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  • Yu Shyr
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
3 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
1 Citation (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

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
3 Citations (Scopus)

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
2016

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)

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)

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
51 Citations (Scopus)
2019

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

1 Citation (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 Jan 1, In : Molecular Cancer Research. 17, 9, p. 1842-1853 12 p.

Research output: Contribution to journalArticle

3 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

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

6 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)
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

2 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)
2016

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)
2018

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

7 Citations (Scopus)
2017

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
17 Citations (Scopus)
2018

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

60 Citations (Scopus)
2017

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)

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
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

9 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
31 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

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
5 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
9 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 Jan 1, (Accepted/In press) In : Journal of Cancer Education.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2020

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

1 Citation (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 Jan 1, (Accepted/In press) In : Oncologist.

Research output: Contribution to journalArticle

Open Access
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

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

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
30 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)
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

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

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)

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

8 Citations (Scopus)
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)
2017

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)

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)
2018

Interplay between miRNAs and host genes and their role in cancer

Liu, B., Shyr, Y., Cai, J. & Liu, Q., 2018 Jan 1, In : Briefings in functional genomics. 18, 4, p. 255-266 12 p.

Research output: Contribution to journalArticle

Open Access
8 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)
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)

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)
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
7 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

5 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
24 Citations (Scopus)
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)