Yu Shyr
VICC Faculty Member
Last active: 4/3/2018

Profile

statistical bioinformatics

Publications

The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. Feasibility trial for primary stroke prevention in children with sickle cell anemia in Nigeria (SPIN trial). Galadanci NA, Umar Abdullahi S, Vance LD, Musa Tabari A, Ali S, Belonwu R, Salihu A, Amal Galadanci A, Wudil Jibir B, Bello-Manga H, Neville K, Kirkham FJ, Shyr Y, Phillips S, Covert BV, Kassim AA, Jordan LC, Aliyu MH, DeBaun MR (2018) Am J Hematol 93(3): E83
    › Primary publication · 29411418 (PubMed)
  2. 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 IC, Lou X (2018) J Proteome Res 17(3): 1300-1308
    › Primary publication · 29369637 (PubMed)
  3. The Impact of Smoking and TP53 Mutations in Lung Adenocarcinoma Patients with Targetable Mutations-The Lung Cancer Mutation Consortium (LCMC2). Aisner DL, Sholl LM, Berry LD, Rossi MR, Chen H, Fujimoto J, Moreira AL, Ramalingam SS, Villaruz LC, Otterson GA, Haura E, Politi K, Glisson B, Cetnar J, Garon EB, Schiller J, Waqar SN, Sequist LV, Brahmer J, Shyr Y, Kugler K, Wistuba II, Johnson BE, Minna JD, Kris MG, Bunn PA, Kwiatkowski DJ, LCMC2 investigators (2018) Clin Cancer Res 24(5): 1038-1047
    › Primary publication · 29217530 (PubMed)
  4. Shanghai Score: A Prognostic and Adjuvant Treatment-evaluating System Constructed for Chinese Patients with Hepatocellular Carcinoma after Curative Resection. Sun HC, Xie L, Yang XR, Li W, Yu J, Zhu XD, Xia Y, Zhang T, Xu Y, Hu B, Du LP, Zeng LY, Ouyang J, Zhang W, Song TQ, Li Q, Shi YH, Zhou J, Qiu SJ, Liu Q, Li YX, Tang ZY, Shyr Y, Shen F, Fan J (2017) Chin Med J (Engl) 130(22): 2650-2660
    › Primary publication · 29133751 (PubMed) · PMC5695048 (PubMed Central)
  5. The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data. Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y (2017) BMC Genomics 18(Suppl 6): 690
    › Primary publication · 28984205 (PubMed) · PMC5629567 (PubMed Central)
  6. Longitudinal Cell-Free DNA Analysis in Patients with Small Cell Lung Cancer Reveals Dynamic Insights into Treatment Efficacy and Disease Relapse. Almodovar K, Iams WT, Meador CB, Zhao Z, York S, Horn L, Yan Y, Hernandez J, Chen H, Shyr Y, Lim LP, Raymond CK, Lovly CM (2018) J Thorac Oncol 13(1): 112-123
    › Primary publication · 28951314 (PubMed) · PMC5827950 (PubMed Central)
  7. Corrigendum to "Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control". Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y (2017) Biomed Res Int : 7409598
    › Primary publication · 28804721 (PubMed) · PMC5540237 (PubMed Central)
  8. Genomic profiling of ER breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance. Giltnane JM, Hutchinson KE, Stricker TP, Formisano L, Young CD, Estrada MV, Nixon MJ, Du L, Sanchez V, Ericsson PG, Kuba MG, Sanders ME, Mu XJ, Van Allen EM, Wagle N, Mayer IA, Abramson V, Gόmez H, Rizzo M, Toy W, Chandarlapaty S, Mayer EL, Christiansen J, Murphy D, Fitzgerald K, Wang K, Ross JS, Miller VA, Stephens PJ, Yelensky R, Garraway L, Shyr Y, Meszoely I, Balko JM, Arteaga CL (2017) Sci Transl Med 9(402)
    › Primary publication · 28794284 (PubMed) · PMC5723145 (PubMed Central)
  9. Estimating relative mitochondrial DNA copy number using high throughput sequencing data. Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao YY, Shyr Y, Guo Y (2017) Genomics 109(5-6): 457-462
    › Primary publication · 28734953 (PubMed)
  10. Power and sample size calculations for high-throughput sequencing-based experiments. Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y (2018) Brief Bioinform 19(6): 1247-1255
    › Primary publication · 28605403 (PubMed) · PMC6291796 (PubMed Central)
  11. Multisite external validation of a risk prediction model for the diagnosis of blood stream infections in febrile pediatric oncology patients without severe neutropenia. Esbenshade AJ, Zhao Z, Aftandilian C, Saab R, Wattier RL, Beauchemin M, Miller TP, Wilkes JJ, Kelly MJ, Fernbach A, Jeng M, Schwartz CL, Dvorak CC, Shyr Y, Moons KGM, Sulis ML, Friedman DL (2017) Cancer 123(19): 3781-3790
    › Primary publication · 28542918 (PubMed) · PMC5610619 (PubMed Central)
  12. Feasibility trial for primary stroke prevention in children with sickle cell anemia in Nigeria (SPIN trial). Galadanci NA, Umar Abdullahi S, Vance LD, Musa Tabari A, Ali S, Belonwu R, Salihu A, Amal Galadanci A, Wudil Jibir B, Bello-Manga H, Neville K, Kirkham FJ, Shyr Y, Phillips S, Covert BV, Kassim AA, Jordan LC, Aliyu MH, DeBaun MR (2017) Am J Hematol 92(8): 780-788
    › Primary publication · 28439953 (PubMed) · PMC5523858 (PubMed Central)
  13. StrandScript: evaluation of Illumina genotyping array design and strand correction. Wang J, Samuels DC, Shyr Y, Guo Y (2017) Bioinformatics 33(15): 2399-2401
    › Primary publication · 28402386 (PubMed)
  14. Strategies for processing and quality control of Illumina genotyping arrays. Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y (2018) Brief Bioinform 19(5): 765-775
    › Primary publication · 28334151 (PubMed) · PMC6171493 (PubMed Central)
  15. IGFBP3 Modulates Lung Tumorigenesis and Cell Growth through IGF1 Signaling. Wang YA, Sun Y, Palmer J, Solomides C, Huang LC, Shyr Y, Dicker AP, Lu B (2017) Mol Cancer Res 15(7): 896-904
    › Primary publication · 28330997 (PubMed)
  16. Integrated expression analysis identifies transcription networks in mouse and human gastric neoplasia. Chen Z, Soutto M, Rahman B, Fazili MW, Peng D, Blanca Piazuelo M, Chen H, Kay Washington M, Shyr Y, El-Rifai W (2017) Genes Chromosomes Cancer 56(7): 535-547
    › Primary publication · 28281307 (PubMed) · PMC5524517 (PubMed Central)
  17. 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. Jovanović B, Mayer IA, Mayer EL, Abramson VG, Bardia A, Sanders ME, Kuba MG, Estrada MV, Beeler JS, Shaver TM, Johnson KC, Sanchez V, Rosenbluth JM, Dillon PM, Forero-Torres A, Chang JC, Meszoely IM, Grau AM, Lehmann BD, Shyr Y, Sheng Q, Chen SC, Arteaga CL, Pietenpol JA (2017) Clin Cancer Res 23(15): 4035-4045
    › Primary publication · 28270498 (PubMed) · PMC5540799 (PubMed Central)
  18. Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset. Su PF, Mau YL, Guo Y, Li CI, Liu Q, Boice JD, Shyr Y (2017) Stat Appl Genet Mol Biol 16(1): 47-58
    › Primary publication · 28248637 (PubMed)
  19. The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Zhang P, Lehmann BD, Shyr Y, Guo Y (2017) Int J Genomics : 1926304
    › Primary publication · 28246590 (PubMed) · PMC5299160 (PubMed Central)
  20. Etoposide and cisplatin versus paclitaxel and carboplatin with concurrent thoracic radiotherapy in unresectable stage III non-small cell lung cancer: a multicenter randomized phase III trial. Liang J, Bi N, Wu S, Chen M, Lv C, Zhao L, Shi A, Jiang W, Xu Y, Zhou Z, Wang W, Chen D, Hui Z, Lv J, Zhang H, Feng Q, Xiao Z, Wang X, Liu L, Zhang T, Du L, Chen W, Shyr Y, Yin W, Li J, He J, Wang L (2017) Ann Oncol 28(4): 777-783
    › Primary publication · 28137739 (PubMed)
  21. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis. Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y (2017) Genomics 109(2): 83-90
    › Primary publication · 28131802 (PubMed)
  22. 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) Sci Rep : 40729
    › Primary publication · 28102292 (PubMed) · PMC5244375 (PubMed Central)
  23. 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 MJ, Pendyala P, Chen SC, Shyr Y, Cmelak AJ (2017) Radiat Oncol 12(1): 13
    › Primary publication · 28086954 (PubMed) · PMC5237132 (PubMed Central)
  24. Determining Penetration of Prostate-Specific Antigen Screening Recommendations. Thomas CR, Shyr Y (2017) JAMA Oncol 3(5): 707
    › Primary publication · 28033437 (PubMed)
  25. PS01.68: Heterogeneous Clinical Syndromes Existing Within Patients with Stage IV KRAS Mutant Non-Small Cell Lung Cancer: Topic: Medical Oncology. Iams WT, Yu H, Shyr Y, Patil T, Horn L, McCoach C, Kelly K, Doebele R, Camidge DR (2016) J Thorac Oncol 11(11S): S313
    › Primary publication · 27969535 (PubMed)
  26. Transcriptome-wide signatures of tumor stage in kidney renal clear cell carcinoma: connecting copy number variation, methylation and transcription factor activity. Liu Q, Su PF, Zhao S, Shyr Y (2014) Genome Med 6(12): 117
    › Primary publication · 25648588 (PubMed) · PMC4293006 (PubMed Central)
  27. Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data. Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R (2015) Mol Cell Proteomics 14(2): 405-17
    › Primary publication · 25435543 (PubMed) · PMC4350035 (PubMed Central)
  28. Nationwide trends in mastectomy for early-stage breast cancer. Kummerow KL, Du L, Penson DF, Shyr Y, Hooks MA (2015) JAMA Surg 150(1): 9-16
    › Primary publication · 25408966 (PubMed)
  29. RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment. Guo Y, Zhao S, Li CI, Sheng Q, Shyr Y (2014) Cancer Inform 13(Suppl 6): 1-5
    › Primary publication · 25374457 (PubMed) · PMC4213196 (PubMed Central)
  30. Detection of internal exon deletion with exon Del. Guo Y, Zhao S, Lehmann BD, Sheng Q, Shaver TM, Stricker TP, Pietenpol JA, Shyr Y (2014) BMC Bioinformatics : 332
    › Primary publication · 25322818 (PubMed) · PMC4288651 (PubMed Central)
  31. Illumina human exome genotyping array clustering and quality control. Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J (2014) Nat Protoc 9(11): 2643-62
    › Primary publication · 25321409 (PubMed) · PMC4441213 (PubMed Central)
  32. Genome measures used for quality control are dependent on gene function and ancestry. Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y (2015) Bioinformatics 31(3): 318-23
    › Primary publication · 25297068 (PubMed) · PMC4308666 (PubMed Central)
  33. DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. Sheng Q, Shyr Y, Chen X (2014) BMC Bioinformatics : 323
    › Primary publication · 25267467 (PubMed) · PMC4261523 (PubMed Central)
  34. Statistical strategies for microRNAseq batch effect reduction. Guo Y, Zhao S, Su PF, Li CI, Ye F, Flynn CR, Shyr Y (2014) Transl Cancer Res 3(3): 260-265
    › Primary publication · 25258704 (PubMed) · PMC4171948 (PubMed Central)
  35. Advanced heat map and clustering analysis using heatmap3. Zhao S, Guo Y, Sheng Q, Shyr Y (2014) Biomed Res Int : 986048
    › Primary publication · 25143956 (PubMed) · PMC4124803 (PubMed Central)
  36. MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control. Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y (2014) Biomed Res Int : 248090
    › Primary publication · 24977143 (PubMed) · PMC4058234 (PubMed Central)
  37. Routine clinical evaluation of cerebrovascular reserve capacity using carbogen in patients with intracranial stenosis. 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 (2014) Stroke 45(8): 2335-41
    › Primary publication · 24938845 (PubMed) · PMC4118584 (PubMed Central)
  38. A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods. Guo Y, Bosompem A, Zhong X, Clark T, Shyr Y, Kim AS (2014) Int J Comput Biol Drug Des 7(2-3): 102-12
    › Primary publication · 24878723 (PubMed) · PMC5798231 (PubMed Central)
  39. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. 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 (2014) JAMA 311(19): 1998-2006
    › Primary publication · 24846037 (PubMed) · PMC4163053 (PubMed Central)
  40. LKB1 Loss induces characteristic patterns of gene expression in human tumors associated with NRF2 activation and attenuation of PI3K-AKT. Kaufman JM, Amann JM, Park K, Arasada RR, Li H, Shyr Y, Carbone DP (2014) J Thorac Oncol 9(6): 794-804
    › Primary publication · 24828662 (PubMed) · PMC4026179 (PubMed Central)
  41. Barrett's Esophagus Translational Research Network (BETRNet): the pivotal role of multi-institutional collaboration in esophageal adenocarcinoma research. 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 (2014) Gastroenterology 146(7): 1586-90
    › Primary publication · 24768332 (PubMed) · PMC4224108 (PubMed Central)
  42. Multi-perspective quality control of Illumina exome sequencing data using QC3. Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y (2014) Genomics 103(5-6): 323-8
    › Primary publication · 24703969 (PubMed) · PMC5755963 (PubMed Central)
  43. Phase II trial of sorafenib and erlotinib in advanced pancreatic cancer. 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 (2014) Cancer Med 3(3): 572-9
    › Primary publication · 24574334 (PubMed) · PMC4101748 (PubMed Central)
  44. Sample size determination for paired right-censored data based on the difference of Kaplan-Meier estimates. Su PF, Li CI, Shyr Y (2014) Comput Stat Data Anal : 39-51
    › Primary publication · 24567661 (PubMed) · PMC3931470 (PubMed Central)
  45. Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. Udyavar AR, Hoeksema MD, Clark JE, Zou Y, Tang Z, Li Z, Li M, Chen H, Statnikov A, Shyr Y, Liebler DC, Field J, Eisenberg R, Estrada L, Massion PP, Quaranta V (2013) BMC Syst Biol : S1
    › Primary publication · 24564859 (PubMed) · PMC4029366 (PubMed Central)
  46. Evaluation of read count based RNAseq analysis methods. Guo Y, Li CI, Ye F, Shyr Y (2013) BMC Genomics : S2
    › Primary publication · 24564449 (PubMed) · PMC4092879 (PubMed Central)
  47. Exome sequencing implicates an increased burden of rare potassium channel variants in the risk of drug-induced long QT interval syndrome. 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 (2014) J Am Coll Cardiol 63(14): 1430-7
    › Primary publication · 24561134 (PubMed) · PMC4018823 (PubMed Central)