TY - JOUR AU - Hegde, P. AU - Qi, R. AU - Abernathy, K. AU - Gay, C. AU - Dharap, S. AU - Gaspard, R. AU - Hughes, J. E. AU - Snesrud, E. AU - Lee, N. AU - Quackenbush, J. PY - 2000 DA - 2000// TI - A concise guide to cDNA microarray analysis JO - BioTechniques VL - 29 ID - Hegde2000 ER - TY - JOUR AU - Duggan, D. J. AU - Bittner, M. AU - Chen, Y. AU - Meltzer, P. AU - Trent, J. M. PY - 1999 DA - 1999// TI - Expression profiling using cDNA microarrays JO - Nature Genetics VL - 21 UR - https://doi.org/10.1038/4434 DO - 10.1038/4434 ID - Duggan1999 ER - TY - JOUR AU - Schena, M. AU - Heller, R. A. AU - Theriault, T. P. AU - Konrad, K. AU - Lachenmeier, E. AU - Davis, R. W. PY - 1998 DA - 1998// TI - Microarrays: Biotechnology's discovery platform for functional genomics JO - Trends in Biotechnology VL - 16 UR - https://doi.org/10.1016/S0167-7799(98)01219-0 DO - 10.1016/S0167-7799(98)01219-0 ID - Schena1998 ER - TY - JOUR AU - Ramsay, G. PY - 1998 DA - 1998// TI - DNA chips: State-of-the art JO - Nature Biotechnology VL - 16 UR - https://doi.org/10.1038/nbt0198-40 DO - 10.1038/nbt0198-40 ID - Ramsay1998 ER - TY - BOOK PY - 2000 DA - 2000// TI - Microarray Biochip Technology PB - Eaton Publishing CY - Natick, MA ID - ref5 ER - TY - BOOK PY - 2003 DA - 2003// TI - DNA Microarrays: A molecular cloning manual PB - Cold Spring Harbor Press CY - Cold Spring, NY ID - ref6 ER - TY - CHAP AU - Segal, E. AU - Friedman, N. AU - Kaminski, N. AU - Regev, A. AU - Koller, D. PY - 2005 DA - 2005// TI - From signatures to models: Understanding cancer using microarrays BT - Nature Genetics ID - Segal2005 ER - TY - JOUR AU - Mischel, P. S. AU - Cloughesy, T. F. AU - Nelson, S. F. PY - 2004 DA - 2004// TI - DNA-microarray analysis of brain cancer: Molecular classification for therapy JO - Nature Reviews Neuroscience VL - 5 UR - https://doi.org/10.1038/nrn1518 DO - 10.1038/nrn1518 ID - Mischel2004 ER - TY - CHAP AU - Nevins, J. R. AU - Huang, E. S. AU - Dressman, H. AU - Pittman, J. AU - Huang, A. T. AU - West, M. PY - 2003 DA - 2003// TI - Towards integrated clinico-genomic models for personalized medicine: Combining gene expression signatures and clinical factors in breast cancer outcomes prediction BT - Human Molecular Genetics ID - Nevins2003 ER - TY - JOUR AU - Carr, K. M. AU - Bittner, M. AU - Trent, J. M. PY - 2003 DA - 2003// TI - Gene-expression profiling in human cutaneous melanoma JO - Oncogene VL - 22 UR - https://doi.org/10.1038/sj.onc.1206448 DO - 10.1038/sj.onc.1206448 ID - Carr2003 ER - TY - JOUR AU - Staudt, L. M. PY - 2002 DA - 2002// TI - Gene expression profiling of lymphoid malignancies JO - Annual Review of Medicine VL - 53 UR - https://doi.org/10.1146/annurev.med.53.082901.103941 DO - 10.1146/annurev.med.53.082901.103941 ID - Staudt2002 ER - TY - JOUR AU - Cooper, C. S. PY - 2001 DA - 2001// TI - Applications of microarray technology in breast cancer research JO - Breast Cancer Research VL - 3 UR - https://doi.org/10.1186/bcr291 DO - 10.1186/bcr291 ID - Cooper2001 ER - TY - JOUR AU - Alizadeh, A. A. AU - Ross, D. T. AU - Perou, C. M. AU - Rijn, M. V. a. n. D. e. PY - 2001 DA - 2001// TI - Towards a novel classification of human malignancies based on gene expression patterns JO - Journal of Pathology VL - 195 UR - https://doi.org/10.1002/path.889 DO - 10.1002/path.889 ID - Alizadeh2001 ER - TY - JOUR AU - Belbin, T. J. AU - Singh, B. AU - Barber, I. AU - Socci, N. AU - Wenig, B. AU - Smith, R. AU - Prystowsky, M. B. AU - Childs, G. PY - 2002 DA - 2002// TI - Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays JO - Cancer Research VL - 62 ID - Belbin2002 ER - TY - JOUR AU - West, M. AU - Blanchette, C. AU - Dressman, H. AU - Huang, E. AU - Ishida, S. AU - Spang, R. AU - Zuzan, H. AU - Olson, J. A. AU - Marks, J. R. AU - Nevins, J. R. PY - 2001 DA - 2001// TI - Predicting the clinical status of human breast cancer by using gene expression profiles JO - Proceedings of the National Academy of Sciences of the United States of America VL - 98 UR - https://doi.org/10.1073/pnas.201162998 DO - 10.1073/pnas.201162998 ID - West2001 ER - TY - JOUR AU - Notterman, D. A. AU - Alon, U. AU - Sierk, A. J. AU - Levine, A. J. PY - 2001 DA - 2001// TI - Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays JO - Cancer Research VL - 61 ID - Notterman2001 ER - TY - JOUR AU - Alizadeh, A. A. AU - Elsen, M. B. AU - Davis, R. E. AU - Ma, C. L. AU - Lossos, I. S. AU - Rosenwald, A. AU - Boldrick, J. C. AU - Sabet, H. AU - Tran, T. AU - Yu, X. AU - Powell, J. I. AU - Yang, L. AU - Maru, G. E. AU - Moore, T. AU - Hudson, J. AU - Lu, L. AU - Lewis, D. B. AU - Tibshirani, R. AU - Sherlock, G. AU - Chan, W. C. AU - Greiner, T. C. AU - Weisenburger, D. D. AU - Armitage, J. O. AU - Warnke, R. AU - Levy, R. AU - Wilson, W. AU - Grever, M. R. AU - Byrd, J. C. AU - Botstein, D. AU - Brown, P. O. AU - Staudt, L. M. PY - 2000 DA - 2000// TI - Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling JO - Nature VL - 403 UR - https://doi.org/10.1038/35000501 DO - 10.1038/35000501 ID - Alizadeh2000 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 - CHAP AU - Huber, W. AU - Von Heydebreck, A. PY - 2002 DA - 2002// TI - Variance stabilization applied to microarray data calibration and to the quantification of differential expression BT - Bioinformatics ID - Huber2002 ER - TY - JOUR AU - Jain, N. AU - Thatte, J. AU - Braciale, T. AU - Ley, K. AU - O'Connell, M. AU - Lee, J. K. PY - 2003 DA - 2003// TI - Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg264 DO - 10.1093/bioinformatics/btg264 ID - Jain2003 ER - TY - JOUR AU - Pan, W. PY - 2002 DA - 2002// TI - A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.4.546 DO - 10.1093/bioinformatics/18.4.546 ID - Pan2002 ER - TY - JOUR AU - Pan, W. PY - 2003 DA - 2003// TI - On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg167 DO - 10.1093/bioinformatics/btg167 ID - Pan2003 ER - TY - JOUR AU - Rajagopalan, D. PY - 2003 DA - 2003// TI - A comparison of statistical methods for analysis of high density oligonucleotide array data JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg202 DO - 10.1093/bioinformatics/btg202 ID - Rajagopalan2003 ER - TY - JOUR AU - Rocke, D. M. AU - Durbin, B. PY - 2001 DA - 2001// TI - A model for measurement error for gene expression arrays JO - Journal of Computational Biology VL - 8 UR - https://doi.org/10.1089/106652701753307485 DO - 10.1089/106652701753307485 ID - Rocke2001 ER - TY - JOUR AU - Troyanskaya, O. G. AU - Garber, M. E. AU - Brown, P. O. AU - Botstein, D. AU - Altman, R. B. PY - 2002 DA - 2002// TI - Nonparametric methods for identifying differentially expressed genes in microarray data JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.11.1454 DO - 10.1093/bioinformatics/18.11.1454 ID - Troyanskaya2002 ER - TY - JOUR AU - Tusher, V. G. AU - Tibshirani, R. AU - Chu, G. PY - 2001 DA - 2001// TI - Significance analysis of microarrays applied to the ionizing radiation response JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.091062498 DO - 10.1073/pnas.091062498 ID - Tusher2001 ER - TY - JOUR AU - Wille, A. AU - Gruissem, W. AU - Buhlmann, P. AU - Hennig, L. PY - 2007 DA - 2007// TI - EVE (external variance estimation) increases statistical power for detecting differentially expressed genes JO - Plant J VL - 52 UR - https://doi.org/10.1111/j.1365-313X.2007.03227.x DO - 10.1111/j.1365-313X.2007.03227.x ID - Wille2007 ER - TY - JOUR AU - DeRisi, J. L. AU - Iyer, V. R. AU - Brown, P. O. PY - 1997 DA - 1997// TI - Exploring the metabolic and genetic control of gene expression on a genomic scale JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5338.680 DO - 10.1126/science.278.5338.680 ID - DeRisi1997 ER - TY - JOUR AU - Simon, R. AU - Radmacher, M. D. AU - Dobbin, K. AU - McShane, L. M. PY - 2003 DA - 2003// TI - Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification JO - Journal of the National Cancer Institute VL - 95 UR - https://doi.org/10.1093/jnci/95.1.14 DO - 10.1093/jnci/95.1.14 ID - Simon2003 ER - TY - JOUR AU - Baldi, P. AU - Long, A. D. PY - 2001 DA - 2001// TI - A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences 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 - JOUR AU - Dudoit, S. AU - Fridlyand, J. AU - Speed, T. P. PY - 2002 DA - 2002// TI - Comparison of discrimination methods for the classification of tumors using gene expression data JO - Journal of the American Statistical Association VL - 97 UR - https://doi.org/10.1198/016214502753479248 DO - 10.1198/016214502753479248 ID - Dudoit2002 ER - TY - JOUR AU - Churchill, G. A. PY - 2004 DA - 2004// TI - Using ANOVA to analyze microarray data JO - Biotechniques VL - 37 ID - Churchill2004 ER - TY - JOUR AU - Draghici, S. AU - Kulaeva, O. AU - Hoff, B. AU - Petrov, A. AU - Shams, S. AU - Tainsky, M. A. PY - 2003 DA - 2003// TI - Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg165 DO - 10.1093/bioinformatics/btg165 ID - Draghici2003 ER - TY - JOUR AU - Wolfinger, R. D. AU - Gibson, G. AU - Wolfinger, E. D. AU - Bennett, L. AU - Hamadeh, H. AU - Bushel, P. AU - Afshari, C. AU - Paules, R. S. PY - 2001 DA - 2001// TI - Assessing gene significance from cDNA microarray expression data via mixed models JO - Journal of Computational Biology VL - 8 UR - https://doi.org/10.1089/106652701753307520 DO - 10.1089/106652701753307520 ID - Wolfinger2001 ER - TY - JOUR AU - Valls, J. AU - Grau, M. AU - Sole, X. AU - Hernandez, P. AU - Montaner, D. AU - Dopazo, J. AU - Peinado, M. A. AU - Capella, G. AU - Moreno, V. AU - Pujana, M. A. PY - 2008 DA - 2008// TI - CLEAR-test: Combining inference for differential expression and variability in microarray data analysis JO - Journal of Biomedical Informatics VL - 41 UR - https://doi.org/10.1016/j.jbi.2007.05.005 DO - 10.1016/j.jbi.2007.05.005 ID - Valls2008 ER - TY - JOUR AU - Oleksiak, M. F. AU - Churchill, G. A. AU - Crawford, D. L. PY - 2002 DA - 2002// TI - Variation in gene expression within and among natural populations JO - Nat Genet VL - 32 UR - https://doi.org/10.1038/ng983 DO - 10.1038/ng983 ID - Oleksiak2002 ER - TY - JOUR AU - Lambrechts, D. AU - Robberecht, W. AU - Carmeliet, P. PY - 2007 DA - 2007// TI - Heterogeneity in motoneuron disease JO - Trends in Neurosciences VL - 30 UR - https://doi.org/10.1016/j.tins.2007.07.002 DO - 10.1016/j.tins.2007.07.002 ID - Lambrechts2007 ER - TY - JOUR AU - Bijlani, R. AU - Cheng, Y. AU - Pearce, D. A. AU - Brooks, A. I. AU - Ogihara, M. PY - 2003 DA - 2003// TI - Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED) JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.1.62 DO - 10.1093/bioinformatics/19.1.62 ID - Bijlani2003 ER - TY - JOUR AU - Lyons-Weiler, J. AU - Patel, S. AU - Becich, M. J. AU - Godfrey, T. E. PY - 2004 DA - 2004// TI - Tests for finding complex patterns of differential expression in cancers: towards individualized medicine JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-110 DO - 10.1186/1471-2105-5-110 ID - Lyons-Weiler2004 ER - TY - JOUR AU - Seth, G. AU - Philp, R. J. AU - Lau, A. AU - Kok, Y. J. AU - Yap, M. AU - Hu, W. S. PY - 2007 DA - 2007// TI - Molecular portrait of high productivity in recombinant NSO cells JO - Biotechnol Bioeng VL - 97 UR - https://doi.org/10.1002/bit.21234 DO - 10.1002/bit.21234 ID - Seth2007 ER - TY - JOUR AU - Tibshirani, R. AU - Hastie, T. PY - 2007 DA - 2007// TI - Outlier sums for differential gene expression analysis JO - Biostatistics VL - 8 UR - https://doi.org/10.1093/biostatistics/kxl005 DO - 10.1093/biostatistics/kxl005 ID - Tibshirani2007 ER - TY - JOUR AU - Tomlins, S. A. AU - Rhodes, D. R. AU - Perner, S. AU - Dhanasekaran, S. M. AU - Mehra, R. AU - Sun, X. W. AU - Varambally, S. AU - Cao, X. AU - Tchinda, J. AU - Kuefer, R. AU - Lee, C. AU - Montie, J. E. AU - Shah, R. B. AU - Pienta, K. J. AU - Rubin, M. A. AU - Chinnaiyan, A. M. PY - 2005 DA - 2005// TI - Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer JO - Science VL - 310 UR - https://doi.org/10.1126/science.1117679 DO - 10.1126/science.1117679 ID - Tomlins2005 ER - TY - JOUR AU - Wu, B. PY - 2007 DA - 2007// TI - Cancer outlier differential gene expression detection JO - Biostatistics (Oxford, England) VL - 8 UR - https://doi.org/10.1093/biostatistics/kxl029 DO - 10.1093/biostatistics/kxl029 ID - Wu2007 ER - TY - CHAP AU - Lian, H. PY - 2007 DA - 2007// TI - MOST: detecting cancer differential gene expression BT - Biostat ID - Lian2007 ER - TY - CHAP AU - McClave, J. T. AU - Sincich, T. PY - 1999 DA - 1999// BT - Statistics ID - McClave1999 ER - TY - JOUR AU - Jeffery, I. B. AU - Higgins, D. G. AU - Culhane, A. C. PY - 2006 DA - 2006// TI - Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-359 DO - 10.1186/1471-2105-7-359 ID - Jeffery2006 ER - TY - JOUR AU - Alon, U. AU - Barka, N. AU - Notterman, D. A. AU - Gish, K. AU - Ybarra, S. AU - Mack, D. AU - Levine, A. J. PY - 1999 DA - 1999// TI - Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays JO - Proceedings of the National Academy of Sciences of the United States of America VL - 96 UR - https://doi.org/10.1073/pnas.96.12.6745 DO - 10.1073/pnas.96.12.6745 ID - Alon1999 ER - TY - JOUR AU - Singh, D. AU - Febbo, P. G. AU - Ross, K. AU - Jackson, D. G. AU - Manola, J. AU - Ladd, C. AU - Tamayo, P. AU - Renshaw, A. A. AU - D'Amico, A. V. AU - Richie, J. P. AU - Lander, E. S. AU - Loda, M. AU - Kantoff, P. W. AU - Golub, T. R. AU - Sellers, W. R. PY - 2002 DA - 2002// TI - Gene expression correlates of clinical prostate cancer behavior JO - Cancer Cell VL - 1 UR - https://doi.org/10.1016/S1535-6108(02)00030-2 DO - 10.1016/S1535-6108(02)00030-2 ID - Singh2002 ER - TY - JOUR AU - Furey, T. S. AU - Cristianini, N. AU - Duffy, N. AU - Bednarski, D. W. AU - Schummer, M. AU - Haussler, D. PY - 2000 DA - 2000// TI - Support vector machine classification and validation of cancer tissue samples using microarray expression data JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.10.906 DO - 10.1093/bioinformatics/16.10.906 ID - Furey2000 ER - TY - CHAP AU - Dettling, M. PY - 2002 DA - 2002// TI - Supervised clustering of genes BT - Genome biology ID - Dettling2002 ER - TY - JOUR AU - Ben-Dor, A. AU - Bruhn, L. AU - Friedman, N. AU - Nachman, I. AU - Schummer, M. AU - Yakhini, Z. PY - 2000 DA - 2000// TI - Tissue classification with gene expression profiles JO - Journal of Computational Biology VL - 7 UR - https://doi.org/10.1089/106652700750050943 DO - 10.1089/106652700750050943 ID - Ben-Dor2000 ER - TY - JOUR AU - Ding, C. AU - Peng, H. PY - 2005 DA - 2005// TI - Minimum redundancy feature selection from microarray gene expression data JO - Journal of Bioinformatics and Computational Biology VL - 3 UR - https://doi.org/10.1142/S0219720005001004 DO - 10.1142/S0219720005001004 ID - Ding2005 ER - TY - CHAP AU - Liu, X. AU - Krishnan, A. AU - Mondry, A. PY - 2005 DA - 2005// TI - An entropy-based gene selection method for cancer classification using microarray data BT - BMC Bioinformatics ID - Liu2005 ER - TY - JOUR AU - Zhang, J. G. AU - Deng, H. W. PY - 2007 DA - 2007// TI - Gene selection for classification of microarray data based on the Bayes error JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-370 DO - 10.1186/1471-2105-8-370 ID - Zhang2007 ER -