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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
    NSF DMS-1914937     (Debashis Ghosh)Sep 1, 2019 - Aug 31, 2022
    National Science Foundation
    New Methods in High-Dimensional Causal Inference
    Role Description: In this proposal, the PI and team will focus their research in two areas. The first will be to understand the implications of deep learning algorithms and their performance on foundational assumptions for the popular potential outcomes model. The second part of the grant will deal with developing scalable algorithms for causal effect estimation. New computationally scalable algorithms for causal effect estimation will be developed as part of this proposal.
    Role: Principal Investigator
    U01CA235488     (KECHRIS-MAYS, KATHERINA)Sep 18, 2018 - Aug 31, 2022
    NIH
    Addressing Sparsity in Metabolomics Data Analysis
    Role: Co-Principal Investigator
    U01CA235488     (Katherina Kechris-Mays)Sep 18, 2018 - Aug 31, 2022
    NIH/NCI
    Addressing Sparsity in Metabolomics Data Analysis
    Role: Principal Investigator
    R01GM117946     (EPSTEIN, MICHAEL PHILIP)Feb 1, 2016 - Dec 31, 2020
    NIH
    Statistical Tests for Mapping Genetic Determinants of Complex Traits
    Role: Co-Investigator
    T32GM102057     (CHIAROMONTE, FRANCESCA ;GIRIRAJAN, SANTHOSH ;SCHAEFFER, STEPHEN W)Jul 1, 2013 - Dec 31, 2023
    NIH
    Computation, Bioinformatics, and Statistics (CBIOS) Training Program
    Role: Co-Investigator
    NSF ABI-1262538     (Debashis Ghosh)Jul 1, 2013 - Mar 31, 2017
    National Science Foundation
    Multivariate Statistical Methods for Genomic Data Integration
    Role Description: This research focuses on multivariate methods of analysis with high-dimensional genomic data, with the goal of prioritizing the genome for further study. Two classes of problems will be studied during the course of the project. The first is Hidden Markov Models and the second is multiple testing procedures, whose use have become commonplace with genomic datasets. This project proposes novel multivariate extensions of both types of method with a goal of being characterized by sound theoretical statistical principles while simultaneously being computationally feasible on big datasets.
    Role: Principal Investigator
    R01CA129102     (TAYLOR, JEREMY M.G.)Jul 1, 2007 - Jun 30, 2022
    NIH
    Statistical Methods for Cancer Biomarkers
    Role: Co-Investigator
    R01GM072007     (GHOSH, DEBASHIS)Sep 1, 2004 - Aug 31, 2010
    NIH
    Statistical Methods for the Analysis of Functional Genomic Data
    Role: Principal 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. Yang X, Chin BB, Silosky M, Wehrend J, Litwiller DV, Ghosh D, Xing F. Learning Without Real Data Annotations to Detect Hepatic Lesions in PET Images. IEEE Trans Biomed Eng. 2024 Feb; 71(2):679-688. PMID: 37708016.
      View in: PubMed
    2. Wiley LK, Shortt JA, Roberts ER, Lowery J, Kudron E, Lin M, Mayer D, Wilson M, Brunetti TM, Chavan S, Phang TL, Pozdeyev N, Lesny J, Wicks SJ, Moore ET, Morgenstern JL, Roff AN, Shalowitz EL, Stewart A, Williams C, Edelmann MN, Hull M, Patton JT, Axell L, Ku L, Lee YM, Jirikowic J, Tanaka A, Todd E, White S, Peterson B, Hearst E, Zane R, Greene CS, Mathias R, Coors M, Taylor M, Ghosh D, Kahn MG, Brooks IM, Aquilante CL, Kao D, Rafaels N, Crooks KR, Hess S, Barnes KC, Gignoux CR. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. Am J Hum Genet. 2024 Jan 04; 111(1):11-23. PMID: 38181729.
      View in: PubMed
    3. Xing F, Silosky M, Ghosh D, Chin BB. Location-Aware Encoding for Lesion Detection in 68Ga-DOTATATE Positron Emission Tomography Images. IEEE Trans Biomed Eng. 2024 Jan; 71(1):247-257. PMID: 37471190.
      View in: PubMed
    4. Baxter RM, Wang CS, Garcia-Perez JE, Kong DS, Coleman BM, Larchenko V, Schuyler RP, Jackson C, Ghosh T, Rudra P, Paul D, Claassen M, Rochford R, Cambier JC, Ghosh D, Cooper JC, Smith MJ, Hsieh EWY. Expansion of extrafollicular B and T cell subsets in childhood-onset systemic lupus erythematosus. Front Immunol. 2023; 14:1208282. PMID: 37965329.
      View in: PubMed
    5. Carpenter CM, Gillenwater L, Bowler R, Kechris K, Ghosh D. TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes. BMC Bioinformatics. 2023 Oct 25; 24(1):398. PMID: 37880571.
      View in: PubMed
    6. Seal S, Bitler BG, Ghosh D. SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data. PLoS Genet. 2023 Oct; 19(10):e1010983. PMID: 37862362.
      View in: PubMed
    7. Xing F, Yang X, Cornish TC, Ghosh D. Learning with limited target data to detect cells in cross-modality images. Med Image Anal. 2023 12; 90:102969. PMID: 37802010.
      View in: PubMed
    8. Vu T, Seal S, Ghosh T, Ahmadian M, Wrobel J, Ghosh D. FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures. PLoS Comput Biol. 2023 Sep; 19(9):e1011490. PMID: 37756338.
      View in: PubMed
    9. Ahmadian M, Rickert C, Minic A, Wrobel J, Bitler BG, Xing F, Angelo M, Hsieh EWY, Ghosh D, Jordan KR. A platform-independent framework for phenotyping of multiplex tissue imaging data. PLoS Comput Biol. 2023 09; 19(9):e1011432. PMID: 37733781.
      View in: PubMed
    10. Vestal BE, Ghosh D, Est?par RSJ, Kechris K, Fingerlin T, Carlson NE. Quantifying the spatial clustering characteristics of radiographic emphysema explains variability in pulmonary function. Sci Rep. 2023 08 24; 13(1):13862. PMID: 37620507.
      View in: PubMed
    11. Seal S, Neelon B, Angel P, O'Quinn EC, Hill E, Vu T, Ghosh D, Mehta A, Wallace K, Alekseyenko AV. SpaceANOVA: Spatial co-occurrence analysis of cell types in multiplex imaging data using point process and functional ANOVA. bioRxiv. 2023 Jul 09. PMID: 37461579.
      View in: PubMed
    12. Lui VG, Ghosh T, Rymaszewski A, Chen S, Baxter RM, Kong DS, Ghosh D, Routes JM, Verbsky JW, Hsieh EWY. Dysregulated Lymphocyte Antigen Receptor Signaling in Common Variable Immunodeficiency with Granulomatous Lymphocytic Interstitial Lung Disease. J Clin Immunol. 2023 08; 43(6):1311-1325. PMID: 37093407.
      View in: PubMed
    13. Zhuang Y, Xing F, Ghosh D, Hobbs BD, Hersh CP, Banaei-Kashani F, Bowler RP, Kechris K. Deep learning on graphs for multi-omics classification of COPD. PLoS One. 2023; 18(4):e0284563. PMID: 37083575.
      View in: PubMed
    14. Seal S, Bitler BG, Ghosh D. SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data. bioRxiv. 2023 Mar 30. PMID: 36993287.
      View in: PubMed
    15. Prince EW, Ghosh D, G?rg C, Hankinson TC. Uncertainty-Aware Deep Learning Classification of Adamantinomatous Craniopharyngioma from Preoperative MRI. Diagnostics (Basel). 2023 Mar 16; 13(6). PMID: 36980440.
      View in: PubMed
    16. Zuo S, Josey KP, Raghavan S, Yang F, Juar?z-Colunga E, Ghosh D. Transportability Methods for Time-to-Event Outcomes: Application in Adjuvant Colon Cancer Trials. JCO Clin Cancer Inform. 2022 12; 6:e2200088. PMID: 36516368.
      View in: PubMed
    17. Ghosh D, Amini A, Jones BL, Karam SD. Population-level and individual-level explainers for propensity score matching in observational studies. Front Oncol. 2022; 12:958907. PMID: 36338745.
      View in: PubMed
    18. Sanders BE, Wolsky R, Doughty ES, Wells KL, Ghosh D, Ku L, Pressey JG, Bitler BB, Brubaker LW. Small cell carcinoma of the ovary hypercalcemic type (SCCOHT): A review and novel case with dual germline SMARCA4 and BRCA2 mutations. Gynecol Oncol Rep. 2022 Dec; 44:101077. PMID: 36249907.
      View in: PubMed
    19. Jackson CL, Frank DN, Robertson CE, Ir D, Kofonow JM, Montlha MP, Mutsaerts EAML, Nunes MC, Madhi SA, Ghosh D, Weinberg A. Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life. mBio. 2022 10 26; 13(5):e0122922. PMID: 36073815.
      View in: PubMed
    20. Seal S, Ghosh D. MIAMI: mutual information-based analysis of multiplex imaging data. Bioinformatics. 2022 08 02; 38(15):3818-3826. PMID: 35748713.
      View in: PubMed
    21. Suresh K, Severn C, Ghosh D. Survival prediction models: an introduction to discrete-time modeling. BMC Med Res Methodol. 2022 07 26; 22(1):207. PMID: 35883032.
      View in: PubMed
    22. Josey KP, Yang F, Ghosh D, Raghavan S. A calibration approach to transportability and data-fusion with observational data. Stat Med. 2022 10 15; 41(23):4511-4531. PMID: 35848098.
      View in: PubMed
    23. Severn C, Suresh K, G?rg C, Choi YS, Jain R, Ghosh D. A Pipeline for the Implementation and Visualization of Explainable Machine Learning for Medical Imaging Using Radiomics Features. Sensors (Basel). 2022 Jul 12; 22(14). PMID: 35890885.
      View in: PubMed
    24. Seal S, Wrobel J, Johnson AM, Nemenoff RA, Schenk EL, Bitler BG, Jordan KR, Ghosh D. On clustering for cell-phenotyping in multiplex immunohistochemistry (mIHC) and multiplexed ion beam imaging (MIBI) data. BMC Res Notes. 2022 Jun 20; 15(1):215. PMID: 35725622.
      View in: PubMed
    25. Ghosh D, Mastej E, Jain R, Choi YS. Causal Inference in Radiomics: Framework, Mechanisms, and Algorithms. Front Neurosci. 2022; 16:884708. PMID: 35812228.
      View in: PubMed
    26. Vu T, Wrobel J, Bitler BG, Schenk EL, Jordan KR, Ghosh D. SPF: A spatial and functional data analytic approach to cell imaging data. PLoS Comput Biol. 2022 06; 18(6):e1009486. PMID: 35704658.
      View in: PubMed
    27. Seal S, Vu T, Ghosh T, Wrobel J, Ghosh D. DenVar: density-based variation analysis of multiplex imaging data. Bioinform Adv. 2022; 2(1):vbac039. PMID: 36699398.
      View in: PubMed
    28. Dekermanjian JP, Shaddox E, Nandy D, Ghosh D, Kechris K. Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics. BMC Bioinformatics. 2022 May 16; 23(1):179. PMID: 35578165.
      View in: PubMed
    29. Edward JA, Josey K, Bahn G, Caplan L, Reusch JEB, Reaven P, Ghosh D, Raghavan S. Heterogeneous treatment effects of intensive glycemic control on major adverse cardiovascular events in the ACCORD and VADT trials: a machine-learning analysis. Cardiovasc Diabetol. 2022 04 27; 21(1):58. PMID: 35477454.
      View in: PubMed
    30. Johnson MJ, Liu C, Ghosh D, Lang N, Levin MJ, Weinberg A. Cell-Mediated Immune Responses After Administration of the Live or the Recombinant Zoster Vaccine: 5-Year Persistence. J Infect Dis. 2022 04 19; 225(8):1477-1481. PMID: 34850039.
      View in: PubMed
    31. Rudra P, Baxter R, Hsieh EWY, Ghosh D. Compositional Data Analysis using Kernels in mass cytometry data. Bioinform Adv. 2022; 2(1):vbac003. PMID: 35224501.
      View in: PubMed
    32. Zhuang Y, Xing F, Ghosh D, Banaei-Kashani F, Bowler RP, Kechris K. An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning. Front Genet. 2021; 12:760299. PMID: 35154240.
      View in: PubMed
    33. Ghosh D. Sufficient Dimension Reduction: An Information-Theoretic Viewpoint. Entropy (Basel). 2022 Jan 22; 24(2). PMID: 35205462.
      View in: PubMed
    34. Simon OB, Rojas DC, Ghosh D, Yang X, Rogers SE, Martin CS, Holden SK, Kluger BM, Buard I. Profiling Parkinson's disease cognitive phenotypes via resting-state magnetoencephalography. J Neurophysiol. 2022 01 01; 127(1):279-289. PMID: 34936515.
      View in: PubMed
    35. Bear JJ, Sargent JL, O'Neill BR, Chapman KE, Ghosh D, Kirsch HE, Tregellas JR. Spike-Associated Networks Predict Postsurgical Outcomes in Children With Refractory Epilepsy. J Clin Neurophysiol. 2023 Feb 01; 40(2):123-129. PMID: 34817446.
      View in: PubMed
    36. Konigsberg IR, Barnes B, Campbell M, Davidson E, Zhen Y, Pallisard O, Boorgula MP, Cox C, Nandy D, Seal S, Crooks K, Sticca E, Harrison GF, Hopkinson A, Vest A, Arnold CG, Kahn MG, Kao DP, Peterson BR, Wicks SJ, Ghosh D, Horvath S, Zhou W, Mathias RA, Norman PJ, Porecha R, Yang IV, Gignoux CR, Monte AA, Taye A, Barnes KC. Host methylation predicts SARS-CoV-2 infection and clinical outcome. Commun Med (Lond). 2021; 1(1):42. PMID: 35072167.
      View in: PubMed
    37. Konigsberg IR, Barnes B, Campbell M, Davidson E, Zhen Y, Pallisard O, Boorgula MP, Cox C, Nandy D, Seal S, Crooks K, Sticca E, Harrison GF, Hopkinson A, Vest A, Arnold CG, Kahn MG, Kao DP, Peterson BR, Wicks SJ, Ghosh D, Horvath S, Zhou W, Mathias RA, Norman PJ, Porecha R, Yang IV, Gignoux CR, Monte AA, Taye A, Barnes KC. Host methylation predicts SARS-CoV-2 infection and clinical outcome. Commun Med (Lond). 2021 Oct 26; 1(1):42. PMID: 36750622.
      View in: PubMed
    38. Carpenter CM, Zhang W, Gillenwater L, Severn C, Ghosh T, Bowler R, Kechris K, Ghosh D. PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes. PLoS Comput Biol. 2021 10; 17(10):e1008986. PMID: 34679079.
      View in: PubMed
    39. Simon OB, Buard I, Rojas DC, Holden SK, Kluger BM, Ghosh D. A novel approach to understanding Parkinsonian cognitive decline using minimum spanning trees, edge cutting, and magnetoencephalography. Sci Rep. 2021 10 05; 11(1):19704. PMID: 34611218.
      View in: PubMed
    40. Dekermanjian J, Labeikovsky W, Ghosh D, Kechris K. MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools. Metabolites. 2021 Oct 02; 11(10). PMID: 34677393.
      View in: PubMed
    41. Xing F, Cornish TC, Bennett TD, Ghosh D. Bidirectional Mapping-Based Domain Adaptation for Nucleus Detection in Cross-Modality Microscopy Images. IEEE Trans Med Imaging. 2021 10; 40(10):2880-2896. PMID: 33284750.
      View in: PubMed
    42. Ghosh T, Philtron D, Zhang W, Kechris K, Ghosh D. Reproducibility of mass spectrometry based metabolomics data. BMC Bioinformatics. 2021 Sep 07; 22(1):423. PMID: 34493210.
      View in: PubMed
    43. Raghavan S, Josey K, Bahn G, Reda D, Basu S, Berkowitz SA, Emanuele N, Reaven P, Ghosh D. Generalizability of heterogeneous treatment effects based on causal forests applied to two randomized clinical trials of intensive glycemic control. Ann Epidemiol. 2022 01; 65:101-108. PMID: 34280545.
      View in: PubMed
    44. Buchwald AG, Bayham J, Adams J, Bortz D, Colborn K, Zarella O, Buran M, Samet J, Ghosh D, Herlihy R, Carlton EJ. Estimating the Impact of Statewide Policies to Reduce Spread of Severe Acute Respiratory Syndrome Coronavirus 2 in Real Time, Colorado, USA. Emerg Infect Dis. 2021 09; 27(9):2312-2322. PMID: 34193334.
      View in: PubMed
    45. Josey KP, Berkowitz SA, Ghosh D, Raghavan S. Transporting experimental results with entropy balancing. Stat Med. 2021 08 30; 40(19):4310-4326. PMID: 34018204.
      View in: PubMed
    46. Sottnik JL, Vanderlinden L, Joshi M, Chauca-Diaz A, Owens C, Hansel DE, Sempeck C, Ghosh D, Theodorescu D. Androgen Receptor Regulates CD44 Expression in Bladder Cancer. Cancer Res. 2021 06 01; 81(11):2833-2846. PMID: 33687952.
      View in: PubMed
    47. Vestal BE, Carlson NE, Ghosh D. Filtering Spatial Point Patterns Using Kernel Densities. Spat Stat. 2021 Mar; 41. PMID: 33409121.
      View in: PubMed
    48. Okamato Y, Ghosh T, Okamoto T, Schuyler RP, Seifert J, Charry LL, Visser A, Feser M, Fleischer C, Pedrick C, August J, Moss L, Bemis EA, Norris JM, Kuhn KA, Demoruelle MK, Deane KD, Ghosh D, Holers VM, Hsieh EWY. Subjects at-risk for future development of rheumatoid arthritis demonstrate a PAD4-and TLR-dependent enhanced histone H3 citrullination and proinflammatory cytokine production in CD14hi monocytes. J Autoimmun. 2021 02; 117:102581. PMID: 33310262.
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    49. Czaja AS, Anderson HD, Ghosh D, Davidson J, Campbell JD, Valuck RJ. Increased Odds of Ventricular Arrhythmias Associated with Selective Serotonin Reuptake Inhibitor Use among the Pediatric and Young Adult Population: A Case-Control Study. J Pediatr. 2020 11; 226:173-178.e8. PMID: 32645405.
      View in: PubMed
    50. Zhang X, Cornish TC, Yang L, Bennett TD, Ghosh D, Xing F. Generative Adversarial Domain Adaptation for Nucleus Quantification in Images of Tissue Immunohistochemically Stained for Ki-67. JCO Clin Cancer Inform. 2020 07; 4:666-679. PMID: 32730116.
      View in: PubMed
    51. Saltzman AF, Smith DE, Gao D, Ghosh D, Amini A, Aldrink JH, Dasgupta R, Gow KW, Glick RD, Ehrlich PF, Cost NG. Reply to Letter to the Editor. J Pediatr Surg. 2020 11; 55(11):2537-2538. PMID: 32684283.
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    52. Lorberbaum DS, Kishore S, Rosselot C, Sarbaugh D, Brooks EP, Aragon E, Xuan S, Simon O, Ghosh D, Mendelsohn C, Gadue P, Sussel L. Retinoic acid signaling within pancreatic endocrine progenitors regulates mouse and human ? cell specification. Development. 2020 06 22; 147(12). PMID: 32467243.
      View in: PubMed
    53. Zhang W, Ghosh D. A general approach to sensitivity analysis for Mendelian randomization. Stat Biosci. 2021 Apr; 13(1):34-55. PMID: 33737984.
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    54. Warsavage T, Xing F, Bar?n AE, Feser WJ, Hirsch E, Miller YE, Malkoski S, Wolf HJ, Wilson DO, Ghosh D. Quantifying the incremental value of deep learning: Application to lung nodule detection. PLoS One. 2020; 15(4):e0231468. PMID: 32287288.
      View in: PubMed
    55. Czaja AS, Collins K, Valuck RJ, Anderson HD, Ghosh D, Davidson JA. Validity of administrative claims-based algorithms for ventricular arrhythmia and cardiac arrest in the pediatric population. Pharmacoepidemiol Drug Saf. 2020 11; 29(11):1499-1503. PMID: 32283564.
      View in: PubMed
    56. Tiwari P, Colborn KL, Smith DE, Xing F, Ghosh D, Rosenberg MA. Assessment of a Machine Learning Model Applied to Harmonized Electronic Health Record Data for the Prediction of Incident Atrial Fibrillation. JAMA Netw Open. 2020 01 03; 3(1):e1919396. PMID: 31951272.
      View in: PubMed
    57. Ghosh T, Zhang W, Ghosh D, Kechris K. Predictive Modeling for Metabolomics Data. Methods Mol Biol. 2020; 2104:313-336. PMID: 31953824.
      View in: PubMed
    58. Solis-Lemus CR, Fischer ST, Todor A, Liu C, Leslie EJ, Cutler DJ, Ghosh D, Epstein MP. Leveraging Family History in Case-Control Analyses of Rare Variation. Genetics. 2020 02; 214(2):295-303. PMID: 31843756.
      View in: PubMed
    59. Schuyler RP, Jackson C, Garcia-Perez JE, Baxter RM, Ogolla S, Rochford R, Ghosh D, Rudra P, Hsieh EWY. Minimizing Batch Effects in Mass Cytometry Data. Front Immunol. 2019; 10:2367. PMID: 31681275.
      View in: PubMed
    60. Xing F, Bennett T, Ghosh D. Adversarial Domain Adaptation and Pseudo-Labeling for Cross-Modality Microscopy Image Quantification. Med Image Comput Comput Assist Interv. 2019 Oct; 11764:740-749. PMID: 31825019.
      View in: PubMed
    61. Ghosh D. Wavelet-based Benjamini-Hochberg procedures for multiple testing under dependence. Math Biosci Eng. 2019 09 24; 17(1):56-72. PMID: 31731339.
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    62. Major A, Smith DE, Ghosh D, Rabinovitch R, Kamdar M. Risk and subtypes of secondary primary malignancies in diffuse large B-cell lymphoma survivors change over time based on stage at diagnosis. Cancer. 2020 01 01; 126(1):189-201. PMID: 31509235.
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    63. Anantharajan J, Zhou H, Zhang L, Hotz T, Vincent MY, Blevins MA, Jansson AE, Kuan JWL, Ng EY, Yeo YK, Baburajendran N, Lin G, Hung AW, Joy J, Patnaik S, Marugan J, Rudra P, Ghosh D, Hill J, Keller TH, Zhao R, Ford HL, Kang C. Structural and Functional Analyses of an Allosteric EYA2 Phosphatase Inhibitor That Has On-Target Effects in Human Lung Cancer Cells. Mol Cancer Ther. 2019 09; 18(9):1484-1496. PMID: 31285279.
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    64. Saltzman AF, Smith DE, Gao D, Ghosh D, Amini A, Aldrink JH, Dasgupta R, Gow KW, Glick RD, Ehrlich PF, Cost NG. How many lymph nodes are enough? Assessing the adequacy of lymph node yield for staging in favorable histology wilms tumor. J Pediatr Surg. 2019 Nov; 54(11):2331-2335. PMID: 31255328.
      View in: PubMed
    65. Wylie KP, Harris JG, Ghosh D, Olincy A, Tregellas JR. Association of Working Memory With Distributed Executive Control Networks in Schizophrenia. J Neuropsychiatry Clin Neurosci. 2019; 31(4):368-377. PMID: 31117908.
      View in: PubMed
    66. Rao S, Ghosh D, Asturias EJ, Weinberg A. What can we learn about influenza infection and vaccination from transcriptomics? Hum Vaccin Immunother. 2019; 15(11):2615-2623. PMID: 31116679.
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    67. Holleman AM, Broadaway KA, Duncan R, Todor A, Almli LM, Bradley B, Ressler KJ, Ghosh D, Mulle JG, Epstein MP. Powerful and Efficient Strategies for Genetic Association Testing of Symptom and Questionnaire Data in Psychiatric Genetic Studies. Sci Rep. 2019 05 17; 9(1):7523. PMID: 31101869.
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    68. King J, Russell S, Bennett TD, Ghosh D. Kung Faux Pandas Simplifying privacy protection. AMIA Jt Summits Transl Sci Proc. 2019; 2019:267-274. PMID: 31258979.
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    69. Jensen AM, Tregellas JR, Sutton B, Xing F, Ghosh D. Kernel machine tests of association between brain networks and phenotypes. PLoS One. 2019; 14(3):e0199340. PMID: 30897094.
      View in: PubMed
    70. Xing F, Cornish TC, Bennett T, Ghosh D, Yang L. Pixel-to-Pixel Learning With Weak Supervision for Single-Stage Nucleus Recognition in Ki67 Images. IEEE Trans Biomed Eng. 2019 11; 66(11):3088-3097. PMID: 30802845.
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    71. Russell S, Bennett TD, Ghosh D. Software engineering principles to improve quality and performance of R software. PeerJ Comput Sci. 2019; 5:e175. PMID: 33816828.
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    72. Ozdemir T, Bowers DT, Zhan X, Ghosh D, Brown JL. Identification of Key Signaling Pathways Orchestrating Substrate Topography Directed Osteogenic Differentiation Through High-Throughput siRNA Screening. Sci Rep. 2019 01 30; 9(1):1001. PMID: 30700820.
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    73. Bennett TD, Callahan TJ, Feinstein JA, Ghosh D, Lakhani SA, Spaeder MC, Szefler SJ, Kahn MG. Data Science for Child Health. J Pediatr. 2019 05; 208:12-22. PMID: 30686480.
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    74. Oliphant MUJ, Vincent MY, Galbraith MD, Pandey A, Zaberezhnyy V, Rudra P, Johnson KR, Costello JC, Ghosh D, DeGregori J, Espinosa JM, Ford HL. SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program. Cancer Res. 2019 02 15; 79(4):720-734. PMID: 30606720.
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    75. Reinhold D, Pielke-Lombardo H, Jacobson S, Ghosh D, Kechris K. Pre-analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data. Methods Mol Biol. 2019; 1978:323-340. PMID: 31119672.
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    76. Vestal BE, Carlson NE, Est?par RSJ, Fingerlin T, Ghosh D, Kechris K, Lynch D. Using a spatial point process framework to characterize lung computed tomography scans. Spat Stat. 2019 Mar; 29:243-267. PMID: 31750077.
      View in: PubMed
    77. Russell PH, Ghosh D. Radtools: R utilities for smooth navigation of medical image data. F1000Res. 2018; 7. PMID: 31131079.
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    78. Marzec L, Raghavan S, Banaei-Kashani F, Creasy S, Melanson EL, Lange L, Ghosh D, Rosenberg MA. Device-measured physical activity data for classification of patients with ventricular arrhythmia events: A pilot investigation. PLoS One. 2018; 13(10):e0206153. PMID: 30372463.
      View in: PubMed
    79. Philtron D, Lyu Y, Li Q, Ghosh D. Maximum Rank Reproducibility: A Nonparametric Approach to Assessing Reproducibility in Replicate Experiments. J Am Stat Assoc. 2018; 113(523):1028-1039. PMID: 31249430.
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    80. 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 09 17; 9(1):3830. PMID: 30224630.
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    81. Ghosh D. Relaxed covariate overlap and margin-based causal effect estimation. Stat Med. 2018 12 10; 37(28):4252-4265. PMID: 30168168.
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    82. Russell P, Fountain K, Wolverton D, Ghosh D. TCIApathfinder: An R Client for the Cancer Imaging Archive REST API. Cancer Res. 2018 08 01; 78(15):4424-4426. PMID: 29871933.
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    83. Zhu Y, Savage JS, Ghosh D. A Kernel-Based Metric for Balance Assessment. J Causal Inference. 2018 Sep; 6(2). PMID: 30498678.
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    84. 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 06 01; 128(6):2535-2550. PMID: 29757193.
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    85. 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.
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    86. Smith DE, Golden AP, Stange AW, Barker E, Mroz M, Bar?n 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 07; 61(7):592-604. PMID: 29574954.
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    87. 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.
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    88. 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 12 05; 7(1):16954. PMID: 29209073.
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    89. Zhang W, Ghosh D. On the use of kernel machines for Mendelian randomization. Quant Biol. 2017 Dec; 5(4):368-379. PMID: 30221016.
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    90. Cho Y, Hu C, Ghosh D. Covariate adjustment using propensity scores for dependent censoring problems in the accelerated failure time model. Stat Med. 2018 02 10; 37(3):390-404. PMID: 29023972.
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    91. 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.
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    92. 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.
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    93. 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.
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    94. 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.
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    95. 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.
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    96. Choi H, Ghosh D, Qin Z. Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies. Methods Mol Biol. 2017; 1552:135-148. PMID: 28224496.
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    97. 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.
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    98. 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.
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    99. Ghosh D. A modified risk set approach to biomarker evaluation studies. Stat Biosci. 2016 Oct; 8(2):395-406. PMID: 28989545.
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    100. 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.
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    101. 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.
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    102. 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.
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    103. 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.
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    104. 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 01; 65(1):115-130. PMID: 27182090.
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    105. 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.
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    106. 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.
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    107. 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.
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    108. 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.
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    109. 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.
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    110. 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.
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    111. 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.
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    112. 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.
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    113. Ghosh D, Li S. Unsupervised outlier profile analysis. Cancer Inform. 2014; 13(Suppl 4):25-33. PMID: 25452686.
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    114. 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.
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    115. 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.
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    116. Huda MM, Chowdhury R, Ghosh D, Dash AP, Bhattacharya SK, Mondal D. Visceral leishmaniasis-associated mortality in Bangladesh: a retrospective cross-sectional study. BMJ Open. 2014 Jul 22; 4(7):e005408. PMID: 25052172.
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    117. 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.
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    118. 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.
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    119. Hua WY, Nichols TE, Ghosh D. Multiple comparison procedures for neuroimaging genomewide association studies. Biostatistics. 2015 Jan; 16(1):17-30. PMID: 24963012.
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    120. 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.
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    121. 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.
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    122. 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.
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    123. Gonzalez-Fernandez F, Sung D, Haswell KM, Tsin A, Ghosh D. Thiol-dependent antioxidant activity of interphotoreceptor retinoid-binding protein. Exp Eye Res. 2014 Mar; 120:167-74. PMID: 24424263.
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    124. 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.
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    125. 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.
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    126. 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.
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    127. Ghosh D. Genomic outlier detection in high-throughput data analysis. Methods Mol Biol. 2013; 972:141-53. PMID: 23385536.
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    128. Ghosh D. Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Stat Appl Genet Mol Biol. 2012 Jul 26; 11(4). PMID: 22850065.
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    129. 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.
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    130. Ghosh D. A causal framework for surrogate endpoints with semi-competing risks data. Stat Probab Lett. 2012 Oct; 82(11):1898-1902. PMID: 22899873.
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    131. 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.
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    132. Jiang W, Ghosh D. Motion and flexibility in human cytochrome p450 aromatase. PLoS One. 2012; 7(2):e32565. PMID: 22384274.
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    133. 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.
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    134. 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.
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    135. 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.
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    136. 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.
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    137. Poisson LM, Taylor JM, Ghosh D. Integrative set enrichment testing for multiple omics platforms. BMC Bioinformatics. 2011 Nov 25; 12:459. PMID: 22118224.
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    138. 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.
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    139. Ghosh D. Propensity score modelling in observational studies using dimension reduction methods. Stat Probab Lett. 2011 Jul 01; 81(7):813-820. PMID: 21617766.
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    140. 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.
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    141. 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.
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    142. Chen F, Ding X, Ding Y, Xiang Z, Li X, Ghosh D, Schurig GG, Sriranganathan N, Boyle SM, He Y. Proinflammatory caspase-2-mediated macrophage cell death induced by a rough attenuated Brucella suis strain. Infect Immun. 2011 Jun; 79(6):2460-9. PMID: 21464087.
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    143. 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.
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    144. 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.
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    145. Ghosh D. Discrete nonparametric algorithms for outlier detection with genomic data. J Biopharm Stat. 2010 Mar; 20(2):193-208. PMID: 20309754.
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    146. 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.
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    147. 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.
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    148. Ghosh D, Sabel M. Spline-based models for predictiveness curves and surfaces. Stat Interface. 2010 Jan 01; 3(1):445-454. PMID: 22003414.
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    149. 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.
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    150. Khankal R, Chin JW, Ghosh D, Cirino PC. Transcriptional effects of CRP* expression in Escherichia coli. J Biol Eng. 2009 Aug 24; 3:13. PMID: 19703305.
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    151. Ghosh D, Chakrabarti R. Joint variable selection and classification with immunohistochemical data. Biomark Insights. 2009 Jul 22; 4:103-10. PMID: 19684846.
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    152. Gudjonsson JE, Ding J, Li X, Nair RP, Tejasvi T, Qin ZS, Ghosh D, Aphale A, Gumucio DL, Voorhees JJ, Abecasis GR, Elder JT. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J Invest Dermatol. 2009 Dec; 129(12):2795-804. PMID: 19571819.
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    153. 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.
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    154. Patwa TH, Li C, Poisson LM, Kim HY, Pal M, Ghosh D, Simeone DM, Lubman DM. The identification of phosphoglycerate kinase-1 and histone H4 autoantibodies in pancreatic cancer patient serum using a natural protein microarray. Electrophoresis. 2009 Jun; 30(12):2215-26. PMID: 19582723.
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    155. Ghosh D. On assessing surrogacy in a single trial setting using a semicompeting risks paradigm. Biometrics. 2009 Jun; 65(2):521-9. PMID: 18759839.
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    156. Choi H, Nesvizhskii AI, Ghosh D, Qin ZS. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics. 2009 Jul 15; 25(14):1715-21. PMID: 19447789.
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    157. Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA. Genetics, gene expression and bioinformatics of the pituitary gland. Horm Res. 2009 Apr; 71 Suppl 2:101-15. PMID: 19407506.
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    158. 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.
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    159. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12; 457(7231):910-4. PMID: 19212411.
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    160. Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA. Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches. Genomics. 2009 May; 93(5):449-60. PMID: 19121383.
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    161. den Hollander AI, McGee TL, Ziviello C, Banfi S, Dryja TP, Gonzalez-Fernandez F, Ghosh D, Berson EL. A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2009 Apr; 50(4):1864-72. PMID: 19074801.
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    162. Varambally S, Laxman B, Mehra R, Cao Q, Dhanasekaran SM, Tomlins SA, Granger J, Vellaichamy A, Sreekumar A, Yu J, Gu W, Shen R, Ghosh D, Wright LM, Kladney RD, Kuefer R, Rubin MA, Fimmel CJ, Chinnaiyan AM. Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer. Neoplasia. 2008 Nov; 10(11):1285-94. PMID: 18953438.
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    163. Shen R, Taylor JM, Ghosh D. Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. Bioinformatics. 2008 Dec 15; 24(24):2880-6. PMID: 18922808.
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    164. Col?n-L?pez V, Haan MN, Aiello AE, Ghosh D. The effect of age at migration on cardiovascular mortality among elderly Mexican immigrants. Ann Epidemiol. 2009 Jan; 19(1):8-14. PMID: 18922703.
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    165. Ghosh D, Poisson LM. "Omics" data and levels of evidence for biomarker discovery. Genomics. 2009 Jan; 93(1):13-6. PMID: 18723089.
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    166. Shen R, Chinnaiyan AM, Ghosh D. Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. BMC Med Genomics. 2008 Jun 27; 1:28. PMID: 18588682.
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    167. 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.
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    168. Ghosh D, Chinnaiyan AM. Genomic outlier profile analysis: mixture models, null hypotheses, and nonparametric estimation. Biostatistics. 2009 Jan; 10(1):60-9. PMID: 18539648.
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    169. 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.
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    170. 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.
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    171. Ghosh D, Banerjee M, Biswas P. Inference for constrained estimation of tumor size distributions. Biometrics. 2008 Dec; 64(4):1009-17. PMID: 18371123.
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    172. Yuan Z, Ghosh D. Combining multiple biomarker models in logistic regression. Biometrics. 2008 Jun; 64(2):431-9. PMID: 18325068.
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    173. 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.
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    174. 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.
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    175. Ghosh D. On the Plackett distribution with bivariate censored data. Int J Biostat. 2008; 4(1):Article 7. PMID: 22462114.
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    176. Yu J, Yu J, Cordero KE, Johnson MD, Ghosh D, Rae JM, Chinnaiyan AM, Lippman ME. A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival. Neoplasia. 2008 Jan; 10(1):79-88. PMID: 18231641.
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    177. Choi H, Ghosh D, Nesvizhskii AI. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res. 2008 Jan; 7(1):286-92. PMID: 18078310.
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    178. Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A. Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics. 2008 Mar; 7(3):600-11. PMID: 18077443.
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    179. 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.
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    180. 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.
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    181. Yu J, Cao Q, Mehra R, Laxman B, Yu J, Tomlins SA, Creighton CJ, Dhanasekaran SM, Shen R, Chen G, Morris DS, Marquez VE, Shah RB, Ghosh D, Varambally S, Chinnaiyan AM. Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer. Cancer Cell. 2007 Nov; 12(5):419-31. PMID: 17996646.
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    182. 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.
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    183. 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.
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    184. Ghosh D. Semiparametric inference for surrogate endpoints with bivariate censored data. Biometrics. 2008 Mar; 64(1):149-56. PMID: 17651457.
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    185. Ghosh D. Proportional hazards regression for cancer studies. Biometrics. 2008 Mar; 64(1):141-8. PMID: 17573863.
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    186. Tsai HJ, Tsai AC, Nriagu J, Ghosh D, Gong M, Sandretto A. Associations of BMI, TV-watching time, and physical activity on respiratory symptoms and asthma in 5th grade schoolchildren in Taipei, Taiwan. J Asthma. 2007 Jun; 44(5):397-401. PMID: 17613637.
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    187. 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.
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    188. Rhodes DR, Kalyana-Sundaram S, Tomlins SA, Mahavisno V, Kasper N, Varambally R, Barrette TR, Ghosh D, Varambally S, Chinnaiyan AM. Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia. 2007 May; 9(5):443-54. PMID: 17534450.
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    189. 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.
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    190. Yu J, Yu J, Almal AA, Dhanasekaran SM, Ghosh D, Worzel WP, Chinnaiyan AM. Feature selection and molecular classification of cancer using genetic programming. Neoplasia. 2007 Apr; 9(4):292-303. PMID: 17460773.
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    191. 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.
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    192. Mehra R, Tomlins SA, Shen R, Nadeem O, Wang L, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM, Shah RB. Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Mod Pathol. 2007 May; 20(5):538-44. PMID: 17334343.
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    193. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007 Feb; 9(2):166-80. PMID: 17356713.
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    194. Ghosh D, Chinnaiyan AM. Empirical Bayes identification [correction of identication] of tumor progression genes from microarray data. Biom J. 2007 Feb; 49(1):68-77. PMID: 17342950.
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    195. Slotnick MJ, Meliker JR, AvRuskin GA, Ghosh D, Nriagu JO. Toenails as a biomarker of inorganic arsenic intake from drinking water and foods. J Toxicol Environ Health A. 2007 Jan 15; 70(2):148-58. PMID: 17365576.
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    196. Ghosh D. Shrunken p-values for assessing differential expression with applications to genomic data analysis. Biometrics. 2006 Dec; 62(4):1099-106. PMID: 17156284.
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    197. Xie J, Juliao PC, Gilsdorf JR, Ghosh D, Patel M, Marrs CF. Identification of new genetic regions more prevalent in nontypeable Haemophilus influenzae otitis media strains than in throat strains. J Clin Microbiol. 2006 Dec; 44(12):4316-25. PMID: 17005745.
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    198. Chang ST, Ghosh D, Kirschner DE, Linderman JJ. Peptide length-based prediction of peptide-MHC class II binding. Bioinformatics. 2006 Nov 15; 22(22):2761-7. PMID: 17000752.
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    199. 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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    200. Shen R, Ghosh D, Chinnaiyan A, Meng Z. Eigengene-based linear discriminant model for tumor classification using gene expression microarray data. Bioinformatics. 2006 Nov 01; 22(21):2635-42. PMID: 16926220.
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    201. Ghosh D. Incorporating monotonicity into the evaluation of a biomarker. Biostatistics. 2007 Apr; 8(2):402-13. PMID: 16905591.
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    202. MacDonald JW, Ghosh D. COPA--cancer outlier profile analysis. Bioinformatics. 2006 Dec 01; 22(23):2950-1. PMID: 16895932.
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    203. Ghosh D. Semi-parametric inferences for association with semi-competing risks data. Stat Med. 2006 Jun 30; 25(12):2059-70. PMID: 16196081.
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    204. Ghosh D. Modelling tumour biology-progression relationships in screening trials. Stat Med. 2006 Jun 15; 25(11):1872-84. PMID: 16220483.
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    205. Tsai HJ, Tsai AC, Nriagu J, Ghosh D, Gong M, Sandretto A. Risk factors for respiratory symptoms and asthma in the residential environment of 5th grade schoolchildren in Taipei, Taiwan. J Asthma. 2006 Jun-Jul; 43(5):355-61. PMID: 16801139.
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    206. McEwen LN, Kim C, Haan M, Ghosh D, Lantz PM, Mangione CM, Safford MM, Marrero D, Thompson TJ, Herman WH. Diabetes reporting as a cause of death: results from the Translating Research Into Action for Diabetes (TRIAD) study. Diabetes Care. 2006 Feb; 29(2):247-53. PMID: 16443868.
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    207. 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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    208. Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell. 2005 Nov; 8(5):393-406. PMID: 16286247.
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    209. Wang X, Yu J, Sreekumar A, Varambally S, Shen R, Giacherio D, Mehra R, Montie JE, Pienta KJ, Sanda MG, Kantoff PW, Rubin MA, Wei JT, Ghosh D, Chinnaiyan AM. Autoantibody signatures in prostate cancer. N Engl J Med. 2005 Sep 22; 353(12):1224-35. PMID: 16177248.
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    210. Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. Probabilistic model of the human protein-protein interaction network. Nat Biotechnol. 2005 Aug; 23(8):951-9. PMID: 16082366.
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    211. Ghosh D, Chinnaiyan AM. Classification and selection of biomarkers in genomic data using LASSO. J Biomed Biotechnol. 2005 Jun 30; 2005(2):147-54. PMID: 16046820.
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    212. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Barrette TR, Ghosh D, Chinnaiyan AM. Mining for regulatory programs in the cancer transcriptome. Nat Genet. 2005 Jun; 37(6):579-83. PMID: 15920519.
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    213. Rubin MA, Bismar TA, Andr?n 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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    214. 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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    215. 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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    216. 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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    217. 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.
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    218. 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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    219. Shen R, Ghosh D, Chinnaiyan AM. Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. BMC Genomics. 2004 Dec 14; 5(1):94. PMID: 15598354.
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    220. 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.
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    221. 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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    222. 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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    223. Yu J, He S, Friedman JS, Akimoto M, Ghosh D, Mears AJ, Hicks D, Swaroop A. Altered expression of genes of the Bmp/Smad and Wnt/calcium signaling pathways in the cone-only Nrl-/- mouse retina, revealed by gene profiling using custom cDNA microarrays. J Biol Chem. 2004 Oct 01; 279(40):42211-20. PMID: 15292180.
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    224. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A. 2004 Jun 22; 101(25):9309-14. PMID: 15184677.
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    225. Sreekumar A, Laxman B, Rhodes DR, Bhagavathula S, Harwood J, Giacherio D, Ghosh D, Sanda MG, Rubin MA, Chinnaiyan AM. Humoral immune response to alpha-methylacyl-CoA racemase and prostate cancer. J Natl Cancer Inst. 2004 Jun 02; 96(11):834-43. PMID: 15173267.
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    226. Sen S, Burmeister M, Ghosh D. Meta-analysis of the association between a serotonin transporter promoter polymorphism (5-HTTLPR) and anxiety-related personality traits. Am J Med Genet B Neuropsychiatr Genet. 2004 May 15; 127B(1):85-9. PMID: 15108187.
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    227. Zhang L, Srinivasan U, Marrs CF, Ghosh D, Gilsdorf JR, Foxman B. Library on a slide for bacterial comparative genomics. BMC Microbiol. 2004 Mar 22; 4:12. PMID: 15035675.
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    228. 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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    229. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004 Jan-Feb; 6(1):1-6. PMID: 15068665.
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    230. Ghosh D. Penalized discriminant methods for the classification of tumors from gene expression data. Biometrics. 2003 Dec; 59(4):992-1000. PMID: 14969478.
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    231. Ghosh D, Lin DY. Semiparametric analysis of recurrent events data in the presence of dependent censoring. Biometrics. 2003 Dec; 59(4):877-85. PMID: 14969466.
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    232. Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, Ghosh D, Sewalt RG, Otte AP, Hayes DF, Sabel MS, Livant D, Weiss SJ, Rubin MA, Chinnaiyan AM. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20):11606-11. PMID: 14500907.
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    233. Smolkin M, Ghosh D. Cluster stability scores for microarray data in cancer studies. BMC Bioinformatics. 2003 Sep 06; 4:36. PMID: 12959646.
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    234. 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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    235. 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.
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    236. Wu JH, Haan MN, Liang J, Ghosh D, Gonzalez HM, Herman WH. Impact of diabetes on cognitive function among older Latinos: a population-based cohort study. J Clin Epidemiol. 2003 Jul; 56(7):686-93. PMID: 12921938.
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    237. Wu JH, Haan MN, Liang J, Ghosh D, Gonzalez HM, Herman WH. Impact of antidiabetic medications on physical and cognitive functioning of older Mexican Americans with diabetes mellitus: a population-based cohort study. Ann Epidemiol. 2003 May; 13(5):369-76. PMID: 12821276.
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    238. 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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    239. 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.
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    240. Rubin MA, Zhou M, Dhanasekaran SM, Varambally S, Barrette TR, Sanda MG, Pienta KJ, Ghosh D, Chinnaiyan AM. alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. JAMA. 2002 Apr 03; 287(13):1662-70. PMID: 11926890.
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    241. Ghosh D. Singular value decomposition regression models for classification of tumors from microarray experiments. Pac Symp Biocomput. 2002; 18-29. PMID: 11928474.
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