Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Debashis Ghosh

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentCSPH-Bio Info General Ops
Phone303/724-4365
    Other Positions
    TitleChair
    InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
    DepartmentCSPH-Bio Info General Ops


    Collapse Research 
    Collapse research activities and funding
    R01GM072007     (GHOSH, DEBASHIS)Sep 1, 2004 - Aug 31, 2010
    NIH
    Statistical Methods for the Analysis of Functional Genomic Data
    Role: Principal Investigator

    R01CA129102     (TAYLOR, JEREMY M.G.)Jul 1, 2007 - Jun 30, 2022
    NIH
    Statistical Methods for Cancer Biomarkers
    Role: Co-Investigator

    R01GM117946     (EPSTEIN, MICHAEL PHILIP)Feb 1, 2016 - Dec 31, 2019
    NIH
    Statistical Tests for Mapping Genetic Determinants of Complex Traits
    Role: Co-Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Zhang L, Zhou H, Li X, Vartuli RL, Rowse M, Xing Y, Rudra P, Ghosh D, Zhao R, Ford HL. Author Correction: Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression. Nat Commun. 2018 Sep 17; 9(1):3830. PMID: 30224630.
      View in: PubMed
    2. Ghosh D. Relaxed covariate overlap and margin-based causal effect estimation. Stat Med. 2018 Aug 30. PMID: 30168168.
      View in: PubMed
    3. Russell P, Fountain K, Wolverton D, Ghosh D. TCIApathfinder: An R Client for the Cancer Imaging Archive REST API. Cancer Res. 2018 Aug 01; 78(15):4424-4426. PMID: 29871933.
      View in: PubMed
    4. Vartuli RL, Zhou H, Zhang L, Powers RK, Klarquist J, Rudra P, Vincent MY, Ghosh D, Costello JC, Kedl RM, Slansky JE, Zhao R, Ford HL. Eya3 promotes breast tumor-associated immune suppression via threonine phosphatase-mediated PD-L1 upregulation. J Clin Invest. 2018 Jun 01; 128(6):2535-2550. PMID: 29757193.
      View in: PubMed
    5. Rudra P, Broadaway KA, Ware EB, Jhun MA, Bielak LF, Zhao W, Smith JA, Peyser PA, Kardia SLR, Epstein MP, Ghosh D. Testing cross-phenotype effects of rare variants in longitudinal studies of complex traits. Genet Epidemiol. 2018 06; 42(4):320-332. PMID: 29601641.
      View in: PubMed
    6. Smith DE, Golden AP, Stange AW, Barker E, Mroz M, Barón AE, Ghosh D, Maier L, Cragle D, Newman LS. Clinical and laboratory factors contributing to uninterpretable beryllium lymphocyte proliferation tests (BeLPT). Am J Ind Med. 2018 Jul; 61(7):592-604. PMID: 29574954.
      View in: PubMed
    7. Zhang L, Zhou H, Li X, Vartuli RL, Rowse M, Xing Y, Rudra P, Ghosh D, Zhao R, Ford HL. Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression. Nat Commun. 2018 03 13; 9(1):1047. PMID: 29535359.
      View in: PubMed
    8. Zhu B, Song N, Shen R, Arora A, Machiela MJ, Song L, Landi MT, Ghosh D, Chatterjee N, Baladandayuthapani V, Zhao H. Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers. Sci Rep. 2017 Dec 05; 7(1):16954. PMID: 29209073.
      View in: PubMed
    9. Zhang W, Ghosh D. On the use of kernel machines for Mendelian randomization. Quant Biol. 2017 Dec; 5(4):368-379. PMID: 30221016.
      View in: PubMed
    10. Cho Y, Hu C, Ghosh D. Covariate adjustment using propensity scores for dependent censoring problems in the accelerated failure time model. Stat Med. 2018 Feb 10; 37(3):390-404. PMID: 29023972.
      View in: PubMed
    11. Amini A, Jones BL, Stumpf P, Leong S, Lieu CH, Weekes C, Davis SL, Messersmith WA, Purcell WT, Ghosh D, Schefter T, Goodman KA. Patterns of Care for Locally Advanced Pancreatic Adenocarcinoma Using the National Cancer Database. Pancreas. 2017 08; 46(7):904-912. PMID: 28697131.
      View in: PubMed
    12. Lutz SM, Thwing A, Schmiege S, Kroehl M, Baker CD, Starling AP, Hokanson JE, Ghosh D. Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications. BMC Bioinformatics. 2017 Jul 19; 18(1):344. PMID: 28724417.
      View in: PubMed
    13. Duex JE, Owens C, Chauca-Diaz A, Dancik GM, Vanderlinden LA, Ghosh D, Leivo MZ, Hansel DE, Theodorescu D. Nuclear CD24 Drives Tumor Growth and Is Predictive of Poor Patient Prognosis. Cancer Res. 2017 09 15; 77(18):4858-4867. PMID: 28674079.
      View in: PubMed
    14. Kim D, Volk H, Girirajan S, Pendergrass S, Hall MA, Verma SS, Schmidt RJ, Hansen RL, Ghosh D, Ludena-Rodriguez Y, Kim K, Ritchie MD, Hertz-Picciotto I, Selleck SB. The joint effect of air pollution exposure and copy number variation on risk for autism. Autism Res. 2017 Sep; 10(9):1470-1480. PMID: 28448694.
      View in: PubMed
    15. Stokes WA, Amini A, Jones BL, McDermott JD, Raben D, Ghosh D, Goddard JA, Bowles DW, Karam SD. Survival impact of induction chemotherapy in advanced head and neck cancer: A National Cancer Database analysis. Head Neck. 2017 06; 39(6):1113-1121. PMID: 28301079.
      View in: PubMed
    16. Vora A, Naik A, Lokhandwala Y, Chopra A, Varma J, Wander GS, Jaswal A, Srikanthan V, Singh B, Kahali D, Gupta A, Mantri RR, Mishra A, Pandurangi U, Ghosh D, Makkar JS, Sahu S, Radhakrishnan R. Profiling cardiac arrhythmia and heart failure patients in India: The Pan-arrhythmia and Heart Failure Observational Study. Indian Heart J. 2017 Mar - Apr; 69(2):226-239. PMID: 28460772.
      View in: PubMed
    17. Choi H, Ghosh D, Qin Z. Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies. Methods Mol Biol. 2017; 1552:135-148. PMID: 28224496.
      View in: PubMed
    18. Amini A, Waxweiler TV, Brower JV, Jones BL, McDermott JD, Raben D, Ghosh D, Bowles DW, Karam SD. Association of Adjuvant Chemoradiotherapy vs Radiotherapy Alone With Survival in Patients With Resected Major Salivary Gland Carcinoma: Data From the National Cancer Data Base. JAMA Otolaryngol Head Neck Surg. 2016 11 01; 142(11):1100-1110. PMID: 27541166.
      View in: PubMed
    19. Amini A, Jones BL, Ghosh D, Schefter TE, Goodman KA. Impact of facility volume on outcomes in patients with squamous cell carcinoma of the anal canal: Analysis of the National Cancer Data Base. Cancer. 2017 01 01; 123(2):228-236. PMID: 27571233.
      View in: PubMed
    20. Ghosh D. A modified risk set approach to biomarker evaluation studies. Stat Biosci. 2016 Oct; 8(2):395-406. PMID: 28989545.
      View in: PubMed
    21. Zhan X, Girirajan S, Zhao N, Wu MC, Ghosh D. A novel copy number variants kernel association test with application to autism spectrum disorders studies. Bioinformatics. 2016 12 01; 32(23):3603-3610. PMID: 27497442.
      View in: PubMed
    22. Traynor AJ, Aragon M, Ghosh D, Choi RS, Dingmann C, Vu Tran Z, Bucklin BA. Obstetric Anesthesia Workforce Survey: A 30-Year Update. Anesth Analg. 2016 06; 122(6):1939-46. PMID: 27088993.
      View in: PubMed
    23. Amini A, Jones BL, McDermott JD, Serracino HS, Jimeno A, Raben D, Ghosh D, Bowles DW, Karam SD. Survival outcomes with concurrent chemoradiation for elderly patients with locally advanced head and neck cancer according to the National Cancer Data Base. Cancer. 2016 05 15; 122(10):1533-43. PMID: 26969811.
      View in: PubMed
    24. Broadaway KA, Cutler DJ, Duncan R, Moore JL, Ware EB, Jhun MA, Bielak LF, Zhao W, Smith JA, Peyser PA, Kardia SLR, Ghosh D, Epstein MP. A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants. Am J Hum Genet. 2016 Mar 03; 98(3):525-540. PMID: 26942286; PMCID: PMC4800053.
    25. Zhu Y, Ghosh D, Coffman DL, Savage JS. Estimating controlled direct effects of restrictivefeeding practices in the 'Early dieting in girls' study. J R Stat Soc Ser C Appl Stat. 2016 Jan; 65(1):115-130. PMID: 27182090.
      View in: PubMed
    26. Daniels M, Frangakis C, Charu V, Ghosh D. University of Pennsylvania 7th annual conference on statistical issues in clinical trials: Current issues regarding the use of biomarkers and surrogate endpoints in clinical trials (morning panel discussion). Clin Trials. 2015 Aug; 12(4):323-32. PMID: 26062596.
      View in: PubMed
    27. Hua WY, Ghosh D. Equivalence of kernel machine regression and kernel distance covariance for multidimensional phenotype association studies. Biometrics. 2015 Sep; 71(3):812-20. PMID: 25939365.
      View in: PubMed
    28. Cho Y, Ghosh D. Weighted estimation of the accelerated failure time model in the presence of dependent censoring. PLoS One. 2015; 10(4):e0124381. PMID: 25909753; PMCID: PMC4409295.
    29. Zhan X, Patterson AD, Ghosh D. Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data. BMC Bioinformatics. 2015 Mar 11; 16:77. PMID: 25887233; PMCID: PMC4359587.
    30. Ghosh D, Zhu Y, Coffman DL. Penalized regression procedures for variable selection in the potential outcomes framework. Stat Med. 2015 May 10; 34(10):1645-58. PMID: 25628185; PMCID: PMC4390482.
    31. Ge T, Nichols TE, Ghosh D, Mormino EC, Smoller JW, Sabuncu MR. A kernel machine method for detecting effects of interaction between multidimensional variable sets: an imaging genetics application. Neuroimage. 2015 Apr 01; 109:505-514. PMID: 25600633.
      View in: PubMed
    32. Zhan X, Ghosh D. Incorporating auxiliary information for improved prediction using combination of kernel machines. Stat Methodol. 2015 Jan 01; 22:47-57. PMID: 25419198.
      View in: PubMed
    33. Almli LM, Duncan R, Feng H, Ghosh D, Binder EB, Bradley B, Ressler KJ, Conneely KN, Epstein MP. Correcting systematic inflation in genetic association tests that consider interaction effects: application to a genome-wide association study of posttraumatic stress disorder. JAMA Psychiatry. 2014 Dec 01; 71(12):1392-9. PMID: 25354142; PMCID: PMC4293022.
    34. Ghosh D, Li S. Unsupervised outlier profile analysis. Cancer Inform. 2014; 13(Suppl 4):25-33. PMID: 25452686; PMCID: PMC4218656.
    35. de Bekker C, Quevillon LE, Smith PB, Fleming KR, Ghosh D, Patterson AD, Hughes DP. Species-specific ant brain manipulation by a specialized fungal parasite. BMC Evol Biol. 2014 Aug 29; 14:166. PMID: 25085339.
      View in: PubMed
    36. Zhu Y, Coffman DL, Ghosh D. A Boosting Algorithm for Estimating Generalized Propensity Scores with Continuous Treatments. J Causal Inference. 2015 Mar 01; 3(1):25-40. PMID: 26877909.
      View in: PubMed
    37. Li Y, Ghosh D. Meta-analysis based on weighted ordered P-values for genomic data with heterogeneity. BMC Bioinformatics. 2014 Jun 28; 15:226. PMID: 24972803; PMCID: PMC4089554.
    38. Zhan X, Epstein MP, Ghosh D. An Adaptive Genetic Association Test Using Double Kernel Machines. Stat Biosci. 2015 Oct 01; 7(2):262-281. PMID: 26640602.
      View in: PubMed
    39. Hua WY, Nichols TE, Ghosh D. Multiple comparison procedures for neuroimaging genomewide association studies. Biostatistics. 2015 Jan; 16(1):17-30. PMID: 24963012.
      View in: PubMed
    40. Lee Y, Ghosh D, Zhang Y. Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells. BMC Genomics. 2014 May 12; 15:360. PMID: 24884369.
      View in: PubMed
    41. Li Y, Ghosh D. A two-step hierarchical hypothesis set testing framework, with applications to gene expression data on ordered categories. BMC Bioinformatics. 2014 Apr 14; 15:108. PMID: 24731138; PMCID: PMC4000433.
    42. Lee Y, Ghosh D, Hardison RC, Zhang Y. MRHMMs: multivariate regression hidden Markov models and the variantS. Bioinformatics. 2014 Jun 15; 30(12):1755-6. PMID: 24558116.
      View in: PubMed
    43. Teo G, Vogel C, Ghosh D, Kim S, Choi H. PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation. J Proteome Res. 2014 Jan 03; 13(1):29-37. PMID: 24229407.
      View in: PubMed
    44. Lee Y, Ghosh D, Zhang Y. Association testing to detect gene-gene interactions on sex chromosomes in trio data. Front Genet. 2013; 4:239. PMID: 24312118.
      View in: PubMed
    45. Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS. Sparsely correlated hidden Markov models with application to genome-wide location studies. Bioinformatics. 2013 Mar 01; 29(5):533-41. PMID: 23325620.
      View in: PubMed
    46. Ghosh D. Genomic outlier detection in high-throughput data analysis. Methods Mol Biol. 2013; 972:141-53. PMID: 23385536.
      View in: PubMed
    47. Ghosh D. Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Stat Appl Genet Mol Biol. 2012 Jul 26; 11(4). PMID: 22850065.
      View in: PubMed
    48. Chen W, Ghosh D, Raghunathan TE, Norkin M, Sargent DJ, Bepler G. On Bayesian methods of exploring qualitative interactions for targeted treatment. Stat Med. 2012 Dec 10; 31(28):3693-707. PMID: 22733620; PMCID: PMC3528020.
    49. Ghosh D. A causal framework for surrogate endpoints with semi-competing risks data. Stat Probab Lett. 2012 Oct; 82(11):1898-1902. PMID: 22899873.
      View in: PubMed
    50. Poisson LM, Sreekumar A, Chinnaiyan AM, Ghosh D. Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data. Genomics. 2012 May; 99(5):265-74. PMID: 22497771.
      View in: PubMed
    51. Li Y, Ghosh D. Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data. Bioinformatics. 2012 Mar 15; 28(6):807-14. PMID: 22285559.
      View in: PubMed
    52. Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res. 2012 May; 40(9):3785-99. PMID: 22262733.
      View in: PubMed
    53. Begum F, Ghosh D, Tseng GC, Feingold E. Comprehensive literature review and statistical considerations for GWAS meta-analysis. Nucleic Acids Res. 2012 May; 40(9):3777-84. PMID: 22241776.
      View in: PubMed
    54. Chang ST, Tchitchek N, Ghosh D, Benecke A, Katze MG. A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections. BMC Syst Biol. 2011 Dec 22; 5:202. PMID: 22189154.
      View in: PubMed
    55. Poisson LM, Taylor JM, Ghosh D. Integrative set enrichment testing for multiple omics platforms. BMC Bioinformatics. 2011 Nov 25; 12:459. PMID: 22118224; PMCID: PMC3329720.
    56. Mortensen AH, MacDonald JW, Ghosh D, Camper SA. Candidate genes for panhypopituitarism identified by gene expression profiling. Physiol Genomics. 2011 Oct 06; 43(19):1105-16. PMID: 21828248.
      View in: PubMed
    57. Ghosh D. Propensity score modelling in observational studies using dimension reduction methods. Stat Probab Lett. 2011 Jul 01; 81(7):813-820. PMID: 21617766.
      View in: PubMed
    58. Ghosh D, Taylor JM, Sargent DJ. Meta-analysis for surrogacy: accelerated failure time models and semicompeting risks modeling. Biometrics. 2012 Mar; 68(1):226-32. PMID: 21668903.
      View in: PubMed
    59. Ghosh D, Taylor JM, Sargent DJ. Rejoinder for "Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modelling" Biometrics. 2012 Mar; 68(1):245-247. PMID: 22547832.
      View in: PubMed
    60. Ghosh D, Elliott MR, Taylor JM. Links between analysis of surrogate endpoints and endogeneity. Stat Med. 2010 Dec 10; 29(28):2869-79. PMID: 20803482; PMCID: PMC2997195.
    61. Ghosh D, Qin ZS. Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data. Genes (Basel). 2010 Sep 27; 1(2):317-34. PMID: 24710049.
      View in: PubMed
    62. Ghosh D. Discrete nonparametric algorithms for outlier detection with genomic data. J Biopharm Stat. 2010 Mar; 20(2):193-208. PMID: 20309754; PMCID: PMC2845329.
    63. Choi H, Qin ZS, Ghosh D. A double-layered mixture model for the joint analysis of DNA copy number and gene expression data. J Comput Biol. 2010 Feb; 17(2):121-37. PMID: 20170400.
      View in: PubMed
    64. Ghosh D. Semiparametric analysis of recurrent events: artificial censoring, truncation, pairwise estimation and inference. Lifetime Data Anal. 2010 Oct; 16(4):509-24. PMID: 20063182; PMCID: PMC2939236.
    65. Ghosh D, Sabel M. Spline-based models for predictiveness curves and surfaces. Stat Interface. 2010 Jan 01; 3(1):445-454. PMID: 22003414.
      View in: PubMed
    66. Chen W, Ghosh D, Raghunathan TE, Sargent DJ. Bayesian variable selection with joint modeling of categorical and survival outcomes: an application to individualizing chemotherapy treatment in advanced colorectal cancer. Biometrics. 2009 Dec; 65(4):1030-40. PMID: 19210736; PMCID: PMC2870722.
    67. Wu J, Patwa TH, Lubman DM, Ghosh D. Identification of differentially expressed spatial clusters using humoral response microarray data. Comput Stat Data Anal. 2009 Jun 15; 53(8):3094-3102. PMID: 19759808.
      View in: PubMed
    68. Ghosh D. On assessing surrogacy in a single trial setting using a semicompeting risks paradigm. Biometrics. 2009 Jun; 65(2):521-9. PMID: 18759839; PMCID: PMC2752047.
    69. McEwen LN, Kim C, Haan MN, Ghosh D, Lantz PM, Thompson TJ, Herman WH. Are health-related quality-of-life and self-rated health associated with mortality? Insights from Translating Research Into Action for Diabetes (TRIAD). Prim Care Diabetes. 2009 Feb; 3(1):37-42. PMID: 19269911; PMCID: PMC4138696.
    70. Liu D, Ghosh D, Lin X. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics. 2008 Jun 24; 9:292. PMID: 18577223; PMCID: PMC2483287.
    71. Ghosh D, Chinnaiyan AM. Genomic outlier profile analysis: mixture models, null hypotheses, and nonparametric estimation. Biostatistics. 2009 Jan; 10(1):60-9. PMID: 18539648; PMCID: PMC2605210.
    72. Chen W, Ghosh D, Raghunathan TE, Sargent DJ. A false-discovery-rate-based loss framework for selection of interactions. Stat Med. 2008 May 20; 27(11):2004-21. PMID: 17979139.
      View in: PubMed
    73. Shen R, Ghosh D, Taylor JM. Modeling intra-tumor protein expression heterogeneity in tissue microarray experiments. Stat Med. 2008 May 20; 27(11):1944-59. PMID: 18300332; PMCID: PMC2753194.
    74. Yuan Z, Ghosh D. Combining multiple biomarker models in logistic regression. Biometrics. 2008 Jun; 64(2):431-9. PMID: 18325068.
      View in: PubMed
    75. Gu W, Choi H, Ghosh D. Global associations between copy number and transcript mRNA microarray data: an empirical study. Cancer Inform. 2008; 6:17-23. PMID: 19259399; PMCID: PMC2623285.
    76. Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP. A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet. 2008 Feb; 82(2):386-97. PMID: 18252219; PMCID: PMC2664991.
    77. Ghosh D. On the Plackett distribution with bivariate censored data. Int J Biostat. 2008; 4(1):Article 7. PMID: 22462114.
      View in: PubMed
    78. Liu D, Lin X, Ghosh D. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics. 2007 Dec; 63(4):1079-88. PMID: 18078480; PMCID: PMC2665800.
    79. Yu J, Yu J, Rhodes DR, Tomlins SA, Cao X, Chen G, Mehra R, Wang X, Ghosh D, Shah RB, Varambally S, Pienta KJ, Chinnaiyan AM. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Res. 2007 Nov 15; 67(22):10657-63. PMID: 18006806.
      View in: PubMed
    80. Choi H, Shen R, Chinnaiyan AM, Ghosh D. A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments. BMC Bioinformatics. 2007 Sep 27; 8:364. PMID: 17900369; PMCID: PMC2246152.
    81. Kim JH, Dhanasekaran SM, Mehra R, Tomlins SA, Gu W, Yu J, Kumar-Sinha C, Cao X, Dash A, Wang L, Ghosh D, Shedden K, Montie JE, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM. Integrative analysis of genomic aberrations associated with prostate cancer progression. Cancer Res. 2007 Sep 01; 67(17):8229-39. PMID: 17804737.
      View in: PubMed
    82. Ghosh D. Semiparametric inference for surrogate endpoints with bivariate censored data. Biometrics. 2008 Mar; 64(1):149-56. PMID: 17651457.
      View in: PubMed
    83. Ghosh D. Proportional hazards regression for cancer studies. Biometrics. 2008 Mar; 64(1):141-8. PMID: 17573863.
      View in: PubMed
    84. Poisson LM, Ghosh D. Statistical issues and analyses of in vivo and in vitro genomic data in order to identify clinically relevant profiles. Cancer Inform. 2007 May 10; 3:231-43. PMID: 19079768.
      View in: PubMed
    85. McEwen LN, Kim C, Karter AJ, Haan MN, Ghosh D, Lantz PM, Mangione CM, Thompson TJ, Herman WH. Risk factors for mortality among patients with diabetes: the Translating Research Into Action for Diabetes (TRIAD) Study. Diabetes Care. 2007 Jul; 30(7):1736-41. PMID: 17468353.
      View in: PubMed
    86. Chen G, Wang X, Yu J, Varambally S, Yu J, Thomas DG, Lin MY, Vishnu P, Wang Z, Wang R, Fielhauer J, Ghosh D, Giordano TJ, Giacherio D, Chang AC, Orringer MB, El-Hefnawy T, Bigbee WL, Beer DG, Chinnaiyan AM. Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma. Cancer Res. 2007 Apr 01; 67(7):3461-7. PMID: 17409457.
      View in: PubMed
    87. Shah RB, Ghosh D, Elder JT. Epidermal growth factor receptor (ErbB1) expression in prostate cancer progression: correlation with androgen independence. Prostate. 2006 Sep 15; 66(13):1437-44. PMID: 16741920.
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    88. MacDonald JW, Ghosh D. COPA--cancer outlier profile analysis. Bioinformatics. 2006 Dec 01; 22(23):2950-1. PMID: 16895932.
      View in: PubMed
    89. Ghosh D. Semi-parametric inferences for association with semi-competing risks data. Stat Med. 2006 Jun 30; 25(12):2059-70. PMID: 16196081.
      View in: PubMed
    90. Ghosh D. Modelling tumour biology-progression relationships in screening trials. Stat Med. 2006 Jun 15; 25(11):1872-84. PMID: 16220483.
      View in: PubMed
    91. Mehra R, Varambally S, Ding L, Shen R, Sabel MS, Ghosh D, Chinnaiyan AM, Kleer CG. Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. Cancer Res. 2005 Dec 15; 65(24):11259-64. PMID: 16357129.
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    92. Witkiewicz AK, Varambally S, Shen R, Mehra R, Sabel MS, Ghosh D, Chinnaiyan AM, Rubin MA, Kleer CG. Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis. Cancer Epidemiol Biomarkers Prev. 2005 Jun; 14(6):1418-23. PMID: 15941950.
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    93. Rubin MA, Bismar TA, Andrén O, Mucci L, Kim R, Shen R, Ghosh D, Wei JT, Chinnaiyan AM, Adami HO, Kantoff PW, Johansson JE. Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific death. Cancer Epidemiol Biomarkers Prev. 2005 Jun; 14(6):1424-32. PMID: 15941951.
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    94. Abecasis GR, Ghosh D, Nichols TE. Linkage disequilibrium: ancient history drives the new genetics. Hum Hered. 2005; 59(2):118-24. PMID: 15838181.
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    95. Levin AM, Ghosh D, Cho KR, Kardia SL. A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors. Bioinformatics. 2005 Jun 15; 21(12):2867-74. PMID: 15814559.
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    96. Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S. Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. BMC Bioinformatics. 2005 Feb 10; 6:26. PMID: 15705192; PMCID: PMC550659.
    97. Shah RB, Mehra R, Chinnaiyan AM, Shen R, Ghosh D, Zhou M, Macvicar GR, Varambally S, Harwood J, Bismar TA, Kim R, Rubin MA, Pienta KJ. Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program. Cancer Res. 2004 Dec 15; 64(24):9209-16. PMID: 15604294.
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    98. Ghosh D, Chinnaiyan AM. Covariate adjustment in the analysis of microarray data from clinical studies. Funct Integr Genomics. 2005 Jan; 5(1):18-27. PMID: 15378393.
      View in: PubMed
    99. Ghosh D. Nonparametric methods for analyzing replication origins in genomewide data. Funct Integr Genomics. 2005 Jan; 5(1):28-31. PMID: 15599787.
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    100. Ghosh D. Accelerated rates regression models for recurrent failure time data. Lifetime Data Anal. 2004 Sep; 10(3):247-61. PMID: 15456106.
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    101. Ghosh D. Mixture models for assessing differential expression in complex tissues using microarray data. Bioinformatics. 2004 Jul 22; 20(11):1663-9. PMID: 14988124.
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    102. Smolkin M, Ghosh D. Cluster stability scores for microarray data in cancer studies. BMC Bioinformatics. 2003 Sep 06; 4:36. PMID: 12959646; PMCID: PMC200969.
    103. Ghosh D. Goodness-of-fit methods for additive-risk models in tumorigenicity experiments. Biometrics. 2003 Sep; 59(3):721-6. PMID: 14601774.
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    104. Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics. 2003 Dec; 3(4):180-8. PMID: 12884057.
      View in: PubMed
    105. Wu JH, Haan MN, Liang J, Ghosh D, Gonzalez HM, Herman WH. Diabetes as a predictor of change in functional status among older Mexican Americans: a population-based cohort study. Diabetes Care. 2003 Feb; 26(2):314-9. PMID: 12547855.
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    106. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 2002 Aug 01; 62(15):4427-33. PMID: 12154050.
      View in: PubMed
    107. Ghosh D. Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments. Funct Integr Genomics. 2002 Aug; 2(3):92-7. PMID: 12185456.
      View in: PubMed
    108. Ghosh D, Chinnaiyan AM. Mixture modelling of gene expression data from microarray experiments. Bioinformatics. 2002 Feb; 18(2):275-86. PMID: 11847075.
      View in: PubMed
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