.

Research output: Contribution to journalArticle

Open Access
15 Citations (Scopus)

LNK deficiency promotes acute aortic dissection and rupture

Laroumanie, F., Korneva, A., Bersi, M. R., Alexander, M. R., Xiao, L., Zhong, X., Van Beusecum, J. P., Chen, Y., Saleh, M. A., McMaster, W. G., Gavulic, K. A., Dale, B. L., Zhao, S., Guo, Y., Shyr, Y., Perrien, D. S., Cox, N. J., Curci, J. A., Humphrey, J. D. & Madhur, M. S., 2018 Oct 18, In : JCI Insight. 3, 20

Research output: Contribution to journalArticle

Open Access
6 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
30 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)

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 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)

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)

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)

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)
2019

Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer

Formisano, L., Lu, Y., Servetto, A., Hanker, A. B., Jansen, V. M., Bauer, J. A., Sudhan, D. R., Guerrero-Zotano, A. L., Croessmann, S., Guo, Y., Ericsson, P. G., Lee, K. M., Nixon, M. J., Schwarz, L. J., Sanders, M. E., Dugger, T. C., Cruz, M. R., Behdad, A., Cristofanilli, M., Bardia, A. & 11 others, O’Shaughnessy, J., Nagy, R. J., Lanman, R. B., Solovieff, N., He, W., Miller, M., Su, F., Shyr, Y., Mayer, I. A., Balko, J. M. & Arteaga, C. L., 2019 Dec 1, In : Nature communications. 10, 1, 1373.

Research output: Contribution to journalArticle

Open Access
41 Citations (Scopus)

BeRBP: Binding estimation for human RNA-binding proteins

Yu, H., Wang, J., Sheng, Q., Liu, Q. & Shyr, Y., 2019 Mar 18, In : Nucleic acids research. 47, 5, e26.

Research output: Contribution to journalArticle

Open Access
9 Citations (Scopus)

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

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)

Extramedullary leukemia behaving as solid cancer: clinical, histologic, and genetic clues to chemoresistance in organ sites

Cunningham, I., Hamele-Bena, D., Guo, Y., Shiomi, T., Papp, A. C., Chakravarti, B., Yang, J., Shyr, Y. & Fisher, R. A., 2019 Nov 1, In : American Journal of Hematology. 94, 11, p. 1200-1207 8 p.

Research output: Contribution to journalArticle

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
10 Citations (Scopus)

Human PAH is characterized by a pattern of lipid-related insulin resistance

Hemnes, A. R., Luther, J. M., Rhodes, C. J., Burgess, J. P., Carlson, J., Fan, R., Fessel, J. P., Fortune, N., Gerszten, R. E., Halliday, S. J., Hekmat, R., Howard, L., Newman, J. H., Niswender, K. D., Pugh, M. E., Robbins, I. M., Sheng, Q., Shibao, C. A., Shyr, Y., Sumner, S. & 7 others, Talati, M., Wharton, J., Wilkins, M. R., Ye, F., Yu, C., West, J. & Brittain, E. L., 2019 Jan 10, In : JCI Insight. 4, 1

Research output: Contribution to journalArticle

Open Access
14 Citations (Scopus)

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, In : Molecular Cancer Research. 17, 9, p. 1842-1853 12 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

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

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)

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)

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)
2020

Bayesian Inference of Lymph Node Ratio Estimation and Survival Prognosis for Breast Cancer Patients

Teng, J., Abdygametova, A., Du, J., Ma, B., Zhou, R., Shyr, Y. & Ye, F., 2020 Feb, In : IEEE Journal of Biomedical and Health Informatics. 24, 2, p. 354-364 11 p., 8847382.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study

COVID-19 and Cancer Consortium, 2020 Jun 20, In : The Lancet. 395, 10241, p. 1907-1918 12 p.

Research output: Contribution to journalArticle

Open Access

Comparative treatment outcomes for patients with idiopathic subglottic stenosis

Gelbard, A., Anderson, C., Berry, L. D., Amin, M. R., Benninger, M. S., Blumin, J. H., Bock, J. M., Bryson, P. C., Castellanos, P. F., Chen, S. C., Clary, M. S., Cohen, S. M., Crawley, B. K., Dailey, S. H., Daniero, J. J., De Alarcon, A., Donovan, D. T., Edell, E. S., Ekbom, D. C., Fernandes-Taylor, S. & 55 others, Fink, D. S., Franco, R. A., Garrett, C. G., Guardiani, E. A., Hillel, A. T., Hoffman, H. T., Hogikyan, N. D., Howell, R. J., Huang, L. C., Hussain, L. K., Johns, M. M., Kasperbauer, J. L., Khosla, S. M., Kinnard, C., Kupfer, R. A., Langerman, A. J., Lentz, R. J., Lorenz, R. R., Lott, D. G., Lowery, A. S., Makani, S. S., Maldonado, F., Mannion, K., Matrka, L., McWhorter, A. J., Merati, A. L., Mori, M. C., Netterville, J. L., ODell, K., Ongkasuwan, J., Postma, G. N., Reder, L. S., Rohde, S. L., Richardson, B. E., Rickman, O. B., Rosen, C. A., Rutter, M. J., Sandhu, G. S., Schindler, J. S., Schneider, G. T., Shah, R. N., Sikora, A. G., Sinard, R. J., Smith, M. E., Smith, L. J., Soliman, A. M. S., Sveinsdóttir, S., Van Daele, D. J., Veivers, D., Verma, S. P., Weinberger, P. M., Weissbrod, P. A., Wootten, C. T., Shyr, Y. & Francis, D. O., 2020 Jan, In : JAMA Otolaryngology - Head and Neck Surgery. 146, 1, p. 20-29 10 p.

Research output: Contribution to journalArticle

Open Access
5 Citations (Scopus)

Immune-Related Adverse Events and Immune Checkpoint Inhibitor Efficacy in Patients with Gastrointestinal Cancer with Food and Drug Administration-Approved Indications for Immunotherapy

Das, S., Ciombor, K. K., Haraldsdottir, S., Pumpalova, Y., Sahin, I. H., Pineda, G., Shyr, Y., Lin, E. P., Hsu, C. Y., Chu, S. K., Goff, L. W., Cardin, D. B., Bilen, M. A., Fisher, G. A., Wu, C. & Berlin, J., 2020 Aug 1, In : Oncologist. 25, 8, p. 669-679 11 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Integrated Omics of Metastatic Colorectal Cancer

Li, C., Sun, Y. D., Yu, G. Y., Cui, J. R., Lou, Z., Zhang, H., Huang, Y., Bai, C. G., Deng, L. L., Liu, P., Zheng, K., Wang, Y. H., Wang, Q. Q., Li, Q. R., Wu, Q. Q., Liu, Q., Shyr, Y., Li, Y. X., Chen, L. N., Wu, J. R. & 2 others, Zhang, W. & Zeng, R., 2020, (Accepted/In press) In : Cancer Cell.

Research output: Contribution to journalArticle

Kidney Stone History and Adverse Outcomes After Percutaneous Coronary Intervention

Lai, C. H., Huang, L. C., Holby, S. N., Lai, Y. J., Su, P. F., Cheng, Y. S., Shyr, Y. & Hsi, R. S., 2020 Feb, In : Urology. 136, p. 75-81 7 p.

Research output: Contribution to journalArticle

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 Sep, In : Chest. 158, 3, p. 973-985 13 p.

Research output: Contribution to journalArticle

Open Access
2 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)

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

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 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)

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