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  • Yu Shyr
2018

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)
2020

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)

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
2 Citations (Scopus)
2017

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

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
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
6 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)
2016

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
69 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)

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)
2018

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

2017

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

10 Citations (Scopus)
2020

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

2016

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
160 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
53 Citations (Scopus)
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
6 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

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

2018

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)
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
8 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)
2016

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)
2018

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
29 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)
2017

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
27 Citations (Scopus)
2018

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
9 Citations (Scopus)
2019

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

7 Citations (Scopus)
2016

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
200 Citations (Scopus)
2019

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)
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
6 Citations (Scopus)
2016

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
294 Citations (Scopus)
2018

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)
2019

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)

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)

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)
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)

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)
3 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)