@PHDTHESIS{alenascott:2006, author = "Scott, A.", title = "Denoising by Wavelet Thresholding Using Multivariate Minimum Distance Partial Density Estimation", school = "Rice University", year = 2006, } @article{amzal:2006, author="Amzal, B. and Bois, F.Y. and Parent, E. and Robert, C.P.", year=2006, title="Bayesian-Optimal Design via Interacting Particle Systems", journal="Journal of the American Statistical Association", volume=474, pages="773-785", } @article{armstrong:2002, author="Armstrong, S.A. and Staunton, J.E. and Silverman, L.B. and Pieters, R. and Boer, M.L. and Minden, M.D. and Sallan, E.S. and Lander, E.S. and Golub, T.R. and Korsmeyer, S.J.", year=2002, title="MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia", journal="Nature Genetics", volume=30, pages="41-47", } @article{auer:2007, author="Auer, H. and Newsom, D.L. and Nowak, N.J. and McHugh, K.M. and Singh, S. and Yu, C.Y. and Yang, Y. and Wenger, G.D. and Gastier-Foster, J.M. Kornacker, K.", year=2007, title="Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays", journal="BMC Genomics", volume=8, pages=111, } @Book{barlow:1972, author="Barlow , R. E. and Bartholomew , D. J. and Bremner, J. M. and Brunk, H. D.", year=1972, title="Statistical Inference under Order Restrictions. The Theory and Application of Isotonic Regression", publisher="Wiley", } @article{barrett:2007, author = {Barrett, T. and Troup, D. B. and Wilhite, S. E. and Ledoux, P. and Rudnev, D. and Evangelista, C. and Kim, I. F. and Soboleva, A. and Tomashevsky, M. and Edgar, R. }, issn = {1362-4962}, journal = {Nucleic Acids Research}, month = {January}, title = {{NCBI GEO}: mining tens of millions of expression profiles--database and tools update.}, volume = {35}, year = {2007} } @article{bartholomew:1961, author="Bartholomew, D.J.", year=1961, title="A test of homogeneity of means under restricted alternatives", journal="Journal of the Royal Statistical Society B", volume=23, pages="239-281", } @article{bayarri:2007, author="Bayarri, M.J. and Garcia-Donato, G.", year=2007, title="Extending conventional priors for testing general hypotheses in linear models", journal="Biometrika", volume=94, pages="135-152", } @article{benjamini:1995, author="Benjamini, Y. and Hochberg, Y.", year=1995, title="Controlling the false discovery rate: A practical and powerful approach to multiple testing", journal="Journal of the Royal Statistical Society B", volume=57, pages="289-300", } @article{benjamini:2001, author="Benjamini, Y. and Yekutieli, D.", year=2001, title="The control of the false discovery rate in multiple testing under dependency", journal="Annals of Statistics", volume=29, pages="1165-1188", } @Inbook{berger:2001, author="Berger, J.O. and Pericchi, R.L.", year=2001, title="Objective {B}ayesian methods for model selection: introduction and comparison", booktitle="Model selection", editor= "P. Lahiri", publisher="Institute of Mathematical Statistics lecture notes - Monograph series", volume="38", pages="135-207", } @book{berry:1985, author="Berry, D.A. and Fristedt, B.", year=1985, title="Bandit problems", publisher="Chapman \& Hall", } @article{berry:1991, author="Berry, D.A.", year=1991, title="Experimental design for drug development: A {B}ayesian approach", journal="Journal of Biopharmaceutical Sciences", volume=1, pages="81-101", } @article{berry:1993, author="Berry, D.A.", year=1993, title="A case for {B}ayesianism in clinical trials", journal="Statistics in Medicine", volume=12, pages="1377-1404", } @article{berry:1999, author="Berry, D.A. and Hochberg, Y.", year=1999, title="Bayesian perspectives of multiple comparisons", journal="Journal of Statistical Planning and Inference", volume=82, pages="215-227", } @Inbook{berry:2001, author="Berry, D.A. and M{\"{u}}ller, P. and Grieve, A.P. and Smith, M. and Parke, T. and Blazed, R. and Mitchard, N. and Krams, M.", year=2001, title="Adaptive {B}ayesian Designs for Dose-Ranging Drug Trials", booktitle="Case Studies in {B}ayesian Statistics", publisher="Springer-Verlag", address="New York", volume="V", } @article{bhattacharjee:2004, author="Bhattacharjee, M. and Pritchard, C.C. and Nelson, P.S. and Arjas, E.", year=2004, title="Bayesian integration functional analysis of microarray data", journal="Bioinformatics", volume=17, pages="2943-2953", } @techreport{bickel:2003, author="Bickel, D.R.", year=2003, title="Selecting an optimal rejection region for multiple testing: A decision-theoretic alternative to FDR control, with an application to microarrays", institution="Medical College of Georgia", } @article{bioconductor, author = {Gentleman, R.C. and Carey, V.J. and Bates,D.M. and Bolstad, B. and Dettling, M. and Dudoit, S. and Ellis, B. and Gautier, L. and Ge, Y. and Gentry, J. and Hornik, K. and Hothorn, T. and Huber, W. and Iacus, S. and Irizarry, R. and Leisch, F. and Li, C. and Maechler, M. and Rossini, A.J. and Sawitzki, G. and Smith, C. and Smyth, G. and Tierney, L. and Yang, J.Y.H. and Zhang, J.}, title = {Bioconductor: Open software development for computational biology and bioinformatics}, journal = {Genome Biology}, volume = {5}, year = {2004}, pages = {R80}, url = {http://genomebiology.com/2004/5/10/R80} } @article{bolstand:2003, author = {Bolstad, B. M. and Irizarry, R. A. and Astrand, M. and Speed, T. P. }, journal = {Bioinformatics}, number = {2}, pages = {185--193}, title = {A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.}, volume = {19}, year = {2003} } @book{box:1992, author = {Box, George E. P. and Tiao, George C.}, title = {Bayesian inference in statistical analysis}, year = {1992}, pages = {588}, publisher = {John Wiley \& Sons} } @article{breiman:2001, author = {Breiman, L.}, journal = {Machine Learning}, number = {1}, pages = {5--32}, title = {Random Forests}, volume = {45}, year = {2001} } @article{brockwell:2003, author="Brockwell, A.E. and Kadane, J.B.", year=2003, title="A gridding method for {B}ayesian sequential decision problems", journal="Journal of Computational and Graphical Statistics", volume=12, pages="566-584", } @article{callow:2000, author="Callow, M.J. and Dudoit, S. and Gong, E.L. and Speed, T.P. and Rubin, E.M.", year=2000, title="Microarray expression profiling identifies genes with altered expression in hdl-deficient mice", journal="Genome research", volume=10, pages="2022-2029", } @article{campodellorto:2007, author="Campo Dell'Orto, M. and Zangrando, A. and Trentin, L. and Li, R. and Liu, W.M. and te Kronnie, G. and Basso, G. and Kohlmann, A.", year=2007, title="New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures", journal="BMC Genomics", volume="8:188", } @inbook{carey:2005, author="Carey, V.J.", year=2005, title="Machine learning concepts and tools for statistical genomics", chapter=16, pages="273-292", publisher="Springer", } @article{carlin:1998, author="Carlin, B. and Kadane, J. and Gelfand, A.", year=1998, title="Approaches for optimal sequential decision analysis in clinical trials", journal="Biometrics", volume=54, pages="964-975", } @techreport{chiogna:2007, author="Chiogna, M. and Massa, M.S. and Romualdi, C.", title="Effect of normalizations on detecting differentially expressed genes with c{DNA} microarray experiments", year=2007, institution="Universita degli studi di {P}adova, {D}ipartimento di scienze statistiche", } @book{chow:2003, author="Chow, S.C. and Shao, J. and Wang, H.", year=2003, title="Sample size calculations in clinical research", publisher="Marcel Dekker", address="New York-Basel", } @techreport{coombes:2007, author="Coombes, K. R. and Wang, J. and Baggerly, K.A.", year=2007, title="A statistical method for finding biomarkers from microarray data, with application to prostate cancer", institution="M.D. {A}nderson Cancer Center", Url="http://www.mdanderson.org/pdf/biostats\_utmdabtr00704.pdf", } @article{cornish:1954, author="Cornish, E.A.", year=1954, title="The Multivariate t-Distribution Associated with a Set of Normal Sample Deviates", journal="Australian journal of physics", volume=7, pages="531-542", } @article{damsleth:1975, author="Damsleth, E.", year=1975, title="Conjugate classes for gamma distributions", journal="Scandinavian Journal of Statistics", volume=2, pages="80-84", } @article{dass:2004, author = {Dass, S.C. and Lee, J.}, title = {A note on the consistency of Bayes factors for testing point null versus non-parametric alternatives}, year = {2004}, journal= {Journal of Statistical Planning and Inference}, volume=119, pages="143-152", } @article{davidsoftware:2003, author= "Dennis, G. and Sherman, B.T. and Hosack, D.A and Yang, J. and Baseler, M.W. and Lane, H.C. and Lempicki, R.A.", year= 2003, title="DAVID: Database for Annotation, Visualization, and Integrated Discovery", journal="Genome Biology", volume=4, pages="(5):P3", } @Book{degroot:1970, author="DeGroot, M.", year=1970, title="Optimal Statistical Decisions", publisher="McGraw Hill", address="New York", } @Book{degroot:2004, author="DeGroot, M.", year=2004, title="Optimal Statistical Decisions", publisher="Wiley-Interscience", } @article{demets:2004, author="De{M}ets, D.L.", year=2004, title="Sequential designs in clinical trials", journal="Cardiac electrophysiology review", volume=2, pages="57-60", } @article{do:2005, author="Do, K. and M{\"{u}}ller, P. and Tang, F.", year=2005, title="A bayesian mixture model for differential gene expression", journal="Journal of the Royal Statistical Society C", volume=54, pages="627-664", } @article{dobbin:2005, author="Dobbin, K. and Simon, R.", year=2005, title="Sample size determination in microarray experiments for class comparison and prognostic classification", journal="Biostatistics", volume=6, pages="27-38", } @article{dudoit:2002, author="Dudoit, S. and Yang, H.Y. and Callow, M.J. and Speed, T.P.", year=2002, title="Statistical Methods for Identifying Differentially Expressed Genes in Replicated c{DNA} Microarray Experiments", journal="Statistica Sinica", volume=12, pages="972-977", } @article{dudoit:2002b, author="Dudoit, S. and Fridlyand, J. and Speed, T.P.", year=2002, title="Comparison of discrimination methods for the classification of tumors using gene expression data", journal="Journal of the Americal Statistical Association", volume=97, pages="77-87", } @article{dudoit:2003, author="Dudoit, S. and Shaffer, J.P. and Boldrick, J.C.", year=2003, title="Multiple Hypothesis Testing in Microarray Experiments", journal="Statistical Science", volume=18, pages="71-103", } @article{dunson:2003, author="Dunson, D. and Neelon, B.", year=2003, title="Bayesian Inference on Order-Constrained Parameters in Generalized Linear Models", journal="Biometrics", volume=59, pages="286-295", } @article{efron:1973, author="Efron, B. and Morris, C.", year=1973, title="Combining possibly related estimation problems (with discussion)", journal="Journal of the {R}oyal Statistical Society, Series B", volume=35, pages="379 –421", } @article{efron:1977, author="Efron, B. and Morris, C.", year=1977, title="Stein’s paradox in statistics", journal="Scientific American", volume=236, pages="119 –127", } @article{efron:2001, author="Efron, B. and Tibshirani, R. and Storey, J.D. and Tusher, V.", year=2001, title="Empirical {B}ayes Analysis of a Microarray Experiment", journal="Journal of the Americal Statistical Association", volume=96, pages="1151-1160", } @article{efron:2002, author="Efron, B. and Tibshirani, R.", year=2002, title="Empirical bayes methods and false discovery rates for microarrays", journal="Genetic Epidemiology", volume=23, pages="70-86", } @article{efron:2004, author="Efron, B.", year=2004, title="Large-scale simultaneous hypothesis testing: the choice of a null hypothesis", journal="Journal of the American Statistical Association", volume=99, pages="96-104", } @inbook{emerson:1983, author="Emerson, J.D. and Hoaglin, D.C.", year= 1983, title="Analysis of two-way tables by medians", booktitle="Understanding Robust and Exploratory Data Analysis", editor="Hoaglin, D.C. and Mosteller, F. and Tukey, J.W.", pages="165-210", publisher="John {W}iley \& Sons", address="New York", } @article{fraley:2003, author = "Fraley, C. and Raftery, A.E.", title = "Enhanced Software for Model-Based Clustering, Density Estimation, and Discriminant Analysis: {MCLUST}", journal = "Journal of Classification", volume = 20, pages = "263-286", year = 2003} @article{fu:2005, author="Fu, W.J. and Dougherty, E.R. and Mallick, B. and Carroll, R.J.", year=2005, title="How Many Sample Are Needed to Build a Classifier: A General Sequential approach", journal="Bioinformatics", volume=21, pages="63-70", } @article{gastwirth:1972, author="Gastwirth, J.L.", year=1972, title="The estimation of the {L}orenz curve and {G}ini index", journal="The review of economics and statistics ({T}he {MIT} press)", volume=54, pages="306-316", } @article{gelfand:1990, author="Gelfand, A.E. and Smith, A.F.M.", year=1990, title="Sampling Based Approaches to Calculating Marginal Densities", journal="Journal of the American Statistical Association", volume=85, pages="398-409", } @article{gelfand:1992, author="Gelfand, A.E. and Smith, A.F.M. and Lee, T.M.", year=1992, title="Bayesian Analysis of Constrained Parameter and Truncated Data Problems Using Gibbs Sampling", journal="Journal of the American Statistical Association", volume=87, pages="523-532", } @Book{gelman:2004, author="Gelman, A. and Carlin, J.B. and Stern, H.S. and Rubin, D.B.", year=2004, title="Bayesian Data Analysis", edition="2nd", publisher="Chapman \& Hall", } @article{geman:1984, author= "Geman, D. and Geman, S.", year=1984, title="Stochastic Relaxation, {G}ibbs Distributions, and the {B}ayesian Restoration of Images", journal="IEEE Transactions on Pattern Analysis and Machine Intelligence", volume= 6, pages="721-741", } @article{geneontology, author= "{Gene Ontology Consortium}", year= 2000, title="Gene Ontology: tool for the unification of biology", journal="Nature Genetics", volume=25, pages="25-29", } @article{genovese:2002, author="Genovese, C. and Wasserman, L.", year=2002, title="Operating characteristics and extensions of the false discovery rate procedure", journal="Journal of the Royal Statistical Society B", volume=64, pages="499-518", } @book{gini:1912, author="Gini, C.", year=1912, title="Variabilita e mutabilita", publisher="C. Cuppini", address="Bologna", } @techreport{ghosal:2002, author="Ghosal, S.", year= 2002, title="A review of consistency and convergence of posterior distribution", institution="Indian Statistical Institute", } @article{golub:1999, author="Golub, T.R. and Slonim, D.K. and Tamayo, P. and Huard, C. and Gaasenbeek, M. and Mesirov, J.P. and Coller, H. and Loh, M.L. and Downing, J.R. and Caligiuri, M.A. and Bloomfield, C.D. and Lander, E.S.", year=1999, title="Molecular classification of cancer: class discovery and class prediction by gene expression monitoring", journal="Science", volume=286, pages="531-537", } @article{gotoolbox:2004, author="Martin, D. and Brun, C. and Remy, E. and Mouren, P. and Thieffry, D. and Jacq, B.", year=2004, title="GOToolBox: functional analysis of gene datasets based on Gene Ontology", journal="Genome Biology", volume=5, pages="R101", } @article{gottardo:2003, author="Gottardo, R. and Pannucci, J.A. and Kuske, C.R. and Brettin, T.", year=2003, title="Statistical analysis of microarray data: a Bayesian approach", volume=4, pages="597-620", } @article{gottardo:2006, author = {Gottardo, R. and Raftery, A.E. and Yeung, K.Y. and Bumgarner, R.E.}, journal = {Biometrics}, title = {Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples}, volume = {62}, pages="10-18", year = {2006} } @Book{gupta:2004, author="Gupta, A.K. and Nadarajah, S.", year=2004, title="Handbook of beta distribution and its applications", publisher="Marcel Dekker, Inc.", } @book{hampel:1986, AUTHOR = "Hampel, F. and Ronchetti, E. and Rousseeuw, P. and Stahel, W.", TITLE = "Robust Statistics - The Approach Based on Influence Functions", PUBLISHER = "Wiley", YEAR = "1986", ADDRESS = "New York" } @article{hardwick:2002, author="Hardwick, J. and Stout, Q.F.", year=2002, title="Optimal few-stage designs", journal="Journal of Statistical Planning and Inference", volume=104, pages="121-145", } @article{hastings:1970, author="Hastings, W.K.", year=1970, title="Monte Carlo Sampling Methods Using Markov Chains and Their Applications", journal="Biometrika", volume=57, pages="97-109", } @article{hayter:1990, author="Hayter, A.J.", year=1990, title="A one-sided studentized range test for testing against a simple ordered alternative", journal="Journal of the American Statistical Association", volume=85, pages="778-785", } @article{hayter:1996, author="Hayter, A.J. and Liu, W.", year=1996, title="Exact calculations for the one-sided studentized range test for testing against a simple ordered alternative", journal="Computational Statistics and Data Analysis", volume=22, pages="17-25", } @article{holmes:2003, author="Holmes, C.C. and Heard, N.A.", year=2003, title="Generalized monotonic regression using random change points", journal="Statistics in medicine", volume=22, pages="623-638", } @book{huber:1981, AUTHOR = "Huber, P.", TITLE = "Robust Statistics", PUBLISHER = "Wiley", YEAR = "1981", ADDRESS = "New York" } @article{huntjens:2006, author="Huntjens, R.J.C. and Peters, M.L. and Woertman, L. and Bovenschen, L.M. and Martin, R.C. and Postma, A.", year=2006, title="Inter-identity amnesia in dissociative identity disorder: a simulated memory impairment?", journal="Psychological medicine", volume=36, pages="857-863", } @article{irizarry:2003, author="Irizarry, R. and Hobbs, B. and Collin, B. and Beazer-Barclay, Y.D. and Antonellis, K.J. and Scherf, U. and Speed, T.S.", year=2003, title="Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data", journal="Biostatistics", volume=4, pages="249-264", } @Misc{jager:2003, author="J{\"{a}}ger, J. and Spang, R.", year=2003, title="Design of a clinical microarray chip", howpublished="The Sevent Annual International Conference on Research in Computational Molecular Biology", } @article{jawitz:2004, author="Jawitz, J.W.", year=2004, title="Moments of truncated continuous univariate distributions", journal="Advances in Water Resources", volume=27, pages="269-281", } @Book{jennison:1999, author="Jennison, C. and Turbull, B.W.", year=1999, title="Group Sequential Methods with Applications to Clinical Trials", publisher="Chapman \& Hall/CRC", } @article{johnson:1992, author="Johnson, V.E.", year=1992, title="A Technique for Estimating Marginal Posterior Densities in Hierarchical Models Using Mixtures of Conditional Densities", journal="Journal of American Statistical Association", volume=87, pages="852-860", } @article{johnson:2006, author = {Johnson, W. E. and Li, W. and Meyer, C. A. and Gottardo, R. and Carroll, J. S. and Brown, M. and Liu, X. S. }, citeulike-article-id = {1120020}, doi = {http://dx.doi.org/10.1073/pnas.0601180103}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, month = {August}, number = {33}, pages = {12457--12462}, posted-at = {2008-12-01 19:36:42}, priority = {0}, title = {Model-based analysis of tiling-arrays for ChIP-chip.}, url = {http://dx.doi.org/10.1073/pnas.0601180103}, volume = {103}, year = {2006} } @Misc{kadane:1997, author="Kadane, J.B.", year=1997, title="Discussion of Robust {B}ayesian design and analysis of clinical trials via prior partitioning by D.J. Sargent and B.P. Carlin", howpublished="In {B}ayesian Robustness, IMS Lecture Notes-Monograph", volume=29, pages="190-191", } @article{kanehisa:2000, author = {Kanehisa, M. and Goto, S. }, journal = {Nucleic Acids Res.}, keywords = {bibtex-import}, pages = {27--30}, posted-at = {2005-03-15 21:56:06}, priority = {2}, title = {{KEGG: Kyoto Encyclopedia of Genes and Genomes}}, volume = {28}, year = {2000}, } @article{kanehisa:2006, author = {Kanehisa, M. and Goto, S. and Hattori, M. and Aoki-Kinoshita, K. F. and Itoh, M. and Kawashima, S. and Katayama, T. and Araki, M. and Hirakawa, M. }, doi = {http://dx.doi.org/10.1093/nar/gkj102\%20}, issn = {1362-4962}, journal = {Nucleic Acids Research}, keywords = {gochebi, kegg}, month = {January}, number = {Database issue}, posted-at = {2007-10-31 11:43:07}, priority = {0}, title = {From genomics to chemical genomics: new developments in KEGG}, url = {http://dx.doi.org/10.1093/nar/gkj102\%20}, volume = {34}, year = {2006}, } @article{kanehisa:2007, author = {Kanehisa, M. and Araki, M. and Goto, S. and Hattori, M. and Hirakawa, M. and Itoh, M. and Katayama, T. and Kawashima, S. and Okuda, S. and Tokimatsu, T. and Yamanishi, Y.}, doi = {http://dx.doi.org/10.1093/nar/gkm882}, journal = {Nucl. Acids Res.}, keywords = {disease, kegg, pathways}, month = {December}, pages = {gkm882+}, title = {KEGG for linking genomes to life and the environment}, url = {http://dx.doi.org/10.1093/nar/gkm882}, year = {2007}, } @book{kaufman:2005, author = "Kaufman, L. and Rousseeuw, P.J.", publisher = "Wiley-Interscience", title = {Finding Groups in Data: An Introduction to Cluster Analysis}, year = {2005}, } @article{kendziorski:2003, author="Kendziorski, C.M. and Newton, M.A. and Lan, H. and Gould, M.N.", year=2003, title="On parametric empirical bayes methods for comparing multiple groups using replicated gene expression profiles", journal="Statistics in Medicine", volume=22, pages="3899-3914", } @article{kerr:2001, author = {Kerr, M. K. and Churchill, G. A. }, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences USA}, number = {16}, pages = {8961--8965}, title = {Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments.}, volume = {98}, year = {2001} } @article{klugkist:2005a, author="Klugkist, I. and Laudy, O. and Hoijtink, H.", year=2005, title="Inequality constrained analysis of variance: a {B}ayesian approach", journal="Psychological methods", volume="10", pages="477-493", } @article{klugkist:2005b, author="Klugkist, I. and Kato, B. and Hoijtink, H.", year=2005, title="Bayesian model selection using encompassing priors", journal="Statistica Neerlandica", volume=59, pages="57-69", } @article{kraemer:1979, author="Kraemer, H.C. and Paik, M.", year=1979, title="A central t approximation to the noncentral t distribution", journal="Tehcnometrics", volume=21, pages="357-360", } @ARTICLE{langaas:2005, AUTHOR = {Langaas, M. and Lindqvist, B. H. and Ferkingstad, E.}, TITLE = {Estimating the proportion of true null hypotheses, with application to {DNA} microarray data}, JOURNAL = {Journal of the Royal Statistical Society B}, Volume = {67}, Pages = {555-572}, YEAR = {2005}, } @article{lapointe:2004, author="Lapointe, J. and Li, C. and Higgins, J.P and Rijn, M. and Bair, E. and Montgomery, K. and Ferrari, M. and Egevad, L. and Rayford, W. and Bergerheim, U. and Ekman, P. and DeMarzo, A.M. and Tibshirani, R. and Botstein, D. and Brown, P.O. and Brooks, J.D. and Pollack, J.R.", year=2004, title="Gene expression profiling identifies clinically relevant subtypes of prostate cancer", journal="Proceedings of the National Academy of Science", volume=101, pages="811-816", } @article{lee:2004, author="Lee, M.L. and Whitmore, G.", year=2004, title="Power and sample size for microarray studies", journal="Statistics in medicine", volume=11, pages="3543-3570", } @article{leung:2001, author="Leung, D.H.Y. and Wang, Y.G.", year=2001, title="Optimal designs for evaluating a series of treaments", journal="Biometrics", volume=57, pages="168-171", } @article{lindley:1957, author="Lindley, D.V.", year=1957, title="A statistical paradox", journal="Biometrika", volume=44, pages="187-192", } @article{lo:2007, author="Lo, K. and Gottardo, R.", year=2007, title="Flexible empirical Bayes models for differential gene expression", journal="Bioinformatics", volume=23, pages="328-335", } @article{lonnstedt:2002, author="L{\"{o}}nnstedt, I. and Speed, T.", year=2002, title="Replicated microarray data", journal="Statistica Sinica", volume=12, number=1, } @article{mack:1981, author="Mack, G.A. and Wolfe, D.A.", year=1981, title="K-Sample Rank Test for Umbrella Alternatives", journal="Journal of the American Statistical Association", volume=76, pages="175-181", } @article{maqc:2006, author="MAQCconsortium", year=2006, title="The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements", journal="Nature Biotechnology", volume=24, pages="1151-1161", } @PhdThesis{meichun:2006, author = {Ding, Meichun}, title = {Bayesian Optimal Design for Phase II Screening Trials}, school = {M.D. Anderson Cancer Center and Rice University}, year = {2006}, } @article{miller:1980, author="Miller, R.B.", year=1980, title="Bayesian Analysis of the Two-Parameter Gamma Distribution", journal="Technometrics", volume=22, pages="65-69", } @article{mootha:2003, author= "Mootha, V.K. and Lindgren, C.M. and Eriksson, K.-F. and Subramanian, A. and Sihag, S. and Lehar, J. and Puigserver, P. and Carlsson, E. and Ridderstrale, A. and Laurila, E. and Houstis, N. and Daly, M.J. and Patterson, N. and Mesirov, J.P. and Golub, T.R. and Tamayo, P. and Spiegelman, B. and Lander, E.S. and Hirschhorn, J.N. and Altshuler, D. and Groop, L.C.", title="PGC-1$\alpha$-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes", journal= "Nature genetics", year=2003, volume=34, pages="267-273", } @article{mortazavi:2008, author= "Mortazavi, A. and Williams, B.A. and McCue, K. and Schaeffer, L. and Wold, B.", year=2008, title="Mapping and quantifying mammalian transcriptomres by RNA-Seq", journal="Nature methods", volume=5, pages="621-628", } @article{mukherjee:2002, author="Mukherjee, S. and Tamayo, P. and Rogers, S. and Rifkin, R. and Eagle, A. Campbell, C. and Golub, T. and Mesirov, J.", year=2002, title="Estimating dataset size requirements for classifying DNA microarray data", journal="Journal of Computational Biology", volume=10, pages="119-142", } @article{mueller:1995, author="M{\"{u}}ller, P. and Parmigiani, G.", year=1995, title="Optimal design via curve fitting of Monte Carlo experiments", journal="Journal of the American Statistical Association", volume=90, pages="1322-1330", } @article{mueller:2004, author="M{\"{u}}ller, P. and Parmigiani, G. and Robert, C. and Rousseau, J.", year=2004, title="Optimal sample size for multiple testing: the case of gene expression microarrays", journal="Journal of the American Statistical Association", volume=99, pages="990-1001", } @article{mullerquintana:2004, author = {M{\"{u}}ller, P. and Quintana, F.A. }, journal = {Statistical Science}, number = {1}, pages = {95-110}, title = {Nonparametric Bayesian Data Analysis}, url = {http://www.projecteuclid.org/Dienst/UI/1.0/Summarize/euclid.ss/1089808275}, volume = {19}, year = {2004} } @Inbook{mueller:2007, author="M{\"{u}}ller, P. and Parmigiani, G. and Rice, K.", year= 2007, title="FDR and Bayesian Multiple Comparisons Rules", booktitle="Bayesian Statistics 8", editor="Bernardo, J.M. and Bayarri, S. and Berger, J.O. and Dawid, A.P. and Heckerman, D. and Smith, A.F.M. and West, M.", publisher="Oxford University Press", } @article{neelon:2004, author="Neelon, B. and Dunson, D.", year=2004, title="Bayesian Isotonic Regression and Trend Analysis", journal="Biometrics", volume=60, pages="398-406", } @article{newton:2001, author="Newton, M.A. and Kendziorski, C.M. and Richmond, C.S and Blattner, F.R. and Tsui, K.W.", year=2001, title="On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data", journal="Journal of Computational Biology", volume=8, pages="37-52", } @Inbook{newton:2003, author="Newton, M.A. and Kendziorski, C.M.", year=2003, title="Parametric Empirical {B}ayes Methods for Microarrays", booktitle="The analysis of gene expression data: methods and software", publisher="Springer Verlag", address="New York", } @article{newton:2004, author="Newton, M.A. and Noueriry, A. and Sarkar, D. and Ahlquist, P.", year=2004, title="Detecting differential gene expression with a semiparametric hierarchical mixture model", journal="Biostatistics", volume=5, pages="155-176", } @article{nguyen:2005, author="Nguyen, D.V.", year=2005, title="A Unified Computational Framework to Compare Direct and Sequential False Discovery Rate Algorithms for Exploratory {DNA} Microarray Studies", journal="Journal of Data Science", volume=3, pages="331-352", } @book{numrecipes:1992, author = "Press, W.H. and Flannery, B.P. and Teukolsky, S.A. and Vetterling, W.T.", title = "Numerical Recipes: The Art of Scientific Computing", edition = "2nd", publisher = "Cambridge University Press", address = "Cambridge (UK) and New York", year = 1992, isbn = "0-521-43064-X", } @article{owen:1965, author="Owen, D.B.", year=1965, title="A special case of a bivariate non-central t-distribution", journal="Biometrika", volume=52, pages="437-446", } @article{pan:2002, author="Pan, W. and Lin, J. and Le, C.T.", year=2002, title="Model-Based Cluster Analysis of Microarray Gene Expression Data", journal="Genome Biology", volume=3, pages="research0009.1-0009.8", } @article{pan:2002b, author="Pan, W. and Lin, J. and Le. C.T.", year=2002, title="How many replicates of arrays are required to detect gene expression changes in microarray experiments?", journal="Genome Biology", volume=3, pages="research0022.1-0022.10", } @Inbook{pan:2003, author="Pan, W. and Lin, J. and Le, C.T.", year=2003, title="A Mixture Model Approach to Detecting Differentially Expressed Genes with Microarray Data", booktitle="Functional \& Integrative Genomics", publisher="Springer-Verlag GmbH", pages="117-124", } @article{parmigiani:2002, author="Parmigiani, G. and Garret, E.S. and Anbazhagan, R. and Gabrielson, E.", year=2002, title="A statistical framework for expression-based molecular classification in cancer", journal="Journal of the Royal Statistical Society B", volume=64, pages="717-736", } @book{parmigiani:2003, title="The Analysis of Gene Expression Data", year=2003, editor="Parmigiani, G. and Garett, E.S. and Irizarry, R.A. and Zeger, S.L.", publisher="Springer", } @article{planet:2012, author="Planet, E. and Stephan-Otto Attolini, C. and Reina, O. and Flores, O. and Rossell, D.", title="htSeqTools: High-Throughput Sequencing Quality Control, Processing and Visualization in R", journal="Bioinformatics (in press)", year=2012, } @article{pounds:2003, author="Pounds, S. and Morris, S.W.", year=2003, title="Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values", journal="Bioinformatics", volume=10, pages="1236-1242", } @Book{robertson:1988, author="Robertson, T. and Wright, F.T. and Dykstra, R.L.", year=1988, title="Order restricted statistical inference", publisher="Wiley", } @article{rossell:2006, author="Rossell, D. and M{\"{u}}ller, P. and Rosner, G.", year=2006, title="Screening designs for drug development", journal="Biostatistics", volume=8, pages="595-608", } @techreport{rossell:2007, author="Rossell, D.", year=2007, title="Ga{G}a: a simple and flexible hierarchical model for microarray data analysis", institution="{M}.{D}. {A}nderson cancer center", url="http://rosselldavid.googlepages.com", } @Inbook{rossell:2007b, author="Rossell, D. and Baladandayuthapani, V. and Johnson, V.E.", year=2007, title="Bayes Factors Based on Test Statistics under Order Restrictions", booktitle="Informed inference", editor= "Hoijtink, H. and Klugkist, I. and Boelen, P.", publisher="To appear", } @article{rossell:2008, author="Rossell, D. and Guerra, R. and Scott, C.", year=2008, title="Semi-parametric Differential Expression Analysis via Partial Mixture Estimation", journal="Statistical Applications in Genetics and Molecular Biology", volume=7, pages="1,15", } @article{rossell:2009, author="Rossell, D.", year=2009, title="Ga{G}a: a simple and flexible hierarchical model for differential expression analysis", journal="Annals of Applied Statistics (to Appear)", } @techreport{rossell:2009suppl, author="Rossell, D.", year=2009, title="Supplement to Ga{G}a: a simple and flexible hierarchical model for differential expression analysis", institution="Institute for {R}esearch in {B}iomedicine of {B}arcelona", } @article{rpkg:ACME, author = {Scacheri, P.C. and Crawford, G.E. and Davis, S.}, title = {Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.}, journal = {Methods Enzymol}, year = {2006}, volume = {411}, pages = {270--282}, } @article{rpkg:affy, author = {Gautier, L. and Cope, L. and Bolstad, B.M. and Irizarry, R.A.}, title = {affy---analysis of Affymetrix GeneChip data at the probe level}, journal = {Bioinformatics}, volume = {20}, number = {3}, year = {2004}, issn = {1367-4803}, pages = {307--315}, doi = {http://dx.doi.org/10.1093/bioinformatics/btg405}, publisher = {Oxford University Press}, address = {Oxford, UK}, note = "Package version 1.16.0", } @Manual{rpkg:bridge, title = {bridge: Bayesian Robust Inference for Differential Gene Expression}, author = {Raphael Gottardo}, year = {2004}, note = {R package version 1.4.0}, } @Manual{rpkg:BSgenome.Dmelanogaster.UCSC.dm3, title = {BSgenome.Dmelanogaster.UCSC.dm3: Drosophila melanogaster full genome (UCSC version dm3)}, author = {H. Pages}, year = {2009}, } @Manual{rpkg:ClassComparison, title = {ClassComparison: Classes and methods for "class comparison" problems on microarrays}, author = {Kevin R. Coombes}, year = {2007}, note = {R package version 2.5.0}, } @Manual{rpkg:ClassDiscovery, title = {ClassDiscovery: Classes and methods for "class discovery" with microarrays or proteomics}, author = {Coombes, K.R.}, year = {2007}, note = {R package version 2.5.0}, } @Manual{rpkg:gaga, title = {gaga: GaGa hierarchical model for microarray data analysis}, author = {Rossell, D.}, year = {2008}, note = {R package version 1.1.0}, } @Manual{rpkg:genefilter, title = {genefilter: methods for filtering genes from microarray experiments}, author = {Gentleman, R. and Carey, V. and Huber, W. and Hahne, F.}, year = {2009}, note = {R package version 1.22.0}, } @Manual{rpkg:EBarrays, title = {EBarrays: Empirical {B}ayes for Microarrays}, author = {Christina Kendziorski and Michael Newton and Deepayan Sarkar}, year = {2005}, note = {R package version 1.2.0}, } @Manual{rpkg:hopach, title = {hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid}, author = {Pollard, K.S. and van der Laan, M.J. and Wall, G.}, year = {2008}, note = {R package version 2.2.0}, } @Manual{rpkg:gcrma, title = {gcrma: Background Adjustment Using Sequence Information}, author = {Wu, J. and Irizarry, R. with contributions from Gentry, J.M.J.}, year = {2007}, note = {R package version 2.8.1}, } @Manual{rpkg:Mclust, author = "Fraley, C. and Raftery, A.E.", title = "{MCLUST} Version 3 for {R}: {N}ormal Mixture Modeling and Model-Based Clustering", number = "504", address = "Department of Statistics", institution = "University of Washington", year = 2006} @Manual{rpkg:MCMCpack, title = {MCMCpack: Markov chain Monte Carlo (MCMC) Package}, author = {Andrew D. Martin and Kevin M. Quinn and Jong Hee Park}, year = {2007}, note = {R package version 0.9-2}, url = {http://mcmcpack.wustl.edu}, } @article{rpkg:mgcv, title= {Stable and efficient multiple smoothing parameter estimation for generalized additive models}, author= {Wood S.N.}, year=2004, journal= {Journal of the American Statistical Association}, volume= 99, pages={673-686}, } @Manual{rpkg:MLInterfaces, title = {MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers}, author = {Carey, V. and Gentleman, R. and Mar, J.}, year = {2009}, note = {R package version 1.22.0}, } @Manual{rpkg:quantreg, title = {quantreg: Quantile Regression}, author = {Roger Koenker}, year = {2007}, note = {R package version 4.10}, url = {http://www.r-project.org}, } @Manual{rpkg:ShortRead, author = {Morgan, M. and Lawrence, M. and Anders, S.}, title = {ShortRead: Base classes and methods for high-throughput short-read sequencing data.}, year = {2009}, } @Manual{rpkg:siggenes, title = {siggenes: Multiple testing using SAM and Efron's empirical Bayes approaches}, author = {Holger Schwender}, year = {2007}, note = {R package version 1.13.2}, } @Manual{rpkg:stats, title = {R: A Language and Environment for Statistical Computing}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, year = {2009}, note = {{ISBN} 3-900051-07-0}, url = {http://www.R-project.org}, } @Manual{rsoftware, title = {R: A language and environment for statistical computing}, author = {{R Development Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2008}, note = {{ISBN} 3-900051-07-0}, url = {http://www.R-project.org}, } @Techreport{schwender:2003, author="Schwender, H. and Krause, A. and Ickstadt, K.", year=2003, title="Comparison of the Empirical {B}ayes and the Significance Analysis of Microarrays", number="44", } @article{scott:2001, author="Scott, D.W.", year=2001, title="Parametric Statistical Modeling by Minimum Integrated Square Error", journal="Technometrics", volume=43, pages="274-285", } @Misc{scott:2004, author="Scott, D.W.", year=2004, title="Oulier detection and clustering by partial mixture modelling", howpublished="Proceedings of COMPTSTAT, Ed. Antoch.", pages= "453-464", } @article{scottm:2004, author="Scott, M. and Lu, G. and Hallett, M. and Thomas, D.Y.", year=2004, title="The Hera database and its use in the characterization of endoplasmic reticulum proteins", journal="Bioinformatics", volume=20, pages= "937-944", } @incollection{scott:2004b, AUTHOR = "D. W. Scott", TITLE = "Partial Mixture Estimation and Outlier Detection in Data and Regression", editor = "M. Hubert and G. Pison and A. Struyf and S. Van Aelst", PAGES = "297--306", booktitle = "Theory and Applications of Recent Robust Methods", series = "Statistics for Industry and Technology", publisher = {Birkh\"{a}user}, address = "Basel, Switzerland", YEAR = "2004"} @article{schwarz:1978, author="Schwarz, G.", year=1978, title="Estimating the dimension of a model", journal="Annals of Statistics", volume=6, pages="461-464", } @book{silvapulle:2004, author="Silvapulle, M.J. and Sen, P.K.", year= 2004, title="Constrained statistical inference", publisher= "Wiley", address= "New York", } @article{simon:1987, author="Simon, R.", year=1987, title="How large should a phase II trial of a new drug be?", journal="Cancer Trt. Rpts.", volume=71, pages="1079-1085", } @article{singh:1993, author="Singh, B. and Wright, F.T.", year=1993, title="The level probabilities for a simple loop ordering", journal="Annals of the Institute of Statistical Mathematics", volume=45, pages="279-292", } @article{smyth:2004, author="Smyth, G.K.", year=2004, title="Linear Models and Empirical {B}ayes Methods for Assessing Differential Expression in Microarray Experiments", journal="Statistical Applications in Genetics and Molecular Biology", volume=3, issue=1, article=3, } @incollection{smyth:2005, author="Smyth, G.K.", year=2005, title="Limma: linear models for microarray data", pages="397-420", editor= "Gentleman, R. and Carey, V. and Dudoit, S. and Irizarry, R. and Huber, W.", booktitle="Bioinformatics and Computational Biology Solutions using R and Bioconductor", publisher="Springer", address="New York", } @article{soft:bowtie, author="Langmead, B. and Trapnell, C. and Pop, M. and Salzberg, S.L.", year=2009, title="Ultrafast and memory-efficient alignment of short DNA sequences to the human genome", journal="Genome Biology", volume="10:R25", } @article{song:2000, author="Song, P.X.-K.", year=2000, title="Multivariate Dispersion Models Generated from Gaussian Copula", journal="Scandinavian Journal of Statistics", volume=27, pages="305-320", } @article{spearman:1904, author="Spearman, C.", year=1904, title="The proof and measurement of association between two rings", journal="American Journal of Psychology", volume=15, pages="72-101", } @article{spiegelhalter:1994, author="Spiegelhalter, D.J. and Freedman, L.S. and Parmar, M.K.B.", year=1994, title="Bayesian approaches to randomised trials", journal="Journal of the Royal Statistical Society A", volume=157, pages="357-416", } @Misc{stangl:1995, author="Stangl, D.K.", year=1995, title="Bayesian methods in the analysis of clinical trials: A discussion", howpublished="Proceedings of the Section on {B}ayesian Statistical Science. Alexandria, Virginia: American Statistical Association", pages="7-9", } @Book{stafford:2008, author="Stafford, P.", year= 2008, title="Methods in Microarray Normalization", publisher="CRC Press", address="USA", } @inproceedings{stein:1956, author="Stein, C.", year= 1956, title="Inadmissibility of the usual estimator for the mean of a multivariate distribution", booktitle="Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability", volume=1, pages="197-206", } @article{storey:2002, author="Storey, J.D.", year=2002, title="A direct approach to false discovery rates", journal="Journal of the Royal Statistical Society B", volume=64, pages="479-498", } @article{storey:2003, author="Storey, J.D.", year=2003, title="The positive false discovery rate: a bayesian interpretation and the q-value", journal="Annals of Statistics", volume=31, pages="2013-2035", } @article{storeytib:2003, author="Storey, J.D. and Tibshirani, R.", year=2003, title="Statistical significance for genome-wide studies", journal="Proceeding of the National Academy of Science", volume=100, pages="9440-9445", } @Techreport{storey:2004, author="Storey, J.D.", year=2004, title="Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach", } @article{storey:2007, author="Storey, J.D.", year=2007, title="The Optimal Discovery Procedure: A New Approach to Simultaneous Significance Testing", journal="Journal of the Royal Statistical Society B", volume=69, pages="347-368", } @article{storey:2007b, author="Storey, J.D. and Day, J.Y. and Leek, J.T.", year=2007, title="The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments", journal="Biostatistics", volume=8, pages="414-432", } @article{stout:1999, author="Stout, Q.F. and Hardwick, J.", year=1999, title="Minimizing the costs of screening trials", journal="Computing Science and Statistics", volume=31, pages="440-444", } @article{stout:2005, author="Stout, Q.F. and Hardwick, J.", year=2005, title="Optimal Screening Designs with Flexible Cost and Constraint Structures", journal="Journal of Sequential Planning and Inference", volume=132, pages="149-162", } @article{strauss:1995, author="Strauss, N. and Simon, R.", year=1995, title="Investigating a Sequence of Randomized Phase-II Trials to Discover Promising Treaments", journal="Statistics in Medicine", volume=14, pages="1479-1489", } @article{subramanian:2005, author = "Subramanian, A. and Tamayoa, P. and Mootha, V.K. and Mukherjeed, S. and Eberta, B.L. and Gillettea, M.A. and Paulovichg, A. and Pomeroyh, S.L. and Goluba, T.R. and Landera, E.S. and Mesirova, J.P.", title = "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles", journal = "PNAS", year = 2005, volume=102, pages="15545-15550", } @Misc{tusch:2005, author="Tusch, G.", year=2005, title="Sequential classification for microarray and clinical data", howpublished="IEEE Computational Systems Bioinformatics Conference Workshops", pages="5-6", } @article{tusher:2001, author="Tusher, V.G. and Tibshirani, R. and Chu, G.", year=2001, title="Significance analysis of microarrays applied to the ionizing radiation response", journal="Proceedings of the National Academy of Science", volume=98, pages="5116-5121", } @article{vejohnson:2005, author="Johnson, V.E.", year=2005, title="{B}ayes factors based on test statistics", journal="Journal of the {R}oyal statistical society B", volume=67, pages="689-701", } @Book{wand:1995, author="Wand, M.P. and Jones, M.C.", year=1995, title="Kernel Smoothing", publisher="Chapman and Hall", address="London", } @article{wang:1998, author="Wand, Y.G. and Leung, D.H.Y.", year=1998, title="An optimal design for screening trials", journal="Biometrics", volume=54, pages="243-250", } @book{whitehead:1997, author="Whitehead, J.", year=1997, title="The Design and Analysis of Sequential Clinical Trials, Revised, 2nd Edition", publisher="Wiley", address="New York", } @article{wood:2004, author="Wood, S.N.", year=2004, title="Stable and efficient multiple smoothing parameter estimation for generalized additive models", journal="Journal of the Americal Statistical Association", volume=99, pages="673-686", } @article{wood:2008, author="Wood, S.N.", year=2008, title="Fast stable direct fitting and smoothness selection for generalized additive models", journal="Journal of the Royal Statistical Association B", volume=70, pages="495-518", } @techreport{wu:2004, author="Wu, Z. and Irizarry, R.A. and Gentleman, R. and Murillo, F.M. and Spencer, F.", year=2004, title="A Model Based Background Adjustment for Oligonucleotide Expression Arrays", institution="Johns Hopkins University, Dept. of Biostatistics", } @article{yang:2003, author="Yang, M.C.K. and Yang, J.J. and McIndoe, R.A. and She, S.X.", year=2003, title="Microarray experimental design: power and sample size considerations", journal="Physiological Genomics", volume=16, pages="24-28", } @article{yao:1996, author="Yao, T.J. and Begg, C.B. and Livingston, P.O.", year=1996, title="Optimal sample size for a series of pilot trials of new agents", journal="Biometrics", volume=52, pages="992-1001", } @article{yao:1998, author="Yao, T.J. and Venkatraman, E.S.", year=1998, title="Optimal two-stage design for a series of pilot trials of new agents", journal="Biometrics", volume=54, pages="1183-1189", } @article{yuan:2006, author="Yuan, M. and Kendziorski, C.", year=2006, title="A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification", journal="Biometrics", volume=62, pages="1089-1098", } @Inbook{zellner:1980, author="Zellner, A. and Siow, A.", year=1980, title="Posterior odds ratios for selected regression hypotheses", booktitle="Bayesian statistics", editor="Bernardo, J.M. and DeGroot, M.H. and Lindley, D.V. and Smith, A.F.M.", publisher="Valencia: University Press", volume=1, } @article{zhao:2005, author="Zhao, Y. and Li, M.C. and Simon, R.", year=2005, title="An adaptive method for c{DNA} microarray normalization", journal="Bioinformatics", volume=6, pages=28, } @article{zhang:2008, author="Zhang, Y. and Liu, T. and Meyer, C.A. and Eeckhoute, J. and Johnson, D.S. and Bernstein, B.E. and Nussbaum, C. and Myers, R.M. and Brown, M. and Li, W. and Liu, X.S.", year=2008, title="Model-based Analysis of ChIP-Seq (MACS)", journal="Genome {B}iology", volume="9", pages="R173", } @article{zien:2003, author="Zien, A. and Fluck, J. and Zimmer, R. and Lengauer, T.", year=2003, title="Microarrays: how many do you need?", journal="Journal of Computational Biology", volume=10, pages="653-667", }