Publications

Publications

2016 2015 2014 2013

 

2016

  1. Zhou X, Updegraff BL, Guo Y, Peyton M, Girard L, Larsen JE, Xie XJ, Zhou Y, Hwang TH, Xie Y, Rodriguez-Canales J, Villalobos P, Behrens C, Wistuba, II, Minna J, O'Donnell KA. PROTOCADHERIN 7 acts through SET and PP2A to potentiate MAPK signaling by EGFR and KRAS during lung tumorigenesis. Cancer Res. 2016. doi: 10.1158/0008-5472.CAN-16-1267-T.

  2. Zhang YA, Ma X, Sathe A, Fujimoto J, Wistuba, II, Lam S, Yatabe Y, Wang YW, Stastny V, Gao B, Larsen JE, Girard L, Liu X, Song K, Behrens C, Kalhor N, Xie Y, Zhang MQ, Minna JD, Gazdar AF. Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers.J Thorac Oncol. 2016;11(3):346-60.

  3. Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XS. High-dimensional genomic data bias correction and data integration using MANCIE. Nat Commun. 2016;7:11305.

  4. Sieberts SK, Zhu F, Garcia-Garcia J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornes O, Guney E, Li H, Marin MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VS, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellon V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C, Members of the Rheumatoid Arthritis Challenge C, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TW, Kurreeman F, Allaart CF, Louis Bridges S, Jr., Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun. 2016;7:12460. doi: 10.1038/ncomms12460.

  5. Piper HG, Fan D, Coughlin LA, Ho EX, McDaniel MM, Channabasappa N, Kim J, Kim M, Zhan X, Xie Y, Koh AY. Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome. JPEN J Parenter Enteral Nutr. 2016. doi: 10.1177/0148607116658762.

  6. Patidar PL, Motea EA, Fattah FJ, Zhou Y, Morales JC, Xie Y, Garner HR, Boothman DA. The Kub5-Hera/RPRD1B interactome: a novel role in preserving genetic stability by regulating DNA mismatch repair. Nucleic Acids Res. 2016;44(4):1718-31.

  7. Meyer JJ, Foster RD, Lev-Cohain N, Yokoo T, Dong Y, Schwarz RE, Rule W, Tian J, Xie Y, Hannan R, Nedzi L, Solberg T, Timmerman R. A Phase I Dose-Escalation Trial of Single-Fraction Stereotactic Radiation Therapy for Liver Metastases. Ann Surg Oncol. 2016;23(1):218-24.

  8. Luo X, Zang X, Yang L, Huang J, Liang F, Rodriguez Canales J, Wistuba, II, Gazdar A, Xie Y, Xiao G. Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis. J Thorac Oncol. 2016. doi: 10.1016/j.jtho.2016.10.017.

  9. Lee S, Kopp F, Chang TC, Sataluri A, Chen B, Sivakumar S, Yu H, Xie Y, Mendell JT. Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins. Cell. 2016;164(1-2):69-80.

  10. Laccetti AL, Chen B, Cai J, Gates S, Xie Y, Lee SJ, Gerber DE. Increase in Cancer Center Staff Effort Related to Electronic Patient Portal Use. J Oncol Pract. 2016;12(12):e981-e90.

  11. Kim J, Kim MS, Koh AY, Xie Y, Zhan X. FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies. BMC Bioinformatics. 2016;17(1):420.

  12. Han T, Goralski M, Capota E, Padrick SB, Kim J, Xie Y, Nijhawan D. The antitumor toxin CD437 is a direct inhibitor of DNA polymerase alpha. Nat Chem Biol. 2016;12(7):511-5.

  13. Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC, Prostate Cancer Challenge DC. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncol. 2016. doi: 10.1016/S1470-2045(16)30560-5.

  14. Girard L, Rodriguez-Canales J, Behrens C, Thompson DM, Botros IW, Tang H, Xie Y, Rekhtman N, Travis WD, Wistuba, II, Minna JD, Gazdar AF. An Expression Signature as an Aid to the Histologic Classification of Non-Small Cell Lung Cancer. Clin Cancer Res. 2016;22(19):4880-9.

  15. Chun SG, Hughes R, Sumer BD, Myers LL, Truelson JM, Khan SA, Ma TW, Xie Y, Yordy JS, Cooley S, Wu J, Choy H, Nedzi LA. A Phase I/II Study of Nab-Paclitaxel, Cisplatin, and Cetuximab With Concurrent Radiation Therapy for Locally Advanced Squamous Cell Cancer of the Head and Neck. Cancer Invest. 2016:1-9.

  16. Chen W, Hill H, Christie A, Kim MS, Holloman E, Pavia-Jimenez A, Homayoun F, Ma Y, Patel N, Yell P, Hao G, Yousuf Q, Joyce A, Pedrosa I, Geiger H, Zhang H, Chang J, Gardner KH, Bruick RK, Reeves C, Hwang TH, Courtney K, Frenkel E, Sun X, Zojwalla N, Wong T, Rizzi JP, Wallace EM, Josey JA, Xie Y, Xie XJ, Kapur P, McKay RM, Brugarolas J. Targeting renal cell carcinoma with a HIF-2 antagonist. Nature. 2016;539(7627):112-7.

  17. Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Frohlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S, Alzheimer's Disease Neuroimaging I. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. 2016;12(6):645-53.

  18. Aboudehen K, Kim MS, Mitsche M, Garland K, Anderson N, Noureddine L, Pontoglio M, Patel V, Xie Y, DeBose-Boyd R, Igarashi P. Transcription Factor Hepatocyte Nuclear Factor-1beta Regulates Renal Cholesterol Metabolism. J Am Soc Nephrol. 2016;27(8):2408-21.

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2015

  1. Fan D, Coughlin LA, Neubauer MM, Kim J, Kim MS, Zhan X, Simms-Waldrip TR, Xie Y, Hooper LV, Koh AY. Activation of HIF-1 and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nat Med. 2015 Jul;21(7):808-14.

  2. Sharma D, Kim MS,D'Mello SR. Transcriptome profiling of expression changes during neuronal death by RNA-Seq. Exp. Biol. Med. 2015 Feb;240(2):242-51.

  3. Zang X, Chen M, Zhou Y, Xiao G, Xie Y, Wang X. Meta-analysis Identification of CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma Cancer Informatics, 2015;Suppl.2:183-91

  4. Sei E, Wang T, Hunter OV, Xie Y, Conrad NK. HITS-CLIP Analysis Uncovers a Link between the Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism. PLoS Pathog. 2015 Feb; 11(2): e1004652.

  5. Tang H, Sebti S, Titone R, Zhou Y, Isidoro C, Ross T, Hibshoosh H, Xiao G, Packer M, Xie Y, and Levine B. Decreased BECN1 mRNA Expression in Human Breast Cancer is Associated with Estrogen Receptor-Negative Subtypes and Poor Prognosis, EBioMedicine. 2015 Mar; 2(3): 255–63.

  6. Ding LH, Park S, Xie Y, Girard L, Minna JD, Story MD. Elucidation of changes in molecular signalling leading to increased cellular transformation in oncogenically progressed human bronchial epithelial cells exposed to radiations of increasing LET. Mutagenesis 2015 Sep; 30(5): 685-94.

  7. Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res. 2015 Jun 23; 43(11): 5263-74.

  8. Elkin SR, Bendris N, Reis C, Zhou Y, Xie Y, Huffman KE, Minna JD, Schmid SL. A systematic analysis reveals heterogeneous changes in the endocytic activities of cancer cells. Cancer Res. 2015 Nov; 75(21): 4640-50.

  9. Gaviria-Agudelo C, Aroh C, Tareen N, Wakeland EK, Kim MS, Copley LA. Genomic Heterogeneity of Methicillin Resistant Staphylococcus aureus Associated with Variation in Severity of Illness among Children with Acute Hematogenous Osteomyelitis. PLoS One. 2015 Jun; 10(6): e0130415.

  10. Ugrankar R, Berglund E, Akdemir F, Tran C, Kim MS, Noh J, Schneider R, Ebert B, Graff JM. Drosophila glucome screening identifies Ck1alpha as a regulator of mammalian glucose metabolim. Nat Commun. 2015 May; 6: 7102.

  11. Gerber DE, Laccetti AL, Chen B, Yan J, Cai J, Gates S, Xie Y, Lee SJC. Predictors and Intensity of Online Access to Electronic Medical Records Among Patients With Cancer. Journal of Oncology Practice 2014 Sep; 10(5): e307-12.

  12. Chu Y, Wang T, Dodd D, Xie Y; Janowski B, Corey D, Intramolecular Circularization Increases Efficiency of RNA Sequencing. Nucleic Acids Res. 2015 Jun 23; 43(11): e75.

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2014

  1. Wang T, Chen B, Kim MSXie Y, Xiao G. A model-based approach to identify binding sites in CLIP-seq data.  PloS one. 2014 Sep; 9(4): e93248.

  2. Chen B, Yun J, Kim MS, Mendell JT, Xie YPIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.  Genome Biol. 2014 Jan; 15(1): R18.

  3. Zhong R, Kim J, Kim HS, Kim MS, Lum L, Levine B, Xiao G, White M and Xie Y Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens.  Nucleic Acids Research. 2014 Jul; 42(13): 8214-22.

  4. Kwon I, Xiang S, Kato M, Wu L, Theodoropoulos P, Wang T, Kim J, Yun J, Xie Y, McKnight SL. Poly-dipeptides encoded by the C9ORF72 repeats bind nucleoli, impede RNA biogenesis, and kill cells.  Science 2014 Sep; 345(6201): 1139-45.

  5. Yang J, Tang H, Li Y, Zhong R, Wang T, Wong S, Xiao G, Xie Y, DIGRE: Drug Induced Genomic Residual Effect Model for Successful Prediction of Multidrug Effects. CPT: Pharmacometrics & Systems Pharmacology. 2015 Feb; 4(2): e1.

  6. Xiao G, Ma S, Minna J, Xie Y. Adaptive prediction model in prospective molecular-signature-based clinical studies, Clinical Cancer Research, 2014 Feb; 20(3): 531-9.

  7. Zhong R, Allen JD, Xiao G, Xie Y. Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PLoS One. 2014 Nov; 9(11): e106319.

  8. Augustyn A, Borromeo M, Wang T, Fujimoto J, Shao C, Dospoy PD, Lee V, Tan C, Sullivan JP, Larsen JE, Girard L, Behrens C, Wistuba II, Xie Y, Cobb MH, Gazdar AF, Johnson JE, Minna JD. ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers. Proc Natl Acad Sci U S A. 2014 Oct; 111(41): 14788-93.

  9. Wang T, Xie Y, Xiao G. dCLIP: a computational approach for comparative CLIP-seq analyses. Genome Biology, 2014 Jan; 15(1): R11.7

  10. Yang J, Wang X, Kim M, Xie Y, Xiao G. Detection of candidate tumor driver genes using a fully integrated Bayesian approach, Statistics in Medicine, 2014 May; 33(10): 1784-800.

  11. Zhong R, Dong X, Levine B, Xie Y, Xiao G. iScreen: Image-Based High-Content RNAi Screening Analysis Tools. J Biomol Screen. 2015 Sep; 20(8): 998-1002.

  12. Gerber DE, Laccetti AL, Chen B, Yan J, Cai J, Gates S, Xie Y, Lee SJ. Predictors and intensity of online access to electronic medical records among patients with cancer. J Oncol Pract. 2014 Sep; 10(5): e307-12.

  13. Gazdar A, Robinson L, Oliver D, Xing C, Travis WD, Soh J, Toyooka S, Watumull L, Xie Y, Kernstine K, Schiller JH. Hereditary lung cancer syndrome targets never smokers with germline EGFR gene T790M mutations. J Thorac Oncol. 2014 Apr; 9(4): 456-63.

  14. Zhao Q, Shi X, Xie Y, Huang J, Shia B, Ma S. Combining multidimensional genomic measurements for predicting cancer prognosis: observations from TCGA. Brief Bioinform. 2015 Mar; 16(2): 291-303.(Epub 2014 Mar 13).

  15. Shi X, Liu J, Huang J, Zhou Y, Xie Y, Ma S. A penalized robust method for identifying gene-environment interactions. Genet Epidemiol. 2014 Apr;38(3):220-30.

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2013

  1. Zhong R, Kim MS, White MA, Xie Y, Xiao G. SbacHTS: spatial background noise correction for highthroughput RNAi screening. Bioinformatics. 2013 Sep; 29(17): 2218-20.

  2. Xiao G, Wang X, Laplant Q, Nestler E, and Xie Y. Detection of Epigenetic Changes Using ANOVA with Spatially Varying Coefficients, Statistical Applications in Genetics and Molecular Biology. 2013 Mar; 12(2): 189-205.

  3. Tang H, Xiao G, Behrens C, Schiller J, Allen J, Chow C, Suraokar M, Corvalan A, Mao J, White M, Wistuba I, Minna J, Xie Y. A 12-Gene Set Predicts Survival Benefits from Adjuvant Chemotherapy in Non-Small-Cell Lung Cancer Patients, Clinical Cancer Research 2013 Mar; 19(6): 1577-86.

  4. Wu Q, Ishikawa T, Sirianni R, Tang H, McDonald JG, Yuhanna IS, Thompson B, Girard L, Mineo C, Brekken RA, Umetani M, Euhus DM, Xie Y, Shaul PW. 27-Hydroxycholesterol Promotes Cell-Autonomous, ER-Positive Breast Cancer Growth. Cell Rep. 2013 Nov; 5(3): 637-45.

  5. Ahn DH, Mehta N, Yorio JT, Xie Y, Yan J, Gerber DE. Influence of Medical Comorbidities on the Presentation and Outcomes of Stage I-III Non-Small-Cell Lung Cancer. Clin Lung Cancer. 2013 Nov; 14(6):6 44-50.

  6. Chakraborty S, Li L, Tang H, Xie Y, Puliyappadamba VT, Raisanen J, Burma S, Boothman DA, Cochran B, Wu J, Habib AA. Cytoplasmic TRADD confers a worse prognosis in glioblastoma. Neoplasia. 2013 Aug; 15(8): 888-97.

  7. Ding LH, Park S, Peyton M, Girard L, Xie Y, Minna JD, Story MD. Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy. BMC Genomics. 2013 Jun; 14: 372.

  8. Sato M, Larsen JE, Lee W, Sun H, Shames DS, Dalvi MP, Ramirez RD, Tang H, DiMaio JM, Gao B, Xie Y, Wistuba II, Gazdar AF, Shay JW, Minna JD. Human lung epithelial cells progressed to malignancy through specific oncogenic manipulations. Mol Cancer Res. 2013 Jun; 11(6): 638-50.

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