Microarray


&
Data


Analysis

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PREPRINT, UNPUBLISHED DOCUMENTS, THESIS

  1. Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Tomas Vinar
    "Optimal arrangement of leaves in the tree representing hierarchical clustering of gene expression data",
    preprint #14 (Computer Science Dept, Univ Waterloo, April 2001)
    [ PDF]

  2. Dieter Beule, Johannes Schuchhardt, Hanspeter Herzel,
    "Clustering gene expression time series",
    preprint.

  3. David R Bickel
    "Robust cluster analysis of DNA microarray data: An application of nonparametric correlation dissimilarity",
    2001 Proceedings of the Joint Statistical Meetings of the American Statistical Association (Biometrics Section).

  4. Sven Bilke
    "Shuffling yeast gene expression data",
    LANL e-print physics/0006050

  5. BM Bolstad, RA Irizarry, M Astrand, TP Speed,
    "A comparison of normalization methods for high density oligonucleotide array data based on bias and variance",
    submitted.

  6. Per Broberg
    "Ranking genes with respect to differential expression",
    Genome Biology, deposited research article.
    http://genomebiology.com/2002/3/9/preprint/0007

  7. S Busygin, G Jacobsen, E Krämer
    "Double conjugated clustering applied to Leukemia microarray data", Contentsoft preprint.
    see also: "Double conjugated clustering and its applicability to node-driven algorithms", Contentsoft preprint.

  8. Viann Chan, Nick Hontzeas, Vincent Park,
    "Gene expression",
    preprint (Univ Warterloo).
    [ PDF]

  9. JA Correa, S Dudoit, DR Goldstein,
    "Multiple testing in the survival analysis of microarray data",
    preprint.

  10. X Cui, MK Kerr, GA Churchill,
    "Data transformation for cDNA microarray data",
    preprint.

  11. S Datta , J Arnold,
    "Statistical techniques for microarray data: a partial overview",
    submitted.

  12. S Datta , S Datta,
    "Comparisons of statistical clustering techniques for microarray gene expression data: A case study",
    submitted.

  13. Marcel Dettling, Peter Buhlmann
    "How to use boosting for tumor classification with gene expression data",
    preprint (ETH Zurich, 2002).

  14. Marcel Dettling, Peter Buhlmann
    "Supervised clustering of genes",
    preprint (ETH Zurich, 2001).

  15. JM Deutsch,
    "Algorithm for finding optimal gene sets in microarray prediction",
    arXiv preprint.
    [ abstract]

  16. CHQ Ding ,
    "Unsupervised feature selection in geneexpression analysis: bootstrap via two-way ordering",
    LBNL Tech Report 50006 (Jan 2002).

  17. KA Do, GJ McLachlan, RW Bean, S Wen
    "A comparison of two methods of clustering gene microarray data",
    Technical Report, Centre for Statistics, University of Queensland.

  18. Eytan Domany
    "Cluster analysis of gene expression data",
    arxiv preprint, physics/0206056.
    [abstract]

  19. RO Dror,
    "Noise models in gene array analysis",
    Area exam report, MIT Department of Electrical Engineering and Computer Science (2001).
    [ PDF]

  20. Sandrine Dudoit, J Fridlyand,
    "Bagging to improve the accuracy of a clustering procedure",
    preprint #600 (Statistics Dept, UC Berkeley).

  21. B Durbin, J Hardin, D Hawkins, DM Rocke,
    "A variance-stabilizing transformation for gene expression microarray data",
    preprint.

  22. Bradley Efron, Robert Tibshirani, John D Storey, Virginia Tusher
    "Empirical Bayes analysis of a microarray experiment",
    preprint #11B/216 (Dept Statistics, Stanford Univ, May 2001).

  23. Bradley Efron, Robert Tibshirani, Virginia Goss, Gilbert Chu,
    "Microarrays and their use in a comparative experiment",
    preprint #37B/213 (Dept Statistics, Stanford Univ, Nov 2000).

  24. S Draghici, O Kulaeva, A Petrov, B Hoff, A Kuklin, S Shams, M Tainsky ,
    "Computational methods for the selection of differentially regulated genes in cell immortalization",
    submitted.

  25. Yevgeniya Jane M Fridlyand,
    Resampling Methods for Variable Selection and Classification: Applications to Genomics
    Ph.D Thesis (2001), Department of Statistics, UC Berkeley.

  26. Sue C Geller, Jeff P Gregg, Paul Hagerman, David M Rocke,
    "Transformation and normalization of oligonucleotide microarray data",
    preprint.
    [PDF]

  27. D Ghosh,
    "Penalized regression models for the classification of tumors from gene expression data",
    submitted.

  28. D Ghosh,
    "Finding cancer subtypes in microarray data using random projections",
    submitted. D Ghosh, TR Barrette, D Rhodes, AM Chinnaiyan,
    "Statistical issues and methods for high-throughput cross-validation of microarray data, with applications to prostate cancer",
    preprint.

  29. AJ Hartemink, DK Gifford, TS Jaakkola, RA Young,
    "Maximum likelihood estimation of optimal scaling factors for expression array normalization",
    MIT preprint.

  30. Andrew D Keller, Michel Schummer, Walter L Ruzzo, Lee Hood,
    "Bayesian classification of DNA array expression data",
    preprint #08-01 (Computer Science and Engineering, Univ Washington, Aug 2000).
    [ PDF]

  31. CM Kendziorski, H Lan, AD Attie,
    "The efficiency of mRNA pooling in microarray experiments",
    preprint (Technical Report #168, Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison).

  32. CM Kendziorski, MA Newton, H Lan, MN Gould,
    "On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles",
    preprint (Technical Report #166, Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison).

  33. Michael LeBlanc, Charles Kooperberg, Tom Grogan, Tom Miller,
    "Directed indices for exploring gene expression data",
    preprint (Fred Hutchinson Cancer Research Center)

  34. L Lazzeroni, Art Owen,
    "Plaid models for gene expression data",
    preprint #211 (Dept Statistics, Stanford Univ, June 2000).
    [ PDF or Postscript ]

  35. William J Lemon, Jeffrey JT Palatini, Ralf Krahe, Fred A Wright
    "Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays", submitted.

  36. H Li, C Zhang,
    "A mixture Rasch model for microarray gene expression data", submitted.

  37. Yi Lin, Samuel T Nadler, Alan D Attie, Brian S Yandell,
    "Mining for low-abundance transcripts in microarray data",
    preprint (Technical Report #1031, Univ Wisconsin, Department of Statistics)

  38. Felix Naef, Daniel A. Lim, Nila Patil, Marcelo O. Magnasco ,
    "From features to expression: High-density oligonucleotide array analysis revisited",
    LANL e-print physics/0102010
    [ PDF]

  39. W Pan, J Lin, C Le,
    "A Mixture model approach to detecting differentially expressed genes with microarray data",
    preprint (Biostat, U Minnesota, #2001-011)

  40. P Pavlidis, J Weston, J Cai, WS Nobel,
    "Learning gene functional classifications from multiple data types."
    preprint.

  41. P Pavlidis, WN Grundy
    "Classification of genes using probabilistic models of microarray expression profiles",
    preprint.

  42. P Pavlidis, WN Grundy
    "Statistical analysis of strain and regional variation in gene expression in mouse brain",
    preprint.

  43. Leif E Peterson, Kwong Lau
    "Observation of intermittency in gene expression on cDNA microarrays",
    Genome Biology, deposited research article.
    http://genomebiology.com/2002/3/7/preprint/0005

  44. M Smolkin, D Ghosh,
    "Cluster stability scores for microarray data in cancer studies",
    submitted.

  45. JD Storey False Discovery Rates: Theory and Applications to DNA Microarrays ,
    PhD Thesis, Department of Statistics, Stanford University.

  46. J Sunil Rao, Jingjin Li ,
    "Parametric and nonparametric analysis of gene expression curves",
    preprint.

  47. M Rattray, N Morrison, D Hoyle, A Brass,
    "DNA microarray normalisation, PCA and a related latent variable model",
    preprint.
    [ PDF ]

  48. JE Steinbachs
    "Microarray analysis: statistical perils and data-mining conundrums",
    preprint.

  49. Mike West,
    "Bayesian regression analysis in the large p, small n paradigm",
    preprint (Duke Univ).

  50. Mike West, Joseph R Nevins, Jeffrey R Marks, Rainer Spang, Carrie Blanchette, Harry Zuzan
    "DNA microarray data analysis and regression modeling for genetic expression profiling",
    preprint (Duke Univ), ISDS Discussion Paper 00-15.

  51. Ka Yee Yeung, David R Haynor, Walter L Ruzzo,
    "Validating clustering for gene expression data",
    preprint.