TY - JOUR AU - Schena, M. AU - Shalon, D. AU - Davis, R. W. AU - Brown, P. O. PY - 1995 DA - 1995// TI - Quantitative monitoring of gene expression patterns with a complementary DNA microarray JO - Science VL - 270 UR - https://doi.org/10.1126/science.270.5235.467 DO - 10.1126/science.270.5235.467 ID - Schena1995 ER - TY - JOUR AU - Lockhart, D. J. AU - Dong, H. AU - Byrne, M. C. AU - Follettie, M. T. AU - Gallo, M. V. AU - Chee, M. S. AU - Mittmann, M. AU - Wang, C. AU - Kobayashi, M. AU - Horton, H. AU - Brown, E. L. PY - 1996 DA - 1996// TI - Expression monitoring by hybridization to high-density oligonucleotide arrays JO - Nat Biotechnol VL - 14 UR - https://doi.org/10.1038/nbt1296-1675 DO - 10.1038/nbt1296-1675 ID - Lockhart1996 ER - TY - JOUR AU - Slonim, D. K. PY - 2002 DA - 2002// TI - From pattern to pathways: gene expression data analysis comes of age JO - Nature Genetics VL - 32 UR - https://doi.org/10.1038/ng1033 DO - 10.1038/ng1033 ID - Slonim2002 ER - TY - JOUR AU - Quackenbush, J. PY - 2001 DA - 2001// TI - Computational Analysis of Microarray Data JO - Nature Reviews Genetics VL - 2 UR - https://doi.org/10.1038/35076576 DO - 10.1038/35076576 ID - Quackenbush2001 ER - TY - JOUR AU - Eisen, M. B. AU - Spellman, P. T. AU - Brown, P. O. AU - Botstein, D. PY - 1998 DA - 1998// TI - Cluster analysis and display of genome-wide expression patterns JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.25.14863 DO - 10.1073/pnas.95.25.14863 ID - Eisen1998 ER - TY - JOUR AU - Tavazoie, S. AU - Hughes, J. D. AU - Campbell, M. J. AU - Cho, R. J. AU - Church, G. M. PY - 1999 DA - 1999// TI - Systematic determination of genetic network architecture JO - Nat Genet VL - 22 UR - https://doi.org/10.1038/10343 DO - 10.1038/10343 ID - Tavazoie1999 ER - TY - JOUR AU - Tamayo, P. AU - Slonim, D. AU - Mesirov, J. AU - Zhu, Q. AU - Kitareewan, S. AU - Dmitrovsky, E. AU - Lander, E. S. AU - Golub, T. R. PY - 1999 DA - 1999// TI - Interpreting patterns of gene expression withself-organizing maps: methods and application to hematopoietic differentiation JO - Proc Natl Acad Sci USA VL - 22 UR - https://doi.org/10.1073/pnas.96.6.2907 DO - 10.1073/pnas.96.6.2907 ID - Tamayo1999 ER - TY - JOUR AU - D'haeseleer, P. PY - 2005 DA - 2005// TI - How does gene expression clustering work? JO - Nature Biotechnology VL - 23 UR - https://doi.org/10.1038/nbt1205-1499 DO - 10.1038/nbt1205-1499 ID - D'haeseleer2005 ER - TY - JOUR AU - Fraley, C. AU - Raftery, A. E. PY - 2002 DA - 2002// TI - Model-based clustering, discriminant analysis and density estimation JO - J Am Stat Assoc VL - 97 UR - https://doi.org/10.1198/016214502760047131 DO - 10.1198/016214502760047131 ID - Fraley2002 ER - TY - JOUR AU - Yeung, K. Y. AU - Fraley, C. AU - Murua, A. AU - Raftery, A. E. AU - Ruzzo, W. L. PY - 2001 DA - 2001// TI - Model-based clustering and data transformations for gene expression data JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.10.977 DO - 10.1093/bioinformatics/17.10.977 ID - Yeung2001 ER - TY - JOUR AU - Siegmund, K. D. AU - Laird, P. W. AU - Laird-Offringa, I. A. PY - 2004 DA - 2004// TI - A comparison of cluster analysis methods using DNA methylation data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth176 DO - 10.1093/bioinformatics/bth176 ID - Siegmund2004 ER - TY - JOUR AU - Lin, K. K. AU - Chudova, D. AU - Hatfield, G. W. AU - Smyth, P. AU - Andersen, B. PY - 2004 DA - 2004// TI - Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance JO - Proceedings of the National Academy of Science USA VL - 101 UR - https://doi.org/10.1073/pnas.0407114101 DO - 10.1073/pnas.0407114101 ID - Lin2004 ER - TY - JOUR AU - Hein, A. M. K. AU - Richardson, S. AU - Causton, H. C. AU - Ambler, G. K. AU - Green, P. J. PY - 2005 DA - 2005// TI - BGX: afully bayesian integrated approach to the analysis of Affymetrix GeneChip data JO - Biostatistics VL - 4 ID - Hein2005 ER - TY - JOUR AU - Li, C. AU - Wong, W. H. PY - 2001 DA - 2001// TI - Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application JO - Genome Biology VL - 2 ID - Li2001 ER - TY - JOUR AU - Rattray, M. AU - Liu, X. AU - Sanguinetti, G. AU - Milo, M. AU - Lawrence, N. PY - 2006 DA - 2006// TI - Propagating Uncertainty in Microarray Data Analysis JO - Briefings in Bioinformatics VL - 7 UR - https://doi.org/10.1093/bib/bbk003 DO - 10.1093/bib/bbk003 ID - Rattray2006 ER - TY - JOUR AU - Sanguinetti, G. AU - Milo, M. AU - Rattray, M. AU - Lawrence, N. D. PY - 2005 DA - 2005// TI - Accounting for probe-level noise in principal component analysis of microarray data JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti617 DO - 10.1093/bioinformatics/bti617 ID - Sanguinetti2005 ER - TY - JOUR AU - Liu, X. AU - Milo, M. AU - Lawrence, N. D. AU - Rattray, M. PY - 2006 DA - 2006// TI - Probe-level measurement error improves accuracy in detecting differential gene expression JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl361 DO - 10.1093/bioinformatics/btl361 ID - Liu2006 ER - TY - JOUR AU - Liu, X. AU - Milo, M. AU - Lawrence, N. D. AU - Rattray, M. PY - 2005 DA - 2005// TI - A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti583 DO - 10.1093/bioinformatics/bti583 ID - Liu2005 ER - TY - STD TI - PUMA – Propagating Uncertainty in Microarray Analysis[http://www.bioinf.manchester.ac.uk/resources/puma/] UR - http://www.bioinf.manchester.ac.uk/resources/puma/ ID - ref19 ER - TY - JOUR AU - Fraley, C. AU - Raftery, A. E. PY - 2002 DA - 2002// TI - Mclust: software for model-based cluster analysis JO - J Classification VL - 16 UR - https://doi.org/10.1007/s003579900058 DO - 10.1007/s003579900058 ID - Fraley2002 ER - TY - JOUR AU - Milligan, G. W. AU - Cooper, M. C. PY - 1986 DA - 1986// TI - A study of the comparability of external criteria for hierarchical cluster analysis JO - Multivariate Behavioral Research VL - 21 UR - https://doi.org/10.1207/s15327906mbr2104_5 DO - 10.1207/s15327906mbr2104_5 ID - Milligan1986 ER - TY - JOUR AU - Hubert, L. AU - Arable, P. PY - 1985 DA - 1985// TI - Comparing partitions JO - Journal of classification VL - 2 UR - https://doi.org/10.1007/BF01908075 DO - 10.1007/BF01908075 ID - Hubert1985 ER - TY - JOUR AU - Yeung, K. Y. AU - Medvedovic, M. AU - Bumgarner, R. E. PY - 2003 DA - 2003// TI - Clustering gene-expression data with repeated measurements JO - Genome Biology VL - 4 UR - https://doi.org/10.1186/gb-2003-4-5-r34 DO - 10.1186/gb-2003-4-5-r34 ID - Yeung2003 ER - TY - JOUR AU - Bolshakova, N. AU - Azuaje, F. PY - 2003 DA - 2003// TI - Cluster validation techniques for genome expression data JO - Signal Process VL - 83 UR - https://doi.org/10.1016/S0165-1684(02)00475-9 DO - 10.1016/S0165-1684(02)00475-9 ID - Bolshakova2003 ER - TY - JOUR AU - Medvedovic, M. AU - Yeung, K. Y. AU - Bumgarner, R. E. PY - 2004 DA - 2004// TI - Bayesian mixture model based clustering of replicated microarray data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth068 DO - 10.1093/bioinformatics/bth068 ID - Medvedovic2004 ER - TY - JOUR AU - Tu, B. P. AU - Kudlicki, A. AU - Rowicka, M. AU - McKnight, S. L. PY - 2005 DA - 2005// TI - Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes JO - Science VL - 310 UR - https://doi.org/10.1126/science.1120499 DO - 10.1126/science.1120499 ID - Tu2005 ER - TY - BOOK PY - 2002 DA - 2002// TI - Statistical algorithms reference guide PB - Affymetrix Inc CY - Santa Clara CA ID - ref27 ER - TY - JOUR AU - Baldi, P. AU - Long, A. D. PY - 2001 DA - 2001// TI - A Baysian framework for the analysis of microarray expression data: regularized t-test and statistical infrence of gene changes JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.6.509 DO - 10.1093/bioinformatics/17.6.509 ID - Baldi2001 ER - TY - STD TI - Gene Expression Omnibus, accession number GDS912[http://www.ncbi.nlm.nih.gov/projects/geo/] UR - http://www.ncbi.nlm.nih.gov/projects/geo/ ID - ref29 ER - TY - JOUR AU - Wu, Z. AU - Irizarry, R. A. AU - Gentleman, R. AU - Martinez-Murillo, F. AU - Spencer, F. PY - 2004 DA - 2004// TI - A model-based background adjustment for oligonucleotide expression arrays JO - Journal of the American Statistical Association VL - 99 UR - https://doi.org/10.1198/016214504000000683 DO - 10.1198/016214504000000683 ID - Wu2004 ER - TY - JOUR AU - Schwartz, G. PY - 1978 DA - 1978// TI - Estimating the dimension of a model JO - Ann Stat VL - 6 UR - https://doi.org/10.1214/aos/1176344136 DO - 10.1214/aos/1176344136 ID - Schwartz1978 ER - TY - CHAP AU - Fraley, C. AU - Raftery, A. E. PY - 2002 DA - 2002// TI - MCLUST: Software for Model-Based Clustering, Discriminant Analysis and Density Estimation BT - Tech Rep 415R PB - Department of Statistics CY - University of Washington ID - Fraley2002 ER - TY - JOUR AU - Dennis, G. AU - Sherman, B. T. AU - Hosack, D. A. AU - Yang, J. AU - Gao, W. AU - Lane, H. C. AU - Lempicki, R. A. PY - 2003 DA - 2003// TI - DAVID: database for annotation, visualization, and integrated discovery JO - Genome Biology VL - 4 UR - https://doi.org/10.1186/gb-2003-4-5-p3 DO - 10.1186/gb-2003-4-5-p3 ID - Dennis2003 ER - TY - JOUR AU - Dempster, A. P. AU - Laird, N. M. AU - Rubin, D. B. PY - 1977 DA - 1977// TI - Maximum likelihood from incomplete data via the EM algorithm JO - Journal of the Royal Statistical Society B VL - 39 ID - Dempster1977 ER - TY - JOUR AU - Banfield, J. D. AU - Raftery, A. E. PY - 1993 DA - 1993// TI - Model-based Gaussian and non-Gaussian clustering JO - Biometrics VL - 49 UR - https://doi.org/10.2307/2532201 DO - 10.2307/2532201 ID - Banfield1993 ER - TY - JOUR AU - Gill, P. E. AU - Murray, W. AU - Saunders, M. A. PY - 2002 DA - 2002// TI - SNOPT: an SQP algorithm for large-scale constrained optimization JO - SIAM Journal on Optimization VL - 12 UR - https://doi.org/10.1137/S1052623499350013 DO - 10.1137/S1052623499350013 ID - Gill2002 ER - TY - JOUR AU - Spellucci, P. A. PY - 1998 DA - 1998// TI - A SQP method for general nonlinear programs using only equality constrained subproblems JO - Mathematical Programming VL - 82 ID - Spellucci1998 ER -