Yu Shyr, Ph.D.

Professor

yu.shyr@vanderbilt.edu
Faculty Appointments
Director of the Center for Quantitative Sciences Professor of Biostatistics Professor of Biomedical InformaticsHarold L. Moses Chair in Cancer ResearchProfessor of Cancer BiologyProfessor of Health Policy
Education
Ph.D., Biostatistics, University of Michigan, Ann Arbor, MichiganM.S., Statistics, Michigan State University, East Lansing, MichiganB.B.A., Tamkang University, Tamsui, Taiwan
Office Address
571 Preston Research Building
Vanderbilt Center for Quantitative Sciences
2220 Pierce Ave
Nasvhille, TN 37232-6848
Research Description
Yu Shyr received his Ph.D. in biostatistics from the University of Michigan and subsequently joined the faculty at Vanderbilt University School of Medicine. He is the Harold L. Moses Chair in Cancer Research, founding director of both the Vanderbilt Center for Quantitative Sciences (CQS) and Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD), as well as professor of biostatistics, biomedical informatics, cancer biology and health policy.

Dr. Shyr is a Fellow of the American Statistical Association and FDA advisory committee voting member. He has delivered more than 200 abstracts at professional meetings and published more than 400 peer-reviewed papers in a variety of journals (h-index = 83). He is the member of the US National Academy of Medicine (IOM) Committee on Policy Issues in the Clinical Development of Biomarkers for Molecularly Targeted Therapies. He has served as a member of the US National Cancer Institute (NCI) Developmental Therapeutics Study Section, Cancer Immunopathology and Immunotherapy Study Section and the Population and Patient-oriented Training Study Section; he also has served on the epidemiology section of the U.S. Army Medical Research and Materiel Command Breast Cancer Research Program (BCRP), and Dr. Shyr is the co-course director for the AACR/ASCO Methods in Clinical Cancer Research Vail Workshop. In addition, he has presented workshops worldwide, in countries such as Belgium, Canada, Germany, China, Japan, Saudi Arabia, and Taiwan. He currently serves on 14 external advisory boards, is the associate editor of JAMA Oncology and the Journal of Thoracic Oncology, directs the biostatistics/bioinformatics cores for the NCI-funded Vanderbilt University Breast Cancer SPORE and GI Cancer SPORE, and is the principle investigator of the NCI U01 Barrett’s Esophagus Translational Research Network Coordinating Center (BETRNetCC).
Research Keywords
statistical bioinformatics, big data, high-dimensional data processing, clinical trial design, sample size estimation, next-generation sequencing
Publications
Shaver TM, Lehmann BD, Beeler JS, Li CI, Li Z, Jin H, Stricker TP, Shyr Y, Pietenpol JA. Diverse, Biologically Relevant, and Targetable Gene Rearrangements in Triple-Negative Breast Cancer and Other Malignancies. Cancer Res [print-electronic]. 2016 Aug 8/15/2016; 76(16): 4850-60. PMID: 27231203, PII: 0008-5472.CAN-16-0058, DOI: 10.1158/0008-5472.CAN-16-0058, ISSN: 1538-7445.

Blum A, Venkitachalam S, Guo Y, Kieber-Emmons AM, Ravi L, Chandar AK, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Shyr Y, Chak A, Varadan V, Guda K. RNA Sequencing Identifies Transcriptionally-Viable Gene Fusions in Esophageal Adenocarcinomas. Cancer Res [print-electronic]. 2016 Aug 8/8/2016; PMID: 27503924, PII: 0008-5472.CAN-16-0979, DOI: 10.1158/0008-5472.CAN-16-0979, ISSN: 1538-7445.

Gilchuk P, Hill TM, Guy C, McMaster SR, Boyd KL, Rabacal WA, Lu P, Shyr Y, Kohlmeier JE, Sebzda E, Green DR, Joyce S. A Distinct Lung-Interstitium-Resident Memory CD8(+) T Cell Subset Confers Enhanced Protection to Lower Respiratory Tract Infection. Cell Rep [print-electronic]. 2016 Aug 8/3/2016; PMID: 27498869, PII: S2211-1247(16)30955-X, DOI: 10.1016/j.celrep.2016.07.037, ISSN: 2211-1247.

Eilertson B, Maruri F, Blackman A, Guo Y, Herrera M, van der Heijden Y, Shyr Y, Sterling TR. A novel resistance mutation in eccC5 of the ESX-5 secretion system confers ofloxacin resistance in Mycobacterium tuberculosis. J. Antimicrob. Chemother [print-electronic]. 2016 Jun 6/3/2016; PMID: 27261264, PII: dkw168, DOI: 10.1093/jac/dkw168, ISSN: 1460-2091.

Vilgelm AE, Johnson CA, Prasad N, Yang J, Chen SC, Ayers GD, Pawlikowski JS, Raman D, Sosman JA, Kelley M, Ecsedy JA, Shyr Y, Levy SE, Richmond A. Connecting the Dots: Therapy-Induced Senescence and a Tumor-Suppressive Immune Microenvironment. J. Natl. Cancer Inst [electronic-print]. 2016 Jun; 108(6): djv406. PMID: 26719346, PMCID: PMC4849355, PII: djv406, DOI: 10.1093/jnci/djv406, ISSN: 1460-2105.

Matsushita K, Yang HC, Mysore MM, Zhong J, Shyr Y, Ma LJ, Fogo AB. Effects of combination PPAR¿ agonist and angiotensin receptor blocker on glomerulosclerosis. Lab. Invest [print-electronic]. 2016 Jun; 96(6): 602-9. PMID: 26999660, PII: labinvest201642, DOI: 10.1038/labinvest.2016.42, ISSN: 1530-0307.

Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y. Mitochondria single nucleotide variation across six blood cell types. Mitochondrion [print-electronic]. 2016 May; 28: 16-22. PMID: 26956645, PII: S1567-7249(16)30011-3, DOI: 10.1016/j.mito.2016.03.001, ISSN: 1872-8278.

Sheng Q, Zhao S, Li CI, Shyr Y, Guo Y. Practicability of detecting somatic point mutation from RNA high throughput sequencing data. Genomics [print-electronic]. 2016 May; 107(5): 163-9. PMID: 27046520, PII: S0888-7543(16)30021-0, DOI: 10.1016/j.ygeno.2016.03.006, ISSN: 1089-8646.

Marshall CB, Mays DJ, Beeler JS, Rosenbluth JM, Boyd KL, Santos Guasch GL, Shaver TM, Tang LJ, Liu Q, Shyr Y, Venters BJ, Magnuson MA, Pietenpol JA. P73 Is Required for Multiciliogenesis and Regulates the Foxj1-Associated Gene Network. Cell Rep [print-electronic]. 2016 Mar 3/15/2016; 14(10): 2289-300. PMID: 26947080, PMCID: PMC4794398, PII: S2211-1247(16)30138-3, DOI: 10.1016/j.celrep.2016.02.035, ISSN: 2211-1247.

Jordan LC, Gindville MC, Scott AO, Juttukonda MR, Strother MK, Kassim AA, Chen SC, Lu H, Pruthi S, Shyr Y, Donahue MJ. Non-invasive imaging of oxygen extraction fraction in adults with sickle cell anaemia. Brain [print-electronic]. 2016 Mar; 139(Pt 3): 738-50. PMID: 26823369, PII: awv397, DOI: 10.1093/brain/awv397, ISSN: 1460-2156.

Johnson DB, Estrada MV, Salgado R, Sanchez V, Doxie DB, Opalenik SR, Vilgelm AE, Feld E, Johnson AS, Greenplate AR, Sanders ME, Lovly CM, Frederick DT, Kelley MC, Richmond A, Irish JM, Shyr Y, Sullivan RJ, Puzanov I, Sosman JA, Balko JM. Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy. Nat Commun. 2016; 7: 10582. PMID: 26822383, PMCID: PMC4740184, PII: ncomms10582, DOI: 10.1038/ncomms10582, ISSN: 2041-1723.

Lehmann BD, Jovanovic B, Chen X, Estrada MV, Johnson KN, Shyr Y, Moses HL, Sanders ME, Pietenpol JA. Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection. PLoS ONE. 2016; 11(6): e0157368. PMID: 27310713, PMCID: PMC4911051, PII: PONE-D-16-14357, DOI: 10.1371/journal.pone.0157368, ISSN: 1932-6203.

Tu C, Li J, Shen S, Sheng Q, Shyr Y, Qu J. Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument. PLoS ONE. 2016; 11(7): e0160160. PMID: 27472422, PII: PONE-D-16-15075, DOI: 10.1371/journal.pone.0160160, ISSN: 1932-6203.

Wang J, Liu Q, Sun J, Shyr Y. Disrupted cooperation between transcription factors across diverse cancer types. BMC Genomics. 2016; 17: 560. PMID: 27496222, PMCID: PMC4975902, PII: 10.1186/s12864-016-2842-8, DOI: 10.1186/s12864-016-2842-8, ISSN: 1471-2164.

Lockney NA, Zhang M, Lu Y, Sopha SC, Washington MK, Merchant N, Zhao Z, Shyr Y, Chakravarthy AB, Xia F. Pyruvate Kinase Muscle Isoenzyme 2 (PKM2) Expression Is Associated with Overall Survival in Pancreatic Ductal Adenocarcinoma. J Gastrointest Cancer. 2015 Dec; 46(4): 390-8. PMID: 26385349, PII: 10.1007/s12029-015-9764-6, DOI: 10.1007/s12029-015-9764-6, ISSN: 1941-6636.

Tu C, Sheng Q, Li J, Ma D, Shen X, Wang X, Shyr Y, Yi Z, Qu J. Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data. J. Proteome Res [print-electronic]. 2015 Nov 11/6/2015; 14(11): 4662-73. PMID: 26390080, PMCID: PMC4859434, DOI: 10.1021/acs.jproteome.5b00536, ISSN: 1535-3907.

Erickson JJ, Lu P, Wen S, Hastings AK, Gilchuk P, Joyce S, Shyr Y, Williams JV. Acute Viral Respiratory Infection Rapidly Induces a CD8+ T Cell Exhaustion-like Phenotype. J. Immunol [print-electronic]. 2015 Nov 11/1/2015; 195(9): 4319-30. PMID: 26401005, PMCID: PMC4733528, PII: jimmunol.1403004, DOI: 10.4049/jimmunol.1403004, ISSN: 1550-6606.

Fata CR, Seeley EH, Desouki MM, Du L, Gwin K, Hanley KZ, Hecht JL, Jarboe EA, Liang SX, Parkash V, Quick CM, Zheng W, Shyr Y, Caprioli RM, Fadare O. Are clear cell carcinomas of the ovary and endometrium phenotypically identical? A proteomic analysis. Hum. Pathol [print-electronic]. 2015 Oct; 46(10): 1427-36. PMID: 26243671, PII: S0046-8177(15)00214-2, DOI: 10.1016/j.humpath.2015.06.009, ISSN: 1532-8392.

Boyd AS, Chen SC, Shyr Y. Intradermal nevi with atypical nuclei in the elderly: The senescent nevus. J. Am. Acad. Dermatol [print-electronic]. 2015 Sep; 73(3): 500-6. PMID: 26188628, PII: S0190-9622(15)01756-9, DOI: 10.1016/j.jaad.2015.06.013, ISSN: 1097-6787.

Goodings C, Smith E, Mathias E, Elliott N, Cleveland SM, Tripathi RM, Layer JH, Chen X, Guo Y, Shyr Y, Hamid R, Du Y, Davé UP. Hhex is Required at Multiple Stages of Adult Hematopoietic Stem and Progenitor Cell Differentiation. Stem Cells [print-electronic]. 2015 Aug; 33(8): 2628-41. PMID: 25968920, PMCID: PMC4641572, DOI: 10.1002/stem.2049, ISSN: 1549-4918.

Cohen DN, Lawson SK, Shaver AC, Du L, Nguyen HP, He Q, Johnson DB, Lumbang WA, Moody BR, Prescott JL, Chandra PK, Boyd AS, Zwerner JP, Robbins JB, Tyring SK, Rady PL, Chappell JD, Shyr Y, Infante JR, Sosman JA. Contribution of Beta-HPV Infection and UV Damage to Rapid-Onset Cutaneous Squamous Cell Carcinoma during BRAF-Inhibition Therapy. Clin. Cancer Res [print-electronic]. 2015 Jun 6/1/2015; 21(11): 2624-34. PMID: 25724524, PMCID: PMC4452444, PII: 1078-0432.CCR-14-2667, DOI: 10.1158/1078-0432.CCR-14-2667, ISSN: 1078-0432.

Shyr Y, Horn L, Berry L. Are We Making Progress in Lung Cancer Using Progression-Free Survival as a Surrogate End Point?. JAMA Oncol. 2015 May; 1(2): 202-3. PMID: 26181024, PII: 2196177, DOI: 10.1001/jamaoncol.2015.0407, ISSN: 2374-2445.

Lammers PE, Lu B, Horn L, Shyr Y, Keedy V. Nab-Paclitaxel in Combination With Weekly Carboplatin With Concurrent Radiotherapy in Stage III Non-Small Cell Lung Cancer. Oncologist [print-electronic]. 2015 May; 20(5): 491-2. PMID: 25845992, PMCID: PMC4425395, PII: theoncologist.2015-0030, DOI: 10.1634/theoncologist.2015-0030, ISSN: 1549-490X.

Samuelson LE, Scherer RL, VanSaun MN, Fan KH, Dozier EA, Carter KJ, Koyama T, Shyr Y, Aschner M, Stanwood GD, Bornhop DJ, Matrisian LM, McIntyre JO. New tools for the quantitative assessment of prodrug delivery and neurotoxicity. Neurotoxicology [print-electronic]. 2015 Mar; 47: 88-98. PMID: 25732874, PMCID: PMC4501381, PII: S0161-813X(15)00023-6, DOI: 10.1016/j.neuro.2015.02.005, ISSN: 1872-9711.

Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R. Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data. Mol. Cell Proteomics [print-electronic]. 2015 Feb; 14(2): 405-17. PMID: 25435543, PMCID: PMC4350035, PII: O114.041376, DOI: 10.1074/mcp.O114.041376, ISSN: 1535-9484.

Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y. Genome measures used for quality control are dependent on gene function and ancestry. Bioinformatics [print-electronic]. 2015 Feb 2/1/2015; 31(3): 318-23. PMID: 25297068, PMCID: PMC4308666, PII: btu668, DOI: 10.1093/bioinformatics/btu668, ISSN: 1367-4811.

Liu Q, Zhong X, Madison BB, Rustgi AK, Shyr Y. Assessing Computational Steps for CLIP-Seq Data Analysis. Biomed Res Int [print-electronic]. 2015; 2015: 196082. PMID: 26539468, PMCID: PMC4619761, DOI: 10.1155/2015/196082, ISSN: 2314-6141.

Hoek KL, Samir P, Howard LM, Niu X, Prasad N, Galassie A, Liu Q, Allos TM, Floyd KA, Guo Y, Shyr Y, Levy SE, Joyce S, Edwards KM, Link AJ. A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination. PLoS ONE. 2015; 10(2): e0118528. PMID: 25706537, PMCID: PMC4338067, PII: PONE-D-14-38979, DOI: 10.1371/journal.pone.0118528, ISSN: 1932-6203.

Goodings C, Tripathi R, Cleveland SM, Elliott N, Guo Y, Shyr Y, Davé UP. Enforced expression of E47 has differential effects on Lmo2-induced T-cell leukemias. Leuk. Res [print-electronic]. 2015 Jan; 39(1): 100-9. PMID: 25499232, PMCID: PMC4277943, PII: S0145-2126(14)00368-3, DOI: 10.1016/j.leukres.2014.11.016, ISSN: 1873-5835.

Kummerow KL, Du L, Penson DF, Shyr Y, Hooks MA. Nationwide trends in mastectomy for early-stage breast cancer. JAMA Surg. 2015 Jan; 150(1): 9-16. PMID: 25408966, PII: 1921808, DOI: 10.1001/jamasurg.2014.2895, ISSN: 2168-6262.

Guo Y, Zhao S, Sheng Q, Guo M, Lehmann B, Pietenpol J, Samuels DC, Shyr Y. RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library. Biomed Res Int [print-electronic]. 2015; 2015: 862130. PMID: 26543871, PMCID: PMC4620295, DOI: 10.1155/2015/862130, ISSN: 2314-6141.

Sidorova TN, Mace LC, Wells KS, Yermalitskaya LV, Su PF, Shyr Y, Atkinson JB, Fogo AB, Prinsen JK, Byrne JG, Petracek MR, Greelish JP, Hoff SJ, Ball SK, Glabe CG, Brown NJ, Barnett JV, Murray KT. Hypertension is associated with preamyloid oligomers in human atrium: a missing link in atrial pathophysiology?. J Am Heart Assoc. 2014 Dec; 3(6): e001384. PMID: 25468655, PMCID: PMC4338732, PII: jah3772, DOI: 10.1161/JAHA.114.001384, ISSN: 2047-9980.

Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J. Illumina human exome genotyping array clustering and quality control. Nat Protoc [print-electronic]. 2014 Nov; 9(11): 2643-62. PMID: 25321409, PMCID: PMC4441213, PII: nprot.2014.174, DOI: 10.1038/nprot.2014.174, ISSN: 1750-2799.

Trott DW, Thabet SR, Kirabo A, Saleh MA, Itani H, Norlander AE, Wu J, Goldstein A, Arendshorst WJ, Madhur MS, Chen W, Li CI, Shyr Y, Harrison DG. Oligoclonal CD8+ T cells play a critical role in the development of hypertension. Hypertension [print-electronic]. 2014 Nov; 64(5): 1108-15. PMID: 25259750, PMCID: PMC4191997, PII: HYPERTENSIONAHA.114.04147, DOI: 10.1161/HYPERTENSIONAHA.114.04147, ISSN: 1524-4563.

Dexheimer JW, Abramo TJ, Arnold DH, Johnson K, Shyr Y, Ye F, Fan KH, Patel N, Aronsky D. Implementation and evaluation of an integrated computerized asthma management system in a pediatric emergency department: a randomized clinical trial. Int J Med Inform [print-electronic]. 2014 Nov; 83(11): 805-13. PMID: 25174321, PII: S1386-5056(14)00143-9, DOI: 10.1016/j.ijmedinf.2014.07.008, ISSN: 1872-8243.

Boyd AS, Su PF, Shyr Y, Tang YW. Squamous cell carcinomas in situ arising in seborrheic keratoses: an association with concomitant immunosuppression?. Int. J. Dermatol [print-electronic]. 2014 Nov; 53(11): 1346-50. PMID: 24898685, DOI: 10.1111/ijd.12086, ISSN: 1365-4632.

Donahue MJ, Dethrage LM, Faraco CC, Jordan LC, Clemmons P, Singer R, Mocco J, Shyr Y, Desai A, O'Duffy A, Riebau D, Hermann L, Connors J, Kirshner H, Strother MK. Routine clinical evaluation of cerebrovascular reserve capacity using carbogen in patients with intracranial stenosis. Stroke [print-electronic]. 2014 Aug; 45(8): 2335-41. PMID: 24938845, PMCID: PMC4118584, PII: STROKEAHA.114.005975, DOI: 10.1161/STROKEAHA.114.005975, ISSN: 1524-4628.

Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Davé UP. LMO2 induces T-cell leukemia with epigenetic deregulation of CD4. Exp. Hematol [print-electronic]. 2014 Jul; 42(7): 581-93.e5. PMID: 24792354, PMCID: PMC4241760, PII: S0301-472X(14)00155-6, DOI: 10.1016/j.exphem.2014.04.010, ISSN: 1873-2399.

Sidorova TN, Mace LC, Wells KS, Yermalitskaya LV, Su PF, Shyr Y, Byrne JG, Petracek MR, Greelish JP, Hoff SJ, Ball SK, Glabe CG, Brown NJ, Barnett JV, Murray KT. Quantitative Imaging of Preamyloid Oligomers, a Novel Structural Abnormality, in Human Atrial Samples. J. Histochem. Cytochem [print-electronic]. 2014 Jul; 62(7): 479-87. PMID: 24789805, PMCID: PMC4072180, PII: 0022155414535782, DOI: 10.1369/0022155414535782, ISSN: 1551-5044.

Strother MK, Anderson MD, Singer RJ, Du L, Moore RD, Shyr Y, Ladner TR, Arteaga D, Day MA, Clemmons PF, Donahue MJ. Cerebrovascular collaterals correlate with disease severity in adult North American patients with Moyamoya disease. AJNR Am J Neuroradiol [print-electronic]. 2014 Jul; 35(7): 1318-24. PMID: 24651814, PMCID: PMC4367488, PII: ajnr.A3883, DOI: 10.3174/ajnr.A3883, ISSN: 1936-959X.

Guo Y, Zhao S, Su PF, Li CI, Ye F, Flynn CR, Shyr Y. Statistical strategies for microRNAseq batch effect reduction. Transl Cancer Res. 2014 Jun 6/1/2014; 3(3): 260-5. PMID: 25258704, PMCID: PMC4171948, DOI: 10.3978/j.issn.2218-676X.2014.06.05, ISSN: 2218-676X.

Kaufman JM, Amann JM, Park K, Arasada RR, Li H, Shyr Y, Carbone DP. LKB1 Loss induces characteristic patterns of gene expression in human tumors associated with NRF2 activation and attenuation of PI3K-AKT. J Thorac Oncol. 2014 Jun; 9(6): 794-804. PMID: 24828662, PMCID: PMC4026179, PII: S1556-0864(15)30302-6, DOI: 10.1097/JTO.0000000000000173, ISSN: 1556-1380.

Abrams JA, Appelman HD, Beer DG, Berry LD, Chak A, Falk GW, Fitzgerald RC, Ginsberg GG, Grady WM, Joshi BP, Lynch JP, Markowitz S, Richmond ES, Rustgi AK, Seibel EJ, Shaheen NJ, Shyr Y, Umar A, Wang KK, Wang TC, Wang TD, Yassin R. Barrett's Esophagus Translational Research Network (BETRNet): the pivotal role of multi-institutional collaboration in esophageal adenocarcinoma research [editorial]. Gastroenterology [print-electronic]. 2014 Jun; 146(7): 1586-90. PMID: 24768332, PMCID: PMC4224108, PII: S0016-5085(14)00540-X, DOI: 10.1053/j.gastro.2014.04.014, ISSN: 1528-0012.

Abramson VG, Cooper Lloyd M, Ballinger T, Sanders ME, Du L, Lai D, Su Z, Mayer I, Levy M, LaFrance DR, Vnencak-Jones CL, Shyr Y, Dahlman KB, Pao W, Arteaga CL. Characterization of breast cancers with PI3K mutations in an academic practice setting using SNaPshot profiling. Breast Cancer Res. Treat [print-electronic]. 2014 Jun; 145(2): 389-99. PMID: 24722917, PMCID: PMC4046906, DOI: 10.1007/s10549-014-2945-3, ISSN: 1573-7217.

Cardin DB, Goff L, Li CI, Shyr Y, Winkler C, DeVore R, Schlabach L, Holloway M, McClanahan P, Meyer K, Grigorieva J, Berlin J, Chan E. Phase II trial of sorafenib and erlotinib in advanced pancreatic cancer. Cancer Med [print-electronic]. 2014 Jun; 3(3): 572-9. PMID: 24574334, PMCID: PMC4101748, DOI: 10.1002/cam4.208, ISSN: 2045-7634.

Su PF, Li CI, Shyr Y. Sample size determination for paired right-censored data based on the difference of Kaplan-Meier estimates. Comput Stat Data Anal. 2014 Jun 6/1/2014; 74: 39-51. PMID: 24567661, PMCID: PMC3931470, DOI: 10.1016/j.csda.2013.12.006, ISSN: 0167-9473.

Lu X, An H, Jin R, Zou M, Guo Y, Su PF, Liu D, Shyr Y, Yarbrough WG. PPM1A is a RelA phosphatase with tumor suppressor-like activity. Oncogene [print-electronic]. 2014 May 5/29/2014; 33(22): 2918-27. PMID: 23812431, PMCID: PMC3897569, PII: onc2013246, DOI: 10.1038/onc.2013.246, ISSN: 1476-5594.

Kris MG, Johnson BE, Berry LD, Kwiatkowski DJ, Iafrate AJ, Wistuba II, Varella-Garcia M, Franklin WA, Aronson SL, Su PF, Shyr Y, Camidge DR, Sequist LV, Glisson BS, Khuri FR, Garon EB, Pao W, Rudin C, Schiller J, Haura EB, Socinski M, Shirai K, Chen H, Giaccone G, Ladanyi M, Kugler K, Minna JD, Bunn PA. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. JAMA. 2014 May 5/21/2014; 311(19): 1998-2006. PMID: 24846037, PMCID: PMC4163053, PII: 1872815, DOI: 10.1001/jama.2014.3741, ISSN: 1538-3598.

Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y. Multi-perspective quality control of Illumina exome sequencing data using QC3. Genomics [print-electronic]. 2014 May; 103(5-6): 323-8. PMID: 24703969, PII: S0888-7543(14)00035-4, DOI: 10.1016/j.ygeno.2014.03.006, ISSN: 1089-8646.

Mikhitarian K, Pollen M, Zhao Z, Shyr Y, Merchant NB, Parikh A, Revetta F, Washington MK, Vnencak-Jones C, Shi C. Epidermal growth factor receptor signaling pathway is frequently altered in ampullary carcinoma at protein and genetic levels. Mod. Pathol [print-electronic]. 2014 May; 27(5): 665-74. PMID: 24186143, PMCID: PMC4007414, PII: modpathol2013185, DOI: 10.1038/modpathol.2013.185, ISSN: 1530-0285.

Weeke P, Mosley JD, Hanna D, Delaney JT, Shaffer C, Wells QS, Van Driest S, Karnes JH, Ingram C, Guo Y, Shyr Y, Norris K, Kannankeril PJ, Ramirez AH, Smith JD, Mardis ER, Nickerson D, George AL, Roden DM. Exome sequencing implicates an increased burden of rare potassium channel variants in the risk of drug-induced long QT interval syndrome. J. Am. Coll. Cardiol [print-electronic]. 2014 Apr 4/15/2014; 63(14): 1430-7. PMID: 24561134, PMCID: PMC4018823, PII: S0735-1097(14)00446-X, DOI: 10.1016/j.jacc.2014.01.031, ISSN: 1558-3597.

Shen EZ, Song CQ, Lin Y, Zhang WH, Su PF, Liu WY, Zhang P, Xu J, Lin N, Zhan C, Wang X, Shyr Y, Cheng H, Dong MQ. Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans. Nature [print-electronic]. 2014 Apr 4/3/2014; 508(7494): 128-32. PMID: 24522532, PII: nature13012, DOI: 10.1038/nature13012, ISSN: 1476-4687.

Lammers PE, Shyr Y, Li CI, Hutchison AS, Sandler A, Carbone DP, Johnson DH, Keedy VL, Horn L. Phase II study of bendamustine in relapsed chemotherapy sensitive or resistant small-cell lung cancer. J Thorac Oncol. 2014 Apr; 9(4): 559-62. PMID: 24736081, PMCID: PMC3990869, PII: S1556-0864(15)30255-0, DOI: 10.1097/JTO.0000000000000079, ISSN: 1556-1380.

Vlacich G, Spratt DE, Diaz R, Phillips JG, Crass J, Li CI, Shyr Y, Cmelak AJ. Dose to the inferior pharyngeal constrictor predicts prolonged gastrostomy tube dependence with concurrent intensity-modulated radiation therapy and chemotherapy for locally-advanced head and neck cancer. Radiother Oncol [print-electronic]. 2014 Mar; 110(3): 435-40. PMID: 24440043, PII: S0167-8140(13)00649-X, DOI: 10.1016/j.radonc.2013.12.007, ISSN: 1879-0887.

Hansen AG, Arnold SA, Jiang M, Palmer TD, Ketova T, Merkel A, Pickup M, Samaras S, Shyr Y, Moses HL, Hayward SW, Sterling JA, Zijlstra A. ALCAM/CD166 is a TGF-ß-responsive marker and functional regulator of prostate cancer metastasis to bone. Cancer Res [print-electronic]. 2014 Mar 3/1/2014; 74(5): 1404-15. PMID: 24385212, PMCID: PMC4149913, PII: 0008-5472.CAN-13-1296, DOI: 10.1158/0008-5472.CAN-13-1296, ISSN: 1538-7445.

Liu Q, Su PF, Zhao S, Shyr Y. Transcriptome-wide signatures of tumor stage in kidney renal clear cell carcinoma: connecting copy number variation, methylation and transcription factor activity. Genome Med. 2014; 6(12): 117. PMID: 25648588, PMCID: PMC4293006, PII: 117, DOI: 10.1186/s13073-014-0117-z, ISSN: 1756-994X.

Guo Y, Zhao S, Li CI, Sheng Q, Shyr Y. RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment. Cancer Inform. 2014; 13(Suppl 6): 1-5. PMID: 25374457, PMCID: PMC4213196, PII: cin-suppl.6-2014-001, DOI: 10.4137/CIN.S17688, ISSN: 1176-9351.

Guo Y, Zhao S, Lehmann BD, Sheng Q, Shaver TM, Stricker TP, Pietenpol JA, Shyr Y. Detection of internal exon deletion with exon Del. BMC Bioinformatics. 2014; 15: 332. PMID: 25322818, PMCID: PMC4288651, PII: 1471-2105-15-332, DOI: 10.1186/1471-2105-15-332, ISSN: 1471-2105.

Sheng Q, Shyr Y, Chen X. DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. BMC Bioinformatics. 2014; 15: 323. PMID: 25267467, PMCID: PMC4261523, PII: 1471-2105-15-323, DOI: 10.1186/1471-2105-15-323, ISSN: 1471-2105.

Zhao S, Guo Y, Sheng Q, Shyr Y. Advanced heat map and clustering analysis using heatmap3. Biomed Res Int [print-electronic]. 2014; 2014: 986048. PMID: 25143956, PMCID: PMC4124803, DOI: 10.1155/2014/986048, ISSN: 2314-6141.

Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y. MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control. Biomed Res Int [print-electronic]. 2014; 2014: 248090. PMID: 24977143, PMCID: PMC4058234, DOI: 10.1155/2014/248090, ISSN: 2314-6141.

Guo Y, Bosompem A, Zhong X, Clark T, Shyr Y, Kim AS. A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods. Int J Comput Biol Drug Des [print-electronic]. 2014; 7(2-3): 102-12. PMID: 24878723, PII: IJCBDD.2014.061642, DOI: 10.1504/IJCBDD.2014.061642, ISSN: 1756-0756.

Guo Y, Li CI, Sheng Q, Winther JF, Cai Q, Boice JD, Shyr Y. Very low-level heteroplasmy mtDNA variations are inherited in humans. J Genet Genomics [print-electronic]. 2013 Dec 12/20/2013; 40(12): 607-15. PMID: 24377867, PMCID: PMC4149221, PII: S1673-8527(13)00196-3, DOI: 10.1016/j.jgg.2013.10.003, ISSN: 1673-8527.

Han D, Zager JS, Shyr Y, Chen H, Berry LD, Iyengar S, Djulbegovic M, Weber JL, Marzban SS, Sondak VK, Messina JL, Vetto JT, White RL, Pockaj B, Mozzillo N, Charney KJ, Avisar E, Krouse R, Kashani-Sabet M, Leong SP. Clinicopathologic predictors of sentinel lymph node metastasis in thin melanoma. J. Clin. Oncol [print-electronic]. 2013 Dec 12/10/2013; 31(35): 4387-93. PMID: 24190111, PII: JCO.2013.50.1114, DOI: 10.1200/JCO.2013.50.1114, ISSN: 1527-7755.

Katsha A, Soutto M, Sehdev V, Peng D, Washington MK, Piazuelo MB, Tantawy MN, Manning HC, Lu P, Shyr Y, Ecsedy J, Belkhiri A, El-Rifai W. Aurora kinase A promotes inflammation and tumorigenesis in mice and human gastric neoplasia. Gastroenterology [print-electronic]. 2013 Dec; 145(6): 1312-22.e1. PMID: 23993973, PMCID: PMC3840093, PII: S0016-5085(13)01270-5, DOI: 10.1053/j.gastro.2013.08.050, ISSN: 1528-0012.

Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet [print-electronic]. 2013 Oct; 29(10): 593-9. PMID: 23972387, PMCID: PMC3926691, PII: S0168-9525(13)00127-3, DOI: 10.1016/j.tig.2013.07.006, ISSN: 0168-9525.

Wang T, Wentz SC, Ausborn NL, Washington MK, Merchant N, Zhao Z, Shyr Y, Chakravarthy AB, Xia F. Pattern of breast cancer susceptibility gene 1 expression is a potential prognostic biomarker in resectable pancreatic ductal adenocarcinoma. Pancreas. 2013 Aug; 42(6): 977-82. PMID: 23851432, PMCID: PMC4026161, PII: 00006676-201308000-00013, DOI: 10.1097/MPA.0b013e318287885c, ISSN: 1536-4828.

Liu Q, Halvey PJ, Shyr Y, Slebos RJ, Liebler DC, Zhang B. Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation. Mol. Cell Proteomics [print-electronic]. 2013 Jul; 12(7): 1900-11. PMID: 23550052, PMCID: PMC3708174, PII: M112.025783, DOI: 10.1074/mcp.M112.025783, ISSN: 1535-9484.

Hansen AG, Freeman TJ, Arnold SA, Starchenko A, Jones-Paris CR, Gilger MA, Washington MK, Fan KH, Shyr Y, Beauchamp RD, Zijlstra A. Elevated ALCAM shedding in colorectal cancer correlates with poor patient outcome. Cancer Res [print-electronic]. 2013 May 5/15/2013; 73(10): 2955-64. PMID: 23539446, PMCID: PMC3660148, PII: 0008-5472.CAN-12-2052, DOI: 10.1158/0008-5472.CAN-12-2052, ISSN: 1538-7445.

Guo Y, Li J, Li CI, Shyr Y, Samuels DC. MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics [print-electronic]. 2013 May 5/1/2013; 29(9): 1210-1. PMID: 23471301, PMCID: PMC4492415, PII: btt118, DOI: 10.1093/bioinformatics/btt118, ISSN: 1367-4811.

Li CI, Su PF, Shyr Y. Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. BMC Bioinformatics. 2013; 14: 357. PMID: 24314022, PMCID: PMC3924199, PII: 1471-2105-14-357, DOI: 10.1186/1471-2105-14-357, ISSN: 1471-2105.

Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y. Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. Biomed Res Int [print-electronic]. 2013; 2013: 915636. PMID: 24303503, PMCID: PMC3835197, DOI: 10.1155/2013/915636, ISSN: 2314-6141.

Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS ONE. 2013; 8(8): e71462. PMID: 23977046, PMCID: PMC3748065, PII: PONE-D-13-05180, DOI: 10.1371/journal.pone.0071462, ISSN: 1932-6203.

Al-Greene NT, Means AL, Lu P, Jiang A, Schmidt CR, Chakravarthy AB, Merchant NB, Washington MK, Zhang B, Shyr Y, Deane NG, Beauchamp RD. Four jointed box 1 promotes angiogenesis and is associated with poor patient survival in colorectal carcinoma. PLoS ONE [electronic-print]. 2013; 8(7): e69660. PMID: 23922772, PMCID: PMC3726759, PII: PONE-D-13-05038, DOI: 10.1371/journal.pone.0069660, ISSN: 1932-6203.

Guo Y, Samuels DC, Li J, Clark T, Li CI, Shyr Y. Evaluation of allele frequency estimation using pooled sequencing data simulation. ScientificWorldJournal [print-electronic]. 2013; 2013: 895496. PMID: 23476151, PMCID: PMC3582166, DOI: 10.1155/2013/895496, ISSN: 1537-744X.

Qiu Q, Lu P, Xiang Y, Shyr Y, Chen X, Lehmann BD, Viox DJ, George AL, Yi Y. A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer. PLoS ONE [print-electronic]. 2013; 8(1): e54979. PMID: 23383020, PMCID: PMC3558433, PII: PONE-D-12-15536, DOI: 10.1371/journal.pone.0054979, ISSN: 1932-6203.

Engelhardt BG, Sengsayadeth SM, Jagasia M, Savani BN, Kassim AA, Lu P, Shyr Y, Yoder SM, Rock MT, Crowe JE. Tissue-specific regulatory T cells: biomarker for acute graft-vs-host disease and survival. Exp. Hematol [print-electronic]. 2012 Dec; 40(12): 974-982.e1. PMID: 22885125, PMCID: PMC3611587, PII: S0301-472X(12)00343-8, DOI: 10.1016/j.exphem.2012.08.002, ISSN: 1873-2399.

Fu Z, Shrubsole MJ, Smalley WE, Wu H, Chen Z, Shyr Y, Ness RM, Zheng W. Lifestyle factors and their combined impact on the risk of colorectal polyps. Am. J. Epidemiol [print-electronic]. 2012 Nov 11/1/2012; 176(9): 766-76. PMID: 23079606, PMCID: PMC3571253, PII: kws157, DOI: 10.1093/aje/kws157, ISSN: 1476-6256.

Fu Z, Shrubsole MJ, Li G, Smalley WE, Hein DW, Chen Z, Shyr Y, Cai Q, Ness RM, Zheng W. Using gene-environment interaction analyses to clarify the role of well-done meat and heterocyclic amine exposure in the etiology of colorectal polyps. Am. J. Clin. Nutr [print-electronic]. 2012 Nov; 96(5): 1119-28. PMID: 23015320, PMCID: PMC3471199, PII: ajcn.112.040345, DOI: 10.3945/ajcn.112.040345, ISSN: 1938-3207.

Abramson RG, Su PF, Shyr Y. Quantitative metrics in clinical radiology reporting: a snapshot perspective from a single mixed academic-community practice. Magn Reson Imaging [print-electronic]. 2012 Nov; 30(9): 1357-66. PMID: 22795791, PMCID: PMC3466403, PII: S0730-725X(12)00202-0, DOI: 10.1016/j.mri.2012.04.018, ISSN: 1873-5894.

Shyr Y. Rigorous quantitative sciences integration--the foundation of high-dimensional genomic research. Clin. Exp. Metastasis [print-electronic]. 2012 Oct; 29(7): 641-3. PMID: 22798219, PMCID: PMC3485411, DOI: 10.1007/s10585-012-9508-y, ISSN: 1573-7276.

Kikuchi T, Hassanein M, Amann JM, Liu Q, Slebos RJ, Rahman SM, Kaufman JM, Zhang X, Hoeksema MD, Harris BK, Li M, Shyr Y, Gonzalez AL, Zimmerman LJ, Liebler DC, Massion PP, Carbone DP. In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers. Mol. Cell Proteomics [print-electronic]. 2012 Oct; 11(10): 916-32. PMID: 22761400, PMCID: PMC3494148, PII: M111.015370, DOI: 10.1074/mcp.M111.015370, ISSN: 1535-9484.

Hong J, Katsha A, Lu P, Shyr Y, Belkhiri A, El-Rifai W. Regulation of ERBB2 receptor by t-DARPP mediates trastuzumab resistance in human esophageal adenocarcinoma. Cancer Res [print-electronic]. 2012 Sep 9/1/2012; 72(17): 4504-14. PMID: 22745369, PMCID: PMC3432752, PII: 0008-5472.CAN-12-1119, DOI: 10.1158/0008-5472.CAN-12-1119, ISSN: 1538-7445.

Zhuang G, Song W, Amato K, Hwang Y, Lee K, Boothby M, Ye F, Guo Y, Shyr Y, Lin L, Carbone DP, Brantley-Sieders DM, Chen J. Effects of cancer-associated EPHA3 mutations on lung cancer. J. Natl. Cancer Inst [print-electronic]. 2012 Aug 8/8/2012; 104(15): 1182-97. PMID: 22829656, PMCID: PMC3611812, PII: djs297, DOI: 10.1093/jnci/djs297, ISSN: 1460-2105.

Talati M, Seeley E, Ihida-Stansbury K, Delisser H, McDonald H, Ye F, Zhang X, Shyr Y, Caprioli R, Meyrick B. Altered expression of nuclear and cytoplasmic histone H1 in pulmonary artery and pulmonary artery smooth muscle cells in patients with IPAH. Pulm Circ. 2012 Jul; 2(3): 340-51. PMID: 23130102, PMCID: PMC3487302, PII: PC-2-340, DOI: 10.4103/2045-8932.101645, ISSN: 2045-8940.

Xu BJ, An QA, Srinivasa Gowda S, Yan W, Pierce LA, Abel TW, Rush SZ, Cooper MK, Ye F, Shyr Y, Weaver KD, Thompson RC. Identification of blood protein biomarkers that aid in the clinical assessment of patients with malignant glioma. Int. J. Oncol [print-electronic]. 2012 Jun; 40(6): 1995-2003. PMID: 22307528, DOI: 10.3892/ijo.2012.1355, ISSN: 1791-2423.

Guo Y, Cai Q, Samuels DC, Ye F, Long J, Li CI, Winther JF, Tawn EJ, Stovall M, Lähteenmäki P, Malila N, Levy S, Shaffer C, Shyr Y, Shu XO, Boice JD. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Mutat. Res [print-electronic]. 2012 May 5/15/2012; 744(2): 154-60. PMID: 22387842, PMCID: PMC3354959, PII: S1383-5718(12)00060-5, DOI: 10.1016/j.mrgentox.2012.02.006, ISSN: 0027-5107.

Pecot CV, Li M, Zhang XJ, Rajanbabu R, Calitri C, Bungum A, Jett JR, Putnam JB, Callaway-Lane C, Deppen S, Grogan EL, Carbone DP, Worrell JA, Moons KG, Shyr Y, Massion PP. Added value of a serum proteomic signature in the diagnostic evaluation of lung nodules. Cancer Epidemiol. Biomarkers Prev [print-electronic]. 2012 May; 21(5): 786-92. PMID: 22374995, PMCID: PMC3660018, PII: 1055-9965.EPI-11-0932, DOI: 10.1158/1055-9965.EPI-11-0932, ISSN: 1538-7755.

Su Y, Vilgelm AE, Kelley MC, Hawkins OE, Liu Y, Boyd KL, Kantrow S, Splittgerber RC, Short SP, Sobolik T, Zaja-Milatovic S, Dahlman KB, Amiri KI, Jiang A, Lu P, Shyr Y, Stuart DD, Levy S, Sosman JA, Richmond A. RAF265 inhibits the growth of advanced human melanoma tumors. Clin. Cancer Res [print-electronic]. 2012 Apr 4/15/2012; 18(8): 2184-98. PMID: 22351689, PMCID: PMC3724517, PII: 1078-0432.CCR-11-1122, DOI: 10.1158/1078-0432.CCR-11-1122, ISSN: 1078-0432.

Li X, Sterling JA, Fan KH, Vessella RL, Shyr Y, Hayward SW, Matrisian LM, Bhowmick NA. Loss of TGF-ß responsiveness in prostate stromal cells alters chemokine levels and facilitates the development of mixed osteoblastic/osteolytic bone lesions. Mol. Cancer Res [print-electronic]. 2012 Apr; 10(4): 494-503. PMID: 22290877, PMCID: PMC3900026, PII: 1541-7786.MCR-11-0506, DOI: 10.1158/1541-7786.MCR-11-0506, ISSN: 1557-3125.

Powell AE, Wang Y, Li Y, Poulin EJ, Means AL, Washington MK, Higginbotham JN, Juchheim A, Prasad N, Levy SE, Guo Y, Shyr Y, Aronow BJ, Haigis KM, Franklin JL, Coffey RJ. The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell. 2012 Mar 3/30/2012; 149(1): 146-58. PMID: 22464327, PMCID: PMC3563328, PII: S0092-8674(12)00280-2, DOI: 10.1016/j.cell.2012.02.042, ISSN: 1097-4172.

Sosman JA, Kim KB, Schuchter L, Gonzalez R, Pavlick AC, Weber JS, McArthur GA, Hutson TE, Moschos SJ, Flaherty KT, Hersey P, Kefford R, Lawrence D, Puzanov I, Lewis KD, Amaravadi RK, Chmielowski B, Lawrence HJ, Shyr Y, Ye F, Li J, Nolop KB, Lee RJ, Joe AK, Ribas A. Survival in BRAF V600-mutant advanced melanoma treated with vemurafenib. N. Engl. J. Med. 2012 Feb 2/23/2012; 366(8): 707-14. PMID: 22356324, PMCID: PMC3724515, DOI: 10.1056/NEJMoa1112302, ISSN: 1533-4406.

Baumann JL, Li M, Poulsen A, Chadwick NS, Cai Q, Chung CH, Shyr Y, Olsen JH, Zheng W, Slebos RJ. Analysis of microsatellite mutations in buccal cells from a case-control study for lung cancer. Cancer Epidemiol [print-electronic]. 2012 Feb; 36(1): e33-9. PMID: 22056752, PMCID: PMC3259162, PII: S1877-7821(11)00103-2, DOI: 10.1016/j.canep.2011.06.003, ISSN: 1877-783X.

Stover DG, Reddy VK, Shyr Y, Savani BN, Reddy N. Long-term impact of prior rituximab therapy and early lymphocyte recovery on auto-SCT outcome for diffuse large B-cell lymphoma. Bone Marrow Transplant [print-electronic]. 2012 Jan; 47(1): 82-7. PMID: 21358691, PII: bmt201129, DOI: 10.1038/bmt.2011.29, ISSN: 1476-5365.

Zhao Z, Huang Y, Zhang B, Shyr Y, Xu H. Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics [print-electronic]. 2012; 13 Suppl 8: S1. PMID: 23281891, PMCID: PMC3535713, PII: 1471-2164-13-S8-S1, DOI: 10.1186/1471-2164-13-S8-S1, ISSN: 1471-2164.

Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y. Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics [print-electronic]. 2012; 13 Suppl 8: S8. PMID: 23281772, PMCID: PMC3535703, PII: 1471-2164-13-S8-S8, DOI: 10.1186/1471-2164-13-S8-S8, ISSN: 1471-2164.

Su PF, Chen X, Chen H, Shyr Y. Statistical aspects of omics data analysis using the random compound covariate. BMC Syst Biol [print-electronic]. 2012; 6 Suppl 3: S11. PMID: 23281681, PMCID: PMC3524312, PII: 1752-0509-6-S3-S11, DOI: 10.1186/1752-0509-6-S3-S11, ISSN: 1752-0509.

Ye F, Bauer JA, Pietenpol JA, Shyr Y. Analysis of high-throughput RNAi screening data in identifying genes mediating sensitivity to chemotherapeutic drugs: statistical approaches and perspectives. BMC Genomics [print-electronic]. 2012; 13 Suppl 8: S3. PMID: 23281588, PMCID: PMC3535706, PII: 1471-2164-13-S8-S3, DOI: 10.1186/1471-2164-13-S8-S3, ISSN: 1471-2164.

Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y. The effect of strand bias in Illumina short-read sequencing data. BMC Genomics. 2012; 13: 666. PMID: 23176052, PMCID: PMC3532123, PII: 1471-2164-13-666, DOI: 10.1186/1471-2164-13-666, ISSN: 1471-2164.

Rao M, Song W, Jiang A, Shyr Y, Lev S, Greenstein D, Brantley-Sieders D, Chen J. VAMP-associated protein B (VAPB) promotes breast tumor growth by modulation of Akt activity. PLoS ONE [print-electronic]. 2012; 7(10): e46281. PMID: 23049696, PMCID: PMC3462209, PII: PONE-D-12-16139, DOI: 10.1371/journal.pone.0046281, ISSN: 1932-6203.

Brantley-Sieders DM, Fan KH, Deming-Halverson SL, Shyr Y, Cook RS. Local breast cancer spatial patterning: a tool for community health resource allocation to address local disparities in breast cancer mortality. PLoS ONE [print-electronic]. 2012; 7(9): e45238. PMID: 23028869, PMCID: PMC3460936, PII: PONE-D-12-12178, DOI: 10.1371/journal.pone.0045238, ISSN: 1932-6203.

Chen X, Li J, Gray WH, Lehmann BD, Bauer JA, Shyr Y, Pietenpol JA. TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer. Cancer Inform [print-electronic]. 2012; 11: 147-56. PMID: 22872785, PMCID: PMC3412597, PII: cin-11-2012-147, DOI: 10.4137/CIN.S9983, ISSN: 1176-9351.

Vlacich G, Diaz R, Thorpe SW, Murphy BA, Kirby W, Sinard RJ, Shakhtour B, Shyr Y, Murphy P, Netterville JL, Yarbrough WG, Cmelak AJ. Intensity-modulated radiation therapy with concurrent carboplatin and paclitaxel for locally advanced head and neck cancer: toxicities and efficacy. Oncologist [print-electronic]. 2012; 17(5): 673-81. PMID: 22550060, PMCID: PMC3360907, PII: theoncologist.2011-0396, DOI: 10.1634/theoncologist.2011-0396, ISSN: 1549-490X.

Fox EM, Miller TW, Balko JM, Kuba MG, Sánchez V, Smith RA, Liu S, González-Angulo AM, Mills GB, Ye F, Shyr Y, Manning HC, Buck E, Arteaga CL. A kinome-wide screen identifies the insulin/IGF-I receptor pathway as a mechanism of escape from hormone dependence in breast cancer. Cancer Res [print-electronic]. 2011 Nov 11/1/2011; 71(21): 6773-84. PMID: 21908557, PMCID: PMC3206206, PII: 0008-5472.CAN-11-1295, DOI: 10.1158/0008-5472.CAN-11-1295, ISSN: 1538-7445.

Murff HJ, Shrubsole MJ, Chen Z, Smalley WE, Chen H, Shyr Y, Ness RM, Zheng W. Nonsteroidal anti-inflammatory drug use and risk of adenomatous and hyperplastic polyps. Cancer Prev Res (Phila) [print-electronic]. 2011 Nov; 4(11): 1799-807. PMID: 21764857, PMCID: PMC3203989, PII: 1940-6207.CAPR-11-0107, DOI: 10.1158/1940-6207.CAPR-11-0107, ISSN: 1940-6215.

Fu Z, Shrubsole MJ, Smalley WE, Wu H, Chen Z, Shyr Y, Ness RM, Zheng W. Association of meat intake and meat-derived mutagen exposure with the risk of colorectal polyps by histologic type. Cancer Prev Res (Phila) [print-electronic]. 2011 Oct; 4(10): 1686-97. PMID: 21803984, PMCID: PMC3188364, PII: 1940-6207.CAPR-11-0191, DOI: 10.1158/1940-6207.CAPR-11-0191, ISSN: 1940-6215.

Novitskiy SV, Pickup MW, Gorska AE, Owens P, Chytil A, Aakre M, Wu H, Shyr Y, Moses HL. TGF-ß receptor II loss promotes mammary carcinoma progression by Th17 dependent mechanisms. Cancer Discov. 2011 Oct; 1(5): 430-41. PMID: 22408746, PMCID: PMC3297196, DOI: 10.1158/2159-8290.CD-11-0100, ISSN: 2159-8290.

Dexheimer JW, Talbot TR, Ye F, Shyr Y, Jones I, Gregg WM, Aronsky D. A computerized pneumococcal vaccination reminder system in the adult emergency department. Vaccine [print-electronic]. 2011 Sep 9/16/2011; 29(40): 7035-41. PMID: 21784117, PMCID: PMC3168965, PII: S0264-410X(11)01053-X, DOI: 10.1016/j.vaccine.2011.07.032, ISSN: 1873-2518.

Miller TW, Balko JM, Fox EM, Ghazoui Z, Dunbier A, Anderson H, Dowsett M, Jiang A, Smith RA, Maira SM, Manning HC, González-Angulo AM, Mills GB, Higham C, Chanthaphaychith S, Kuba MG, Miller WR, Shyr Y, Arteaga CL. ERa-dependent E2F transcription can mediate resistance to estrogen deprivation in human breast cancer. Cancer Discov [print-electronic]. 2011 Sep; 1(4): 338-51. PMID: 22049316, PMCID: PMC3204388, PII: 2159-8290.CD-11-0101, DOI: 10.1158/2159-8290.CD-11-0101, ISSN: 2159-8290.

Villegas R, Xiang YB, Elasy T, Li HL, Yang G, Cai H, Ye F, Gao YT, Shyr Y, Zheng W, Shu XO. Fish, shellfish, and long-chain n-3 fatty acid consumption and risk of incident type 2 diabetes in middle-aged Chinese men and women. Am. J. Clin. Nutr [print-electronic]. 2011 Aug; 94(2): 543-51. PMID: 21677058, PMCID: PMC3142729, PII: ajcn.111.013193, DOI: 10.3945/ajcn.111.013193, ISSN: 1938-3207.

Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, Shyr Y, Pietenpol JA. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J. Clin. Invest. 2011 Jul; 121(7): 2750-67. PMID: 21633166, PMCID: PMC3127435, PII: 45014, DOI: 10.1172/JCI45014, ISSN: 1558-8238.

Borkon MJ, Morrow SE, Koehler EA, Shyr Y, Hilmes MA, Miller RS, Neblett WW, Lovvorn HN. Operative intervention for complete pancreatic transection in children sustaining blunt abdominal trauma: revisiting an organ salvage technique. Am Surg. 2011 May; 77(5): 612-20. PMID: 21679597, ISSN: 1555-9823.

Horn L, Zhao Z, Sandler A, Johnson D, Shyr Y, Wolff S, Devore RF, Laskin J. A phase II study of carboplatin and irinotecan in extensive stage small-cell lung cancer. Clin Lung Cancer [print-electronic]. 2011 May; 12(3): 161-5. PMID: 21663858, PII: S1525-7304(11)00014-3, DOI: 10.1016/j.cllc.2011.03.013, ISSN: 1938-0690.

Funatogawa T, Funatogawa I, Shyr Y. Analysis of covariance with pre-treatment measurements in randomized trials under the cases that covariances and post-treatment variances differ between groups. Biom J. 2011 May; 53(3): 512-24. PMID: 22223254, DOI: 10.1002/bimj.201000200, ISSN: 1521-4036.

Rahman SM, Gonzalez AL, Li M, Seeley EH, Zimmerman LJ, Zhang XJ, Manier ML, Olson SJ, Shah RN, Miller AN, Putnam JB, Miller YE, Franklin WA, Blot WJ, Carbone DP, Shyr Y, Caprioli RM, Massion PP. Lung cancer diagnosis from proteomic analysis of preinvasive lesions. Cancer Res [print-electronic]. 2011 Apr 4/15/2011; 71(8): 3009-17. PMID: 21487035, PMCID: PMC3110721, PII: 0008-5472.CAN-10-2510, DOI: 10.1158/0008-5472.CAN-10-2510, ISSN: 1538-7445.

Miller TW, Balko JM, Ghazoui Z, Dunbier A, Anderson H, Dowsett M, González-Angulo AM, Mills GB, Miller WR, Wu H, Shyr Y, Arteaga CL. A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance. Clin. Cancer Res [print-electronic]. 2011 Apr 4/1/2011; 17(7): 2024-34. PMID: 21346144, PMCID: PMC3221728, PII: 1078-0432.CCR-10-2567, DOI: 10.1158/1078-0432.CCR-10-2567, ISSN: 1078-0432.

Li M, Chen S, Zhang J, Chen H, Shyr Y. Wave-spec: a preprocessing package for mass spectrometry data. Bioinformatics [print-electronic]. 2011 Mar 3/1/2011; 27(5): 739-40. PMID: 21208983, PMCID: PMC3105479, PII: btq724, DOI: 10.1093/bioinformatics/btq724, ISSN: 1367-4811.

Rosenbluth JM, Mays DJ, Jiang A, Shyr Y, Pietenpol JA. Differential regulation of the p73 cistrome by mammalian target of rapamycin reveals transcriptional programs of mesenchymal differentiation and tumorigenesis. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2011 Feb 2/1/2011; 108(5): 2076-81. PMID: 21245298, PMCID: PMC3033306, PII: 1011936108, DOI: 10.1073/pnas.1011936108, ISSN: 1091-6490.

Fohn LE, Rodriguez A, Kelley MC, Ye F, Shyr Y, Stricklin G, Robbins JB. D2-40 lymphatic marker for detecting lymphatic invasion in thin to intermediate thickness melanomas: association with sentinel lymph node status and prognostic value-a retrospective case study. J. Am. Acad. Dermatol. 2011 Feb; 64(2): 336-45. PMID: 21238827, PII: S0190-9622(10)00304-X, DOI: 10.1016/j.jaad.2010.03.005, ISSN: 1097-6787.

Brantley-Sieders DM, Dunaway CM, Rao M, Short S, Hwang Y, Gao Y, Li D, Jiang A, Shyr Y, Wu JY, Chen J. Angiocrine factors modulate tumor proliferation and motility through EphA2 repression of Slit2 tumor suppressor function in endothelium. Cancer Res [print-electronic]. 2011 Feb 2/1/2011; 71(3): 976-87. PMID: 21148069, PMCID: PMC3032824, PII: 0008-5472.CAN-10-3396, DOI: 10.1158/0008-5472.CAN-10-3396, ISSN: 1538-7445.

Brantley-Sieders DM, Jiang A, Sarma K, Badu-Nkansah A, Walter DL, Shyr Y, Chen J. Eph/ephrin profiling in human breast cancer reveals significant associations between expression level and clinical outcome. PLoS ONE [print-electronic]. 2011; 6(9): e24426. PMID: 21935409, PMCID: PMC3174170, PII: PONE-D-11-14906, DOI: 10.1371/journal.pone.0024426, ISSN: 1932-6203.

Boutté AM, McDonald WH, Shyr Y, Yang L, Lin PC. Characterization of the MDSC proteome associated with metastatic murine mammary tumors using label-free mass spectrometry and shotgun proteomics. PLoS ONE [print-electronic]. 2011; 6(8): e22446. PMID: 21853032, PMCID: PMC3154190, PII: PONE-D-11-06025, DOI: 10.1371/journal.pone.0022446, ISSN: 1932-6203.

Tamboli RA, Hajri T, Jiang A, Marks-Shulman PA, Williams DB, Clements RH, Melvin W, Bowen BP, Shyr Y, Abumrad NN, Flynn CR. Reduction in inflammatory gene expression in skeletal muscle from Roux-en-Y gastric bypass patients randomized to omentectomy. PLoS ONE [print-electronic]. 2011; 6(12): e28577. PMID: 22194858, PMCID: PMC3241684, PII: PONE-D-11-17236, DOI: 10.1371/journal.pone.0028577, ISSN: 1932-6203.

Biswas S, Nyman JS, Alvarez J, Chakrabarti A, Ayres A, Sterling J, Edwards J, Rana T, Johnson R, Perrien DS, Lonning S, Shyr Y, Matrisian LM, Mundy GR. Anti-transforming growth factor ß antibody treatment rescues bone loss and prevents breast cancer metastasis to bone. PLoS ONE [print-electronic]. 2011; 6(11): e27090. PMID: 22096521, PMCID: PMC3214031, PII: PONE-D-11-14957, DOI: 10.1371/journal.pone.0027090, ISSN: 1932-6203.

Yu DS, Zhao R, Hsu EL, Cayer J, Ye F, Guo Y, Shyr Y, Cortez D. Cyclin-dependent kinase 9-cyclin K functions in the replication stress response. EMBO Rep [print-electronic]. 2010 Nov; 11(11): 876-82. PMID: 20930849, PMCID: PMC2966956, PII: embor2010153, DOI: 10.1038/embor.2010.153, ISSN: 1469-3178.

Barton CE, Johnson KN, Mays DM, Boehnke K, Shyr Y, Boukamp P, Pietenpol JA. Novel p63 target genes involved in paracrine signaling and keratinocyte differentiation. Cell Death Dis. 2010; 1: e74. PMID: 21151771, PMCID: PMC3000738, DOI: 10.1038/cddis.2010.49, ISSN: 2041-4889.

Hatakeyama H, Cheng H, Wirth P, Counsell A, Marcrom SR, Wood CB, Pohlmann PR, Gilbert J, Murphy B, Yarbrough WG, Wheeler DL, Harari PM, Guo Y, Shyr Y, Slebos RJ, Chung CH. Regulation of heparin-binding EGF-like growth factor by miR-212 and acquired cetuximab-resistance in head and neck squamous cell carcinoma. PLoS ONE. 2010; 5(9): e12702. PMID: 20856931, PMCID: PMC2938338, DOI: 10.1371/journal.pone.0012702, ISSN: 1932-6203.