TY - JOUR AU - Offit, K. PY - 2011 DA - 2011// TI - Personalized medicine: new genomics, old lessons JO - Hum Genet VL - 130 UR - https://doi.org/10.1007/s00439-011-1028-3 DO - 10.1007/s00439-011-1028-3 ID - Offit2011 ER - TY - JOUR AU - Ghosh, D. AU - Poisson, L. M. PY - 2009 DA - 2009// TI - “Omics” data and levels of evidence for biomarker discovery JO - Genomics VL - 93 UR - https://doi.org/10.1016/j.ygeno.2008.07.006 DO - 10.1016/j.ygeno.2008.07.006 ID - Ghosh2009 ER - TY - JOUR AU - Mohr, S. AU - Liew, C. C. PY - 2007 DA - 2007// TI - The peripheral-blood transcriptome: new insights into disease and risk assessment JO - Trends Mol Med VL - 13 UR - https://doi.org/10.1016/j.molmed.2007.08.003 DO - 10.1016/j.molmed.2007.08.003 ID - Mohr2007 ER - TY - BOOK AU - McLachlan, G. AU - Do, K. A. AU - Ambroise, C. PY - 2005 DA - 2005// TI - Analyzing Microarray Gene Expression Data, vol. 422 PB - Wiley CY - Hoboken ID - McLachlan2005 ER - TY - JOUR AU - Ng, S. K. AU - McLachlan, G. J. AU - Wang, K. AU - Nagymanyoki, Z. AU - Liu, S. AU - Ng, S. W. PY - 2015 DA - 2015// TI - Inference on differences between classes using cluster-specific contrasts of mixed effects JO - Biostatistics VL - 16 UR - https://doi.org/10.1093/biostatistics/kxu028 DO - 10.1093/biostatistics/kxu028 ID - Ng2015 ER - TY - JOUR AU - Ben-Dor, A. AU - Shamir, R. AU - Yakhini, Z. PY - 2004 DA - 2004// TI - Clustering gene expression patterns JO - J Comput Biol VL - 6 ID - Ben-Dor2004 ER - TY - JOUR AU - Golub, T. R. AU - Slonim, D. K. AU - Tamayo, P. AU - Huard, C. AU - Gaasenbeek, M. AU - Mesirov, J. P. AU - Coller, H. AU - Loh, M. L. AU - Downing, J. R. AU - Caligiuri, M. A. AU - Bloomfield, C. D. AU - Lander, E. S. PY - 1999 DA - 1999// TI - Molecular classification of cancer: class discovery and class prediction by gene expression monitoring JO - Science VL - 286 UR - https://doi.org/10.1126/science.286.5439.531 DO - 10.1126/science.286.5439.531 ID - Golub1999 ER - TY - JOUR AU - Hartigan, J. A. PY - 1972 DA - 1972// TI - Direct clustering of a data matrix JO - J Am Stat Assoc VL - 67 UR - https://doi.org/10.1080/01621459.1972.10481214 DO - 10.1080/01621459.1972.10481214 ID - Hartigan1972 ER - TY - JOUR AU - Kluger, Y. AU - Basri, R. AU - Chang, J. T. AU - Gerstein, M. PY - 2003 DA - 2003// TI - Spectral biclustering of microarray data: coclustering genes and conditions JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.648603 DO - 10.1101/gr.648603 ID - Kluger2003 ER - TY - JOUR AU - Ward, J. H. PY - 1963 DA - 1963// TI - Hierarchical grouping to optimize an objective function JO - J Am Stat Assoc VL - 58 UR - https://doi.org/10.1080/01621459.1963.10500845 DO - 10.1080/01621459.1963.10500845 ID - Ward1963 ER - TY - JOUR AU - Hartigan, J. A. AU - Wong, M. A. PY - 1979 DA - 1979// TI - A k-means clustering algorithm JO - Appl Stat VL - 28 UR - https://doi.org/10.2307/2346830 DO - 10.2307/2346830 ID - Hartigan1979 ER - TY - STD TI - McLachlan GJ, Basford KE. Mixture models: inference and applications to clustering:1988. ID - ref12 ER - TY - BOOK AU - McNicholas, P. D. PY - 2016 DA - 2016// TI - Mixture Model-Based Classification PB - Hall/CRC Press CY - Boca Raton UR - https://doi.org/10.1201/9781315373577 DO - 10.1201/9781315373577 ID - McNicholas2016 ER - TY - JOUR AU - Spearman, C. PY - 1904 DA - 1904// TI - The proof and measurement of association between two things JO - Am J Psychol VL - 15 UR - https://doi.org/10.2307/1412159 DO - 10.2307/1412159 ID - Spearman1904 ER - TY - STD TI - Ghahramani Z, Hinton GE. The EM algorithm for factor analyzers. Technical Report CRG-TR-96-1, University of Toronto. 1997. ID - ref15 ER - TY - CHAP AU - McLachlan, G. J. AU - Peel, D. PY - 2000 DA - 2000// TI - Mixtures of factor analyzers BT - Proceedings of the Seventeenth International Conference on Machine Learning, ICML ’00 PB - Morgan Kaufmann Publishers Inc CY - San Francisco ID - McLachlan2000 ER - TY - JOUR AU - Tipping, M. E. AU - Bishop, C. M. PY - 1999 DA - 1999// TI - Mixtures of probabilistic principal component analyzers JO - Neural Comput VL - 11 UR - https://doi.org/10.1162/089976699300016728 DO - 10.1162/089976699300016728 ID - Tipping1999 ER - TY - JOUR AU - McNicholas, P. D. AU - Murphy, T. B. PY - 2008 DA - 2008// TI - Parsimonious Gaussian mixture models JO - Stat Comput VL - 18 UR - https://doi.org/10.1007/s11222-008-9056-0 DO - 10.1007/s11222-008-9056-0 ID - McNicholas2008 ER - TY - JOUR AU - Pontes, B. AU - Giráldez, R. AU - Aguilar-Ruiz, J. S. PY - 2015 DA - 2015// TI - Biclustering on expression data: A review JO - J Biomed Inform VL - 57 UR - https://doi.org/10.1016/j.jbi.2015.06.028 DO - 10.1016/j.jbi.2015.06.028 ID - Pontes2015 ER - TY - JOUR AU - Lazzeroni, L. AU - Owen, A. PY - 2000 DA - 2000// TI - Plaid models for gene expression data JO - Stat Sin VL - 12 ID - Lazzeroni2000 ER - TY - JOUR AU - Sheng, Q. AU - Moreau, Y. AU - De Moor, B. PY - 2003 DA - 2003// TI - Biclustering microarray data by gibbs sampling JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1078 DO - 10.1093/bioinformatics/btg1078 ID - Sheng2003 ER - TY - JOUR AU - Gu, J. AU - Liu, J. S. PY - 2008 DA - 2008// TI - Bayesian biclustering of gene expression data JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-1 DO - 10.1186/1471-2164-9-1 ID - Gu2008 ER - TY - STD TI - Martella F, Alfo M, Vichi M. Biclustering of gene expression data by an extension of mixtures of factor analyzers. Int J Biostat. 2008;4(1). https://www.degruyter.com/downloadpdf/j/ijb.2008.4.1/ijb.2008.4.1.1078/ijb.2008.4.1.1078.pdf. UR - https://www.degruyter.com/downloadpdf/j/ijb.2008.4.1/ijb.2008.4.1.1078/ijb.2008.4.1.1078.pdf ID - ref23 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 - J R Stat Soc Ser B Stat Methodol VL - 39 ID - Dempster1977 ER - TY - JOUR AU - Meng, X. L. AU - van Dyk, D. A. PY - 1997 DA - 1997// TI - The EM algorithm – an old folk song sung to a fast new tune (with discussion) JO - J R Stat Soc Ser B Stat Methodol VL - 59 UR - https://doi.org/10.1111/1467-9868.00082 DO - 10.1111/1467-9868.00082 ID - Meng1997 ER - TY - JOUR AU - Woodbury, M. A. PY - 1950 DA - 1950// TI - Inverting modified matrices JO - Memorandum Rep VL - 42 ID - Woodbury1950 ER - TY - JOUR AU - Aitken, A. PY - 1926 DA - 1926// TI - A series formula for the roots of algebraic and transcendental equations JO - Proc R Soc Edinb VL - 45 UR - https://doi.org/10.1017/S0370164600024871 DO - 10.1017/S0370164600024871 ID - Aitken1926 ER - TY - BOOK AU - Krishnan, T. AU - McLachlan, G. PY - 1997 DA - 1997// TI - The EM Algorithm and Extensions PB - Wiley CY - New York ID - Krishnan1997 ER - TY - JOUR AU - Bohning, D. AU - Dietz, E. AU - Schaub, R. AU - Schlattmann, P. AU - Lindsay, B. G. PY - 1994 DA - 1994// TI - The distribution of the likelihood ratio for mixtures of densities from the one-parameter exponential family JO - Ann Inst Stat Math VL - 46 UR - https://doi.org/10.1007/BF01720593 DO - 10.1007/BF01720593 ID - Bohning1994 ER - TY - JOUR AU - McNicholas, P. D. AU - Murphy, T. B. AU - McDaid, A. F. AU - Frost, D. PY - 2010 DA - 2010// TI - Serial and parallel implementations of model-based clustering via parsimonious Gaussian mixture models JO - Comput Stat Data Anal VL - 54 UR - https://doi.org/10.1016/j.csda.2009.02.011 DO - 10.1016/j.csda.2009.02.011 ID - McNicholas2010 ER - TY - JOUR AU - Schwarz, 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 - Schwarz1978 ER - TY - JOUR AU - Hubert, L. AU - Arabie, P. PY - 1985 DA - 1985// TI - Comparing partitions JO - J Classif VL - 2 UR - https://doi.org/10.1007/BF01908075 DO - 10.1007/BF01908075 ID - Hubert1985 ER - TY - JOUR AU - Biernacki, C. AU - Celeux, G. AU - Govaert, G. PY - 2000 DA - 2000// TI - Assessing a mixture model for clustering with the integrated completed likelihood JO - IEEE Trans Pattern Anal Mach Intell VL - 22 UR - https://doi.org/10.1109/34.865189 DO - 10.1109/34.865189 ID - Biernacki2000 ER - TY - CHAP AU - Akaike, H. ED - Petrov, B. N. ED - Csaki, F. PY - 1973 DA - 1973// TI - Information theory and an extension of the maximum likelihood principle BT - Proceedings of the 2nd International Symposium on Information Theory PB - Akademiai Kiado CY - Budapest ID - Akaike1973 ER - TY - JOUR AU - Beaudoin, M. S. AU - Snook, L. A. AU - Arkell, A. M. AU - Simpson, J. A. AU - Holloway, G. P. AU - Wright, D. C. PY - 2013 DA - 2013// TI - Resveratrol supplementation improves white adipose tissue function in a depot-specific manner in Zucker diabetic fatty rats JO - Am J Physiol Regul Integr Comp Physiol VL - 305 UR - https://doi.org/10.1152/ajpregu.00200.2013 DO - 10.1152/ajpregu.00200.2013 ID - Beaudoin2013 ER - TY - JOUR AU - Edgar, R. AU - Domrachev, M. AU - Lash, A. E. PY - 2002 DA - 2002// TI - Gene Expression Omnibus: NCBI gene expression and hybridization array data repository JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.207 DO - 10.1093/nar/30.1.207 ID - Edgar2002 ER - TY - JOUR AU - Gautier, L. AU - Cope, L. AU - Bolstad, B. M. AU - Irizarry, R. A. PY - 2004 DA - 2004// TI - affy–analysis of Affymetrix GeneChip data at the probe level JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg405 DO - 10.1093/bioinformatics/btg405 ID - Gautier2004 ER - TY - JOUR AU - Carvalho, B. S. AU - Irizarry, R. A. PY - 2010 DA - 2010// TI - A framework for oligonucleotide microarray preprocessing JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq431 DO - 10.1093/bioinformatics/btq431 ID - Carvalho2010 ER - TY - BOOK PY - 2016 DA - 2016// TI - R: A Language and Environment for Statistical Computing PB - R Foundation for Statistical Computing CY - Vienna ID - ref39 ER - TY - JOUR AU - Gentleman, R. C. AU - Carey, V. J. AU - Bates, D. M. PY - 2004 DA - 2004// TI - Bioconductor: Open software development for computational biology and bioinformatics JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r80 DO - 10.1186/gb-2004-5-10-r80 ID - Gentleman2004 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2008 DA - 2008// TI - Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2008.211 DO - 10.1038/nprot.2008.211 ID - Huang2008 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn923 DO - 10.1093/nar/gkn923 ID - Huang2009 ER - TY - JOUR PY - 2015 DA - 2015// TI - Gene Ontology Consortium: going forward JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1179 DO - 10.1093/nar/gku1179 ID - ref43 ER - TY - JOUR AU - Issad, T. AU - Masson, E. AU - Pagesy, P. PY - 2010 DA - 2010// TI - O-GlcNAc modification, insulin signaling and diabetic complications JO - Diabetes Metab VL - 36 UR - https://doi.org/10.1016/j.diabet.2010.09.001 DO - 10.1016/j.diabet.2010.09.001 ID - Issad2010 ER - TY - JOUR AU - Saltiel, A. R. AU - Kahn, C. R. PY - 2001 DA - 2001// TI - Insulin signalling and the regulation of glucose and lipid metabolism JO - Nature VL - 414 UR - https://doi.org/10.1038/414799a DO - 10.1038/414799a ID - Saltiel2001 ER - TY - JOUR AU - Nawrocki, A. R. AU - Rajala, M. W. AU - Tomas, E. AU - Pajvani, U. B. AU - Saha, A. K. AU - Trumbauer, M. E. AU - Pang, Z. AU - Chen, A. S. AU - Ruderman, N. B. AU - Chen, H. AU - Rossetti, L. AU - Scherer, P. E. PY - 2006 DA - 2006// TI - Mice lacking adiponectin show decreased hepatic insulin sensitivity and reduced responsiveness to peroxisome proliferator-activated receptor γ agonists JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M505311200 DO - 10.1074/jbc.M505311200 ID - Nawrocki2006 ER - TY - JOUR AU - Laffel, L. PY - 1999 DA - 1999// TI - Ketone bodies: a review of physiology, pathophysiology and application of monitoring to diabetes JO - Diabetes Metab Res Rev VL - 15 UR - https://doi.org/3.0.CO;2-8 DO - 3.0.CO;2-8 ID - Laffel1999 ER - TY - JOUR AU - Yeaman, S. J. PY - 1989 DA - 1989// TI - The 2-oxo acid dehydrogenase complexes: recent advances JO - Biochem J VL - 257 UR - https://doi.org/10.1042/bj2570625 DO - 10.1042/bj2570625 ID - Yeaman1989 ER - TY - JOUR AU - Virkamäki, A. AU - Ueki, K. AU - Kahn, C. R. PY - 1999 DA - 1999// TI - Protein–protein interaction in insulin signaling and the molecular mechanisms of insulin resistance JO - J Clin Investig VL - 103 UR - https://doi.org/10.1172/JCI6609 DO - 10.1172/JCI6609 ID - Virkamäki1999 ER - TY - JOUR AU - Taniguchi, C. M. AU - Emanuelli, B. AU - Kahn, C. R. PY - 2006 DA - 2006// TI - Critical nodes in signalling pathways: insights into insulin action JO - Nat Rev Mol Cell Biol VL - 7 UR - https://doi.org/10.1038/nrm1837 DO - 10.1038/nrm1837 ID - Taniguchi2006 ER - TY - JOUR AU - Kraegen, E. W. AU - Clark, P. W. AU - Jenkins, A. B. AU - Daley, E. A. AU - Chisholm, D. J. AU - Storlien, L. H. PY - 1991 DA - 1991// TI - Development of muscle insulin resistance after liver insulin resistance in high-fat-fed rats JO - Diabetes VL - 40 UR - https://doi.org/10.2337/diab.40.11.1397 DO - 10.2337/diab.40.11.1397 ID - Kraegen1991 ER - TY - JOUR AU - Samuel, V. T. AU - Petersen, K. F. AU - Shulman, G. I. PY - 2010 DA - 2010// TI - Lipid-induced insulin resistance: unravelling the mechanism JO - Lancet VL - 375 UR - https://doi.org/10.1016/S0140-6736(10)60408-4 DO - 10.1016/S0140-6736(10)60408-4 ID - Samuel2010 ER - TY - JOUR AU - Su, A. I. AU - Wiltshire, T. AU - Batalov, S. AU - Lapp, H. AU - Ching, K. A. AU - Block, D. AU - Zhang, J. AU - Soden, R. AU - Hayakawa, M. AU - Kreiman, G. AU - Cooke, M. P. AU - Walker, J. R. AU - Hogenesch, J. B. PY - 2004 DA - 2004// TI - A gene atlas of the mouse and human protein-encoding transcriptomes JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0400782101 DO - 10.1073/pnas.0400782101 ID - Su2004 ER - TY - JOUR AU - Ishii, K. J. AU - Akira, S. PY - 2008 DA - 2008// TI - Potential link between the immune system and metabolism of nucleic acids JO - Curr Opin Immunol VL - 20 UR - https://doi.org/10.1016/j.coi.2008.07.002 DO - 10.1016/j.coi.2008.07.002 ID - Ishii2008 ER - TY - JOUR AU - Neefjes, J. AU - Jongsma, M. L. M. AU - Paul, P. AU - Bakke, O. PY - 2011 DA - 2011// TI - Towards a systems understanding of MHC class I and MHC class II antigen presentation JO - Nat Rev Immunol VL - 11 ID - Neefjes2011 ER - TY - JOUR AU - Paludan, S. AU - Bowie, A. PY - 2013 DA - 2013// TI - Immune sensing of DNA JO - Immunity VL - 38 UR - https://doi.org/10.1016/j.immuni.2013.05.004 DO - 10.1016/j.immuni.2013.05.004 ID - Paludan2013 ER - TY - JOUR AU - Parcej, D. AU - Tampe, R. PY - 2010 DA - 2010// TI - ABC proteins in antigen translocation and viral inhibition JO - Nat Chem Biol VL - 6 UR - https://doi.org/10.1038/nchembio.410 DO - 10.1038/nchembio.410 ID - Parcej2010 ER - TY - JOUR AU - Chaussabel, D. AU - Pascual, V. AU - Banchereau, J. PY - 2010 DA - 2010// TI - Assessing the human immune system through blood transcriptomics JO - BMC Biol VL - 8 UR - https://doi.org/10.1186/1741-7007-8-84 DO - 10.1186/1741-7007-8-84 ID - Chaussabel2010 ER - TY - JOUR AU - Sullivan, P. F. AU - Fan, C. AU - Perou, C. M. PY - 2006 DA - 2006// TI - Evaluating the comparability of gene expression in blood and brain JO - Am J Med Genet B Neuropsychiatr Genet VL - 141B UR - https://doi.org/10.1002/ajmg.b.30272 DO - 10.1002/ajmg.b.30272 ID - Sullivan2006 ER - TY - JOUR AU - Chen, J. AU - Chen, Z. PY - 2008 DA - 2008// TI - Extended Bayesian information criteria for model selection with large model spaces JO - Biometrika VL - 95 UR - https://doi.org/10.1093/biomet/asn034 DO - 10.1093/biomet/asn034 ID - Chen2008 ER - TY - JOUR AU - McNicholas, P. D. AU - Murphy, T. B. PY - 2010 DA - 2010// TI - Model-based clustering of microarray expression data via latent Gaussian mixture models JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq498 DO - 10.1093/bioinformatics/btq498 ID - McNicholas2010 ER - TY - JOUR AU - McLachlan, G. J. AU - Bean, R. W. AU - Peel, D. PY - 2002 DA - 2002// TI - A mixture model-based approach to the clustering of microarray expression data JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.413 DO - 10.1093/bioinformatics/18.3.413 ID - McLachlan2002 ER -