Debashis Ghosh

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. ncbi request reprint Singular value decomposition regression models for classification of tumors from microarray experiments
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Pac Symp Biocomput . 2002
  2. pmc Statistical issues and analyses of in vivo and in vitro genomic data in order to identify clinically relevant profiles
    Laila M Poisson
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Cancer Inform 3:231-43. 2007
  3. pmc Classification and selection of biomarkers in genomic data using LASSO
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    J Biomed Biotechnol 2005:147-54. 2005
  4. pmc Expression of LIM kinase 1 is associated with reversible G1/S phase arrest, chromosomal instability and prostate cancer
    Monica Davila
    Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida, USA
    Mol Cancer 6:40. 2007
  5. pmc Library on a slide for bacterial comparative genomics
    Lixin Zhang
    Department of Epidemiology, University of Michigan School of Public Health, 109 Observatory Street, Ann Arbor, MI48109, USA
    BMC Microbiol 4:12. 2004
  6. ncbi request reprint Mixture models for assessing differential expression in complex tissues using microarray data
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 20:1663-9. 2004
  7. ncbi request reprint Nonparametric methods for analyzing replication origins in genomewide data
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Room M4057, Ann Arbor, MI 48109 2029, USA
    Funct Integr Genomics 5:28-31. 2005
  8. ncbi request reprint Semi-parametric inferences for association with semi-competing risks data
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48105, USA
    Stat Med 25:2059-70. 2006
  9. ncbi request reprint Covariate adjustment in the analysis of microarray data from clinical studies
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, Room M4057, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Funct Integr Genomics 5:18-27. 2005
  10. ncbi request reprint Modelling tumour biology-progression relationships in screening trials
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 2029, USA
    Stat Med 25:1872-84. 2006

Collaborators

Detail Information

Publications85

  1. ncbi request reprint Singular value decomposition regression models for classification of tumors from microarray experiments
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Pac Symp Biocomput . 2002
    ..The regression parameters in the model linking the principal components with the clinical responses are then estimated using maximum likelihood. We demonstrate the application of the methodology to data from a breast cancer study...
  2. pmc Statistical issues and analyses of in vivo and in vitro genomic data in order to identify clinically relevant profiles
    Laila M Poisson
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Cancer Inform 3:231-43. 2007
    ..This method is demonstrated using the in vitro signature of Core Serum Response developed by Chang et al. (PLoS Biology, 2004)...
  3. pmc Classification and selection of biomarkers in genomic data using LASSO
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    J Biomed Biotechnol 2005:147-54. 2005
    ..An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study...
  4. pmc Expression of LIM kinase 1 is associated with reversible G1/S phase arrest, chromosomal instability and prostate cancer
    Monica Davila
    Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida, USA
    Mol Cancer 6:40. 2007
    ..In this study, we investigated the effects of ectopic expression of LIMK1 on cellular morphology, cell cycle progression and expression profile of LIMK1 in prostate tumors...
  5. pmc Library on a slide for bacterial comparative genomics
    Lixin Zhang
    Department of Epidemiology, University of Michigan School of Public Health, 109 Observatory Street, Ann Arbor, MI48109, USA
    BMC Microbiol 4:12. 2004
    ....
  6. ncbi request reprint Mixture models for assessing differential expression in complex tissues using microarray data
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 20:1663-9. 2004
    ..Much of the methodology developed for assessing differential expression with microarray data has assumed that tissue samples are homogeneous...
  7. ncbi request reprint Nonparametric methods for analyzing replication origins in genomewide data
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Room M4057, Ann Arbor, MI 48109 2029, USA
    Funct Integr Genomics 5:28-31. 2005
    ..In this article, we analyze data from a recent yeast study in which candidate replication origins were profiled using cDNA microarrays to test this hypothesis. We find no evidence for such clustering...
  8. ncbi request reprint Semi-parametric inferences for association with semi-competing risks data
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48105, USA
    Stat Med 25:2059-70. 2006
    ..The finite-sample properties of the proposed methodology are assessed using simulation studies, and they are applied to data from a leukaemia transplantation study...
  9. ncbi request reprint Covariate adjustment in the analysis of microarray data from clinical studies
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, Room M4057, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Funct Integr Genomics 5:18-27. 2005
    ..The ideas are illustrated using data from a prostate cancer molecular profiling study...
  10. ncbi request reprint Modelling tumour biology-progression relationships in screening trials
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 2029, USA
    Stat Med 25:1872-84. 2006
    ..Asymptotic properties of these estimators are provided. The proposed methodology is applied to data from a screening study in lung cancer...
  11. ncbi request reprint Incorporating monotonicity into the evaluation of a biomarker
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48105, USA
    Biostatistics 8:402-13. 2007
    ..We apply the various methodologies to data from a prostate cancer study involving a serum biomarker...
  12. ncbi request reprint Shrunken p-values for assessing differential expression with applications to genomic data analysis
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109 2029, USA
    Biometrics 62:1099-106. 2006
    ..Some theoretical results are outlined. The proposed methodology is illustrated using simulation studies and with application to data from a prostate cancer gene expression profiling study...
  13. ncbi request reprint Penalized discriminant methods for the classification of tumors from gene expression data
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48105, USA
    Biometrics 59:992-1000. 2003
    ..We also develop a procedure for ranking genes based on the fitted regression models. The proposed methodologies are applied to two microarray studies in cancer...
  14. ncbi request reprint Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Funct Integr Genomics 3:180-8. 2003
    ..In addition, we develop a simple approach for assessing differential expression using the LASSO method. A combination of the results and the pathway databases are then used to generate candidate biological pathways for cancer...
  15. ncbi request reprint Mixture modelling of gene expression data from microarray experiments
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Room M4057, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 18:275-86. 2002
    ..Within this framework, we present novel algorithms for clustering genes and samples. One of the byproducts of our method is a probabilistic measure for the number of true clusters in the data...
  16. ncbi request reprint Semiparametric inference for surrogate endpoints with bivariate censored data
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48105, USA
    Biometrics 64:149-56. 2008
    ..The finite-sample properties of the estimation methodology are assessed using simulation studies, and the proposed procedures are applied to data from an acute myelogenous leukemia clinical trial...
  17. ncbi request reprint Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments
    Debashis Ghosh
    Department of Biostatistics, School of Public Health, University of Michigan, 1420 Washington Heights, Room M4057, Ann Arbor 48109 2029, USA
    Funct Integr Genomics 2:92-7. 2002
    ..We consider use of this method both when there are replicates and when no replicates exist. The proposed methods are illustrated with an application to two datasets: one involving a human foreskin study, the other involving yeast...
  18. ncbi request reprint Proportional hazards regression for cancer studies
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Biometrics 64:141-8. 2008
    ..Asymptotic results for the regression methodology are provided. The methods are illustrated by application to data from an observational cancer study as well as to simulated data...
  19. ncbi request reprint Semiparametric analysis of recurrent events data in the presence of dependent censoring
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan, USA
    Biometrics 59:877-85. 2003
    ..The finite-sample behavior of the new inference procedures is evaluated through simulation studies. An application to recurrent hospitalization data taken from a study of intravenous drug users is provided...
  20. ncbi request reprint Empirical Bayes identification [correction of identication] of tumor progression genes from microarray data
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109 2029, USA
    Biom J 49:68-77. 2007
    ..The relationship between the proposed method with the false discovery rate is studied. The proposed methods are applied to data from a prostate cancer microarray study...
  21. ncbi request reprint Goodness-of-fit methods for additive-risk models in tumorigenicity experiments
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109 2029, USA
    Biometrics 59:721-6. 2003
    ..The finite-sample properties of the proposed methodology are examined through numerical studies. The methods are then illustrated with data from a tumorigenicity experiment...
  22. ncbi request reprint A polycomb repression signature in metastatic prostate cancer predicts cancer outcome
    Jindan Yu
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
    Cancer Res 67:10657-63. 2007
    ..Therefore, PcG proteins play a central role in the epigenetic silencing of target genes and functionally link stem cells, metastasis, and cancer survival...
  23. pmc Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer
    Sooryanarayana Varambally
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Neoplasia 10:1285-94. 2008
    ..0009) versus 0.495 for serum PSA (P = .902). Our data indicating the up-regulation of GOLM1 expression and its appearance in patients' urine suggest GOLM1 as a potential novel biomarker for clinically localized prostate cancer...
  24. ncbi request reprint Probabilistic model of the human protein-protein interaction network
    Daniel R Rhodes
    Bioinformatics Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Nat Biotechnol 23:951-9. 2005
    ..This integrative analysis provides a comprehensive framework for exploring the human protein interaction network...
  25. ncbi request reprint Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer
    Jindan Yu
    Department of Pathology, Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Cancer Cell 12:419-31. 2007
    ..Taken together, we demonstrate the power of integrating multiple diverse genomic data to decipher targets of disease-related genes...
  26. pmc Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 0940, USA
    Neoplasia 9:166-80. 2007
    ..Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org...
  27. ncbi request reprint Autoantibody signatures in prostate cancer
    Xiaoju Wang
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    N Engl J Med 353:1224-35. 2005
    ..New biomarkers, such as autoantibody signatures, may improve the early detection of prostate cancer...
  28. pmc Molecular concepts analysis links tumors, pathways, mechanisms, and drugs
    Daniel R Rhodes
    Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Neoplasia 9:443-54. 2007
    ..We demonstrate the utility of the approach by highlighting molecular concepts analyses of Myc pathway activation, breast cancer relapse, and retinoic acid treatment...
  29. ncbi request reprint Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression
    Sooryanarayana Varambally
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Cancer Cell 8:393-406. 2005
    ....
  30. ncbi request reprint Integrative analysis of genomic aberrations associated with prostate cancer progression
    Jung H Kim
    Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Program of Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 0940, USA
    Cancer Res 67:8229-39. 2007
    ..Integrative analysis with matched mRNA profiles identified genetic alterations in several proposed candidate genes implicated in prostate cancer progression...
  31. ncbi request reprint The polycomb group protein EZH2 is involved in progression of prostate cancer
    Sooryanarayana Varambally
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Nature 419:624-9. 2002
    ..Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal progression...
  32. ncbi request reprint Eigengene-based linear discriminant model for tumor classification using gene expression microarray data
    Ronglai Shen
    Department of Biostatistics, University of Michigan Ann Arbor, MI 48109 0602, USA
    Bioinformatics 22:2635-42. 2006
    ..The univariate statistics summarize gene expression profiles outside of the gene co-regulation network context, leading to redundant information being included in the selection procedure...
  33. pmc Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, 48109, USA
    Proc Natl Acad Sci U S A 101:9309-14. 2004
    ..Finally, we validated these transcriptional profiles on independent data sets...
  34. pmc Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data
    Kerby Shedden
    Department of Statistics, University of Michigan, Ann Arbor, Michigan, USA
    BMC Bioinformatics 6:26. 2005
    ....
  35. pmc Candidate genes for panhypopituitarism identified by gene expression profiling
    Amanda H Mortensen
    Department of Human Genetics, Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 5618, USA
    Physiol Genomics 43:1105-16. 2011
    ....
  36. pmc Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data
    Ronglai Shen
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Genomics 5:94. 2004
    ..With the accumulating amount of microarray data, one of the most intriguing yet challenging tasks is to develop robust statistical models to integrate the findings...
  37. pmc Feature selection and molecular classification of cancer using genetic programming
    Jianjun Yu
    Bioinformatics Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Neoplasia 9:292-303. 2007
    ..Taken together, our results demonstrate that GP may be valuable for generating effective classifiers containing a practical set of genes for diagnostic/prognostic cancer classification...
  38. pmc Genetics, gene expression and bioinformatics of the pituitary gland
    Shannon W Davis
    University of Michigan, Ann Arbor, MI 48109 0618, USA
    Horm Res 71:101-15. 2009
    ..This approach holds promise for the identification of relevant pathways and candidate genes as risk factors for adenoma formation, understanding mechanisms of progression, and identifying drug targets and clinically relevant biomarkers...
  39. ncbi request reprint Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis
    Rohit Mehra
    Department of Pathology, University of Michigan Medical School, Ann Arbor, 48109, USA
    Cancer Res 65:11259-64. 2005
    ..Our data suggest that immunohistochemical analysis of GATA3 may be the basis for a new clinically applicable test to predict tumor recurrence early in the progression of breast cancer...
  40. ncbi request reprint Mining for regulatory programs in the cancer transcriptome
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Nat Genet 37:579-83. 2005
    ..These results suggest that alterations in pathways activating these transcription factors may be responsible for the observed gene deregulation and cancer pathogenesis...
  41. pmc The identification of phosphoglycerate kinase-1 and histone H4 autoantibodies in pancreatic cancer patient serum using a natural protein microarray
    Tasneem H Patwa
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 0656, USA
    Electrophoresis 30:2215-26. 2009
    ..This work demonstrates the use of natural protein arrays to study the humoral response as a means to search for the potential markers of cancer in serum...
  42. ncbi request reprint Humoral immune response to alpha-methylacyl-CoA racemase and prostate cancer
    Arun Sreekumar
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 0602, USA
    J Natl Cancer Inst 96:834-43. 2004
    ..However, attempts to detect AMACR in circulation have not been successful. Hence, we determined whether an immune response to AMACR could be used as a serum biomarker for prostate cancer...
  43. ncbi request reprint Humoral response profiling reveals pathways to prostate cancer progression
    Barry S Taylor
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Mol Cell Proteomics 7:600-11. 2008
    ..Thus, in addition to functioning as markers in prostate cancer detection, humoral response profiles can serve as powerful tools revealing pathway dysregulation that might otherwise be suppressed by the complexity of the cancer proteome...
  44. pmc Are health-related quality-of-life and self-rated health associated with mortality? Insights from Translating Research Into Action for Diabetes (TRIAD)
    Laura N McEwen
    Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
    Prim Care Diabetes 3:37-42. 2009
    ..To determine if health-related quality-of-life and self-rated health are associated with mortality in persons with diabetes...
  45. pmc Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
    Arun Sreekumar
    The Michigan Center for Translational Pathology, Ann Arbor, USA
    Nature 457:910-4. 2009
    ..Here, by profiling the metabolomic alterations of prostate cancer progression, we reveal sarcosine as a potentially important metabolic intermediary of cancer cell invasion and aggressivity...
  46. ncbi request reprint Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer
    Rohit Mehra
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Mod Pathol 20:538-44. 2007
    ....
  47. ncbi request reprint Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma
    Guoan Chen
    Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
    Cancer Res 67:3461-7. 2007
    ..These studies indicate that autoantibody profiles, as well as individual candidates, may be useful for the noninvasive detection of lung adenocarcinoma...
  48. ncbi request reprint Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program
    Rajal B Shah
    Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
    Cancer Res 64:9209-16. 2004
    ..An appreciation of this heterogeneity is critical to evaluating diagnostic and prognostic biomarkers as well as to designing therapeutic targets for advanced disease...
  49. ncbi request reprint Impact of antidiabetic medications on physical and cognitive functioning of older Mexican Americans with diabetes mellitus: a population-based cohort study
    Jasmanda H Wu
    University of Michigan, School of Public Health, Epidemiology, Ann Arbor, MI 48109, USA
    Ann Epidemiol 13:369-76. 2003
    ..The current study was designed to evaluate the utility of antidiabetic medications in affecting changes in physical and cognitive functioning among older Mexican Americans with diabetes over a 2-year period...
  50. pmc Cluster stability scores for microarray data in cancer studies
    Mark Smolkin
    Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
    BMC Bioinformatics 4:36. 2003
    ..While most work has focused on estimating the number of clusters in a dataset, the question of stability of individual-level clusters has not been addressed...
  51. ncbi request reprint COPA--cancer outlier profile analysis
    James W MacDonald
    University of Michigan Cancer Center, Ann Arbor, MI, USA
    Bioinformatics 22:2950-1. 2006
    ..We have implemented this method, termed Cancer Outlier Profile Analysis (COPA) in an R package (that we call the copa package), and show its applicability on a publicly available dataset...
  52. ncbi request reprint Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Cancer Res 62:4427-33. 2002
    ..Beyond the specific implications for prostate cancer, this work establishes a much-needed model for the evaluation, cross-validation, and comparison of multiple cancer profiling studies...
  53. ncbi request reprint Risk factors for mortality among patients with diabetes: the Translating Research Into Action for Diabetes (TRIAD) Study
    Laura N McEwen
    Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
    Diabetes Care 30:1736-41. 2007
    ..We sought to examine demographic, socioeconomic, and biological predictors of all-cause, cardiovascular, and noncardiovascular mortality in patients with diabetes...
  54. pmc A double-layered mixture model for the joint analysis of DNA copy number and gene expression data
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
    J Comput Biol 17:121-37. 2010
    ....
  55. ncbi request reprint A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors
    Albert M Levin
    Department of Epidemiology, University of Michigan, Ann Arbor, MI 48104 3028, USA
    Bioinformatics 21:2867-74. 2005
    ..However, currently available methods fail to account for variation in the distance between genes, gene density and genomic features (e.g. GC content) in identifying increased or decreased chromosomal regions of gene expression...
  56. pmc ONCOMINE: a cancer microarray database and integrated data-mining platform
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Neoplasia 6:1-6. 2004
    ..Furthermore, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-drug target pairs to facilitate the discovery of novel biomarkers and therapeutic targets...
  57. pmc Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin
    Johann E Gudjonsson
    Department of Dermatology, University of Michigan, 1910 Taubman Center, Ann Arbor, Michigan 48109, USA
    J Invest Dermatol 129:2795-804. 2009
    ..Taken together, our results identify a "pre-psoriatic" gene expression signature, suggesting decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin...
  58. ncbi request reprint Epidermal growth factor receptor (ErbB1) expression in prostate cancer progression: correlation with androgen independence
    Rajal B Shah
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109 0932, USA
    Prostate 66:1437-44. 2006
    ..The role of the epidermal growth factor receptor (ErbB1) in the progression of prostate cancer is incompletely understood...
  59. ncbi request reprint Impact of diabetes on cognitive function among older Latinos: a population-based cohort study
    Jasmanda H Wu
    University of Michigan, School of Public Health, Department of Epidemiology, 611 Church St, Ann Arbor, MI 48104, USA
    J Clin Epidemiol 56:686-93. 2003
    ..Type 2 diabetes, which is highly prevalent in older Mexican Americans, may influence cognitive functioning. We examined the association of diabetes with decline in global cognitive function and memory function over a 2-year period...
  60. pmc Identification of new genetic regions more prevalent in nontypeable Haemophilus influenzae otitis media strains than in throat strains
    Jingping Xie
    Department of Epidemiology, University of Michigan School of Public Health, 109 Observatory Street, Ann Arbor, MI 48109 2029, USA
    J Clin Microbiol 44:4316-25. 2006
    ..Classification tree analysis of lic2B, hmwA, and the nine new potential otitis media virulence genes revealed two H. influenzae pathotypes associated with otitis media...
  61. pmc Comprehensive literature review and statistical considerations for microarray meta-analysis
    George C Tseng
    Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
    Nucleic Acids Res 40:3785-99. 2012
    ..Statistical considerations of such an analysis are further scrutinized and illustrated by a case study. Finally, several open questions are listed and discussed...
  62. pmc EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells
    Celina G Kleer
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 100:11606-11. 2003
    ..This study provides compelling evidence for a functional link between dysregulated cellular memory, transcriptional repression, and neoplastic transformation...
  63. pmc Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:1715-21. 2009
    ..Therefore, it is of interest to see whether the two data sources can be combined to enhance the detection of TFBS...
  64. pmc Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches
    Michelle L Brinkmeier
    Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109 5618, USA
    Genomics 93:449-60. 2009
    ..These genes are exciting candidates for regulators of pituitary development and function...
  65. ncbi request reprint alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer
    Mark A Rubin
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 0602, USA
    JAMA 287:1662-70. 2002
    ..Molecular profiling of prostate cancer has led to the identification of candidate biomarkers and regulatory genes. Discoveries from these genome-scale approaches may have applicability in the analysis of diagnostic prostate specimens...
  66. ncbi request reprint Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling
    Hyungwon Choi
    Department of Pathology and Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
    J Proteome Res 7:286-92. 2008
    ..The statistical approaches presented here require that the data set contain a sufficient number of decoy (known to be incorrect) peptide identifications, which can be obtained using the target-decoy database search strategy...
  67. ncbi request reprint Accelerated rates regression models for recurrent failure time data
    Debashis Ghosh
    Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Lifetime Data Anal 10:247-61. 2004
    ..The finite-sample behavior of the proposed methods is examined in simulation studies, and data from a chronic granulomatous disease study are used to illustrate the methodology...
  68. ncbi request reprint Toenails as a biomarker of inorganic arsenic intake from drinking water and foods
    Melissa J Slotnick
    Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
    J Toxicol Environ Health A 70:148-58. 2007
    ....
  69. ncbi request reprint Meta-analysis of the association between a serotonin transporter promoter polymorphism (5-HTTLPR) and anxiety-related personality traits
    Srijan Sen
    Neuroscience Program, University of Michigan, Ann Arbor, Michigan 48109, USA
    Am J Med Genet B Neuropsychiatr Genet 127:85-9. 2004
    ....
  70. pmc A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments
    Hyungwon Choi
    Department of Statistics and Huck Institute for Life Sciences, Penn State University, University Park, PA, USA
    BMC Bioinformatics 8:364. 2007
    ..With the explosion in data generated using microarray technology by different investigators working on similar experiments, it is of interest to combine results across multiple studies...
  71. ncbi request reprint Linkage disequilibrium: ancient history drives the new genetics
    Goncalo R Abecasis
    Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
    Hum Hered 59:118-24. 2005
    ..Finally, we highlight the importance of using appropriate statistical procedures, such as the false discovery rate, to maximize the chances of success in large scale association studies...
  72. pmc Proinflammatory caspase-2-mediated macrophage cell death induced by a rough attenuated Brucella suis strain
    Fang Chen
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Infect Immun 79:2460-9. 2011
    ..This unique cell death differs from apoptosis, which is not proinflammatory. It is also different from classical pyroptosis, which is caspase-1 mediated...
  73. ncbi request reprint Diabetes reporting as a cause of death: results from the Translating Research Into Action for Diabetes (TRIAD) study
    Laura N McEwen
    Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
    Diabetes Care 29:247-53. 2006
    ..To determine the frequency of reporting of diabetes on death certificates of decedents with known diabetes, define factors associated with reporting of diabetes, and describe trends in reporting over time...
  74. ncbi request reprint 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
    Jindan Yu
    Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan 48015, USA
    J Biol Chem 279:42211-20. 2004
    ..We hypothesize that Bmp/Smad and Wnt/Ca(2+) pathways participate in cell-cell communication in the mature retina, and expression changes observed in the Nrl(-/-) retina reflect their biased utilization in rod versus cone homeostasis...
  75. ncbi request reprint Diabetes as a predictor of change in functional status among older Mexican Americans: a population-based cohort study
    Jasmanda H Wu
    Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor 48109, USA
    Diabetes Care 26:314-9. 2003
    ..This study was designed to examine the impact of diabetes on change in self-reported functional status over a 2-year period among older Mexican Americans with diabetes...
  76. ncbi request reprint Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis
    Agnieszka K Witkiewicz
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Cancer Epidemiol Biomarkers Prev 14:1418-23. 2005
    ..Quantitative image analysis is a novel way to accurately and reproducibly evaluate immunohistochemistry in breast tissue samples using high-density tissue microarrays...
  77. ncbi request reprint Analysis of the 2.0 A crystal structure of the protein-DNA complex of the human PDEF Ets domain bound to the prostate specific antigen regulatory site
    Yangzhou Wang
    Hauptman Woodward Medical Institute, 73 High Street, Buffalo, New York 14203, USA
    Biochemistry 44:7095-106. 2005
    ..Collectively, the common and unique interactions with both the DNA bases and the backbone phosphates lead to substrate specificity and individual preference for certain DNA sites...
  78. ncbi request reprint Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific death
    Mark A Rubin
    Department of Pathology Amory 3 195, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, Massachusetts 02115, USA
    Cancer Epidemiol Biomarkers Prev 14:1424-32. 2005
    ..This is the first study to show that AMACR expression is significantly associated with prostate cancer progression and suggests that not all surrogate end points may be optimal to define biomarkers of aggressive prostate cancer...
  79. pmc Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
    Dawei Liu
    Center for Statistical Sciences, Brown University, Providence, RI 02912, USA
    BMC Bioinformatics 9:292. 2008
    ..The kernel machine method provides a convenient, powerful and unified method for multi-dimensional parametric and nonparametric modeling of the pathway effect...
  80. doi request reprint Combining multiple biomarker models in logistic regression
    Zheng Yuan
    Eli Lilly and Company, Indianapolis, Indiana 46285, USA
    Biometrics 64:431-9. 2008
    ..Simulation studies are performed to assess the finite-sample properties of the proposed model-combining method. It is illustrated with an application to data from an immunohistochemical study in prostate cancer...
  81. pmc Modeling intra-tumor protein expression heterogeneity in tissue microarray experiments
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 307 East 63rd Street, New York, NY 10065, U S A
    Stat Med 27:1944-59. 2008
    ..A general advice is to use the joint model inference whenever results differ between the two-stage methods and the joint analysis...
  82. pmc A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival
    Jianjun Yu
    Bioinformatigram, The University of of Michigan Medical Center, Ann Arbor, MI 48109 USA
    Neoplasia 10:79-88. 2008
    ..Taken together, these data demonstrate the power of using cell culture systems to screen for robust gene signatures of clinical relevance...
  83. pmc Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models
    Dawei Liu
    Center for Statistical Sciences, Brown University, Providence, Rhode Island 02912, USA
    Biometrics 63:1079-88. 2007
    ..A score test is developed to test for the genetic pathway effect. Model/variable selection within the LSKM framework is discussed. The methods are illustrated using a prostate cancer data set and evaluated using simulations...
  84. ncbi request reprint Peptide length-based prediction of peptide-MHC class II binding
    Stewart T Chang
    Program in Bioinformatics, University of Michigan Ann Arbor, MI, USA
    Bioinformatics 22:2761-7. 2006
    ..We investigate whether representing one of these differences, the greater range of peptide lengths binding MHC class II, improves the performance of these algorithms...
  85. ncbi request reprint A false-discovery-rate-based loss framework for selection of interactions
    Wei Chen
    Karmanos Cancer Institute, 4160 John R, Detroit, MI 48201, U S A
    Stat Med 27:2004-21. 2008
    ..Methods are illustrated on data from a colorectal cancer study assessing the chemotherapy treatments and data from a diffuse large-B-cell lymphoma study assessing the prognostic effect of gene expressions...