Citations: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays - Alon, Barkai, Notterman, Gish, Ybarra, Mack, Levine (ResearchIndex)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, and Mack D. Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America, 96:6745--6750, 1999.

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Rule Induction for Classification of Gene Expression Array.. - Liden, Asker, Boström (Correct)

....is a useful measure for ranked feature selection in this domain. 1 Introduction Gene expression array technology has become a standard tool for studying patterns and dynamics of the genetic mechanisms of living cells. Many recent studies have highlighted its usefulness for studying cancer [1] [2], 3] Gene expression profiling does not only provide an attractive alternative to current standard techniques such as histology, genotyping, and immunostaining for tumor classification, but also valuable insights into the molecular characteristics of specific cancer types. In clinical settings, ....

....side effects. To date, a number of methods have been applied to the problem of learning computers to classify cancer types based on gene expression measurements from microarrays. Alon et al. used clustering as a means for classification in their original analysis of the colon cancer data set [2]. Subsequently, methods such as Support Vector Machines (SVMs) 4] 5] Nave Bayesian Classification [6] Artificial Neural Networks (ANNs) 3] and decision trees [7] have been employed to address this task. Some of these studies indicate that besides creating accurate prediction models, an ....

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Alon,U., Barkai,N., Notterman,D.A., Gish,K., Ybarra,S., Mack,S.Y.D. and Levine,A.J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci., 96, 67456750.

Gene Expression Data Analysis of Human Lymphoma Using Support.. - Valentini (2001) (Correct)

.... patterns for both grouping sets of genes, or sets of di erent cells, or di erent functional status of the same cell [7, 20, 25, 43, 47] Using this approach we can discover functionally correlated genes [14, 42, 45] or we can separate expression patterns of normal from pathological tissues [2, 6, 40]. Also, new functional classes not detected using traditional tumor classi cation can be discovered, and these sometimes correspond to di erent diseases with di erent clinical courses [1] Unsupervised methods cannot always correctly separate classes, because they use unlabeled data to ....

U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine. Broad patterns of gene expressions revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. PNAS, 96:6745-6750, National Academy of Sciences, Washington DC, 1999.

Classification of Two-Class Cancer Data Reliably Using - Evolutionary Algorithms.. (Correct)

....changes in gene expression at different stages in the cell cycle and to assign probable functions to newly discovered genes with the expression patterns of known genes. Moreover, DNA array provides a global perspective of gene expression levels, which in turn find applications in gene clustering [1], tissue classification [10] identification of new targets for therapeutic drugs [3] and others. In this paper, we have concentrated on the gene subset identification problem. The gene subset identification problem reduces to an optimization problem consisting of a number of objectives [12, ....

....of diffused large B cell lymphoma (DLBCL) and 54 samples of other types. The lymphoma data containing 4,026 genes is available at http : 11mpp .nih. gov lymphoma data figurel. cdt. The Colon data set is a collection of 62 expression measurements from Colon biopsy samples reported by Alon et al. [1]. It contains 22 normal and 40 Colon cancer samples. The colon data having 2,000 genes is available at http: microaaray.princeton.edu oncology. 3.1 Minimization of Gene Subset Size First, we apply the standard NSGA II on 50 genes which are used in another Leukemia study [10] to minimize two ....

U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. In Proceedings of National Academy of Science, Cell Biology, volume 96, pages 6745-6750, 1999.

Cluster Analysis for Gene Expression Data: A Survey - Jiang, Zhang (2002) (4 citations) (Correct)

....its crucial power as the first step in extracting information from the mass of gene expression data set. Clustering algorithms have proved useful to help group together genes with similar functions based on gene expression patterns under various conditions or across different tissue samples [Alon1999, Tavazoie1999, Eisen1998, Shamir2000]. Co expressed genes found in the same cluster demonstrate significant enrichment for function. By expanding functional families of genes with known function together with poorly characterized or novel genes may help understand the functions of many genes for which information is not previously ....

....cormnon roles in cellular processes and genes of unrelated sequence but similar function cluster tightly together. Similar tendency was also observed in human data [Eisen1998] Gene clustering also becomes the first step to uncover the regulatory elements in transcriptional regulatory networks [Alon1999, Tavazoie1999, Xing2001]. Co expressed genes in the same cluster are probably involved in the same cellular process and strong expression pattern correlation between those genes indicates co regulation. By searching for cormnon DNA sequences at the promoter regions of genes within the same cluster, regulatory motifs ....

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U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine. "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array", Proc. Natl. Acad. Sci. USA, Vol. 96(12):6745-6750, June 1999.

Joint Classifier and Feature Optimization for Cancer.. - Krishnapuram, Carin, .. (2003) (1 citation) (Correct)

....bone marrow or blood samples were taken from 72 patients, 47 with acute myeloid leukemia (AML) and 25 with acute lymphoblastic leukemia (ALL) The second dataset contains expression levels of 2000 genes from 40 tumor and 22 normal colon tissues. The dataset was originally analyzed by Alon, et al. [2] and is available at http: www.molbio.princeton.edu colondata. For all our experiments, we used polynomial kernels with the JCFO. In Table 1, we use a full leave one out crossvalidation study for each of the two datasets to compare the accuracy of the diagnostic classification reported by the ....

U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96:6745--6750, 1999.

Data Mining - Challenges, Models, Methods and Algorithms - Hegland (2003) (Correct)

....are really two dual concepts which can be interchanged. This is in particular exploited in some newer association rule discovery algorithms which are related to formal concept analysis [35] An example of this duality from bioinformatics is in figure 3. 2 which is based on microarray data from [4]. The rows of this bit matrix correspond to tissues tested and the rows correspond to the first 400 of 2000 genes. The bit is set when the expression level is over the 75 percent quantile for that gene which we use here as an example for the gene being switched on . One can now study rules like ....

U. Alon, N. Barkai, D. Notterman, K. Gish, S. Ybarra, D. Mack, and A. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon cancer tissues probed by oligonucleotide arrays. Cell Biology, 96:6745--6750, 1999.

Gene Clustering Using Self-Organizing Maps and.. - Xiao, Dow.. (2003) (Correct)

....low cost. Clustering was used, for example, to understand the functional differences in cultured primary hepatocytes relative to the intact liver[l] In another study, clustering techniques were used on gene expression data for tumor and normal colon tissue probed by oligonucleotide arrays [2]. This latter study was based on the expression data of a collection of 40 tumor and 22 normal colon tissue samples. A two way clustering algorithm was applied to the data and resulted in a separation of cancerous from non cancerous tissue and a strong indication that coregulated genes cluster ....

U.Alon, N.Barkai, D.A.Notterman, K. Gish, S.Ybarra, D.Mack, and A.J.Levine. "Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays," Proc. Natl. Acad. Sci. USA, Vol 96, pp. 6745-6750, Cell Biology, June 1999.

Revealing Predictive Gene Clusters with Supervised Algorithms - Dettling (2003) (Correct)

.... groups of genes with good predictive potential, we report the classification results for 5 binary datasets, the famous AML ALL leukemia dataset of Golub et al. 12] the two breast cancer datasets with estrogen and nodal response of West et al. 13] the colon cancer dataset of Alon et al. [14], the prostate cancer dataset of Singh et al. 15] and a 3 class problem, the lymphoma dataset of Alizadeh et al. 2] For further information about the availability of these data and our preprocessing, see [1] Because, except for the leukemia data, no genuine test sets are available, we base ....

Alon, U., Barkai, N., Notterdam, D., Gish, K., Ybarra, S., Mack, D. and Levine, A. (1999). "Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays". Proceedings of the National Academy of Science, 96, 6745--6750.

Jeffrey R. Spies - University Of Notre (Correct)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, and Mack D. Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America, 96:6745--6750, 1999.

Grid-based Knowledge Discovery in - Clinico-Genomic Data Michael (2006) (Correct)

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Alon, U., et al.: Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Arrays. Proc. Natl. Acad. Sci. 96 (1999) 6745--6750

Simultaneous Gene Clustering and Subset Selection - For Sample Classification (Correct)

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Alon, U., Barkai, N., Notterdam, D.A., Gish, K., Ybarra, S., Mack, D., Levine, A.J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.

Bioinformatics - Vol Suppl Pages (Correct)

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Alon, U., Barkai, N. & et al (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96, 6745--6750.

Experiments with Random Projections for Machine Learning - Fradkin, Madigan (2003) (1 citation) (Correct)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine. Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays. In Proc. Natl. Acad. Sci. USA, volume 96, pages 6745--6750, June 1999.

Feature Selection for Support Vector Machines by Means of.. - Holger Frhlich Holger (Correct)

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U. Alon, N. Barkai, D. Notterman, K. Gish, S. Ybarra, D. Mack, and A. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon cancer tissues probed by oligonucleotide arrays. Cell Biology, 96:6745 -- 6750, 1999.

Bioinformatics - Biomarker Discovery In (Correct)

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Alon, U., N. Barkai, D. Notterman, K. Gish, S. Ybarra, D. Mack, and A. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96:6745-- 6750, 1999.

Selection of the Most Useful Subset of Genes for Gene.. - Paul, Iba (2004) (Correct)

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Alon, U., Barkai, N., et al., "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays", in Proceedings of National Academy of Science, Cell Biology, vol. 96, 1999, pp. 6745--6750.

Identification of Informative Genes for Molecular Classification .. - Paul, Iba (2004) (Correct)

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Alon, U., Barkai, N., et al.: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of National Academy of Science, Cell Biology, vol. 96, 1999, 6745--6750.

Emerging Patterns and Gene Expression Data - Li, Wong (Correct)

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Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D., & Levine, A. J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of National Academy of Sciences of the United States of American, 96, 6745--675.

Use of Built-in Features in the Interpretation of.. - Li, Liu, Wong (Correct)

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Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. & Levine, A. J. (1999), `Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays', Proceedings of National Academy of Sciences of the United States of American 96, 6745-6750.

Mining Succinct Systems of Minimal Generators of Formal.. - Dong, Jiang, Pei, Li, Wong (2005) (1 citation) (Correct)

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U. Alon, et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissue s probed by oligonucleotide arrays. Proc. Nat. Academy of Sciences of the United States of American, 96:6745--675, 1999.

Identifying Good Diagnostic Gene Groups from Gene Expression.. - Li, Wong (2002) (1 citation) (Correct)

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Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. and Levine, A. J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. U.S.A., 96, 6745--6750.

Simple Rules Underlying Gene Expression Profiles of More than Six .. - Li, al. (2003) (1 citation) (Correct)

The Use of Emerging Patterns in the Analysis of Gene.. - Dong, Li, Wong (2003) (Correct)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S.Y.D. Mack, and J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96:6745--6750, 1999.

Genomic Signal Processing: The Salient Issues - Dougherty, al. (2004) (Correct)

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U. Alon, N. Barkai, D. A. Notterman, et al., "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays," Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 12, pp. 6745--6750, 1999.

Unsupervised Clustering of Bioinformatics Data - Tasoulis, Plagianakos, Vrahatis (2004) (Correct)

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U. Alon; N. Barkai; D.A. Notterman; K.Gish; S. Ybarra; D. Mack; A.J. Levine, 1999, "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array", Proc. Natl. Acad. Sci. USA, 96(12), pp. 6745--6750.

Learning Structure and Concepts in Data Through Data Clustering - Hamerly (2003) (Correct)

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U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. In Proceedings of the National Academy Sciences USA, volume 96, pages 6745{ 6750, 1999.

Studies of Microarray Data Analysis with Applications for Human .. - Hautaniemi (Correct)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America, 96(12):6745--6750, June 1999.

E-CAST: A Data Mining Algorithm for Gene Expression Data - Bellaachia, Portnoy, al. (Correct)

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Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D. & Levine, A.J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucle otide arrays,

Bioinformatics: Organisms from Venus, Technology.. - De Moor, Marchal.. (2003) (Correct)

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Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., Levine A.J. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Of the Nat. Ac. Of Sciences, 1999, 96(12), pp6745-6750.

Feature Selection for Support Vector Machines by Means of.. - Fröhlich (2002) (Correct)

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U. Alon, N. Barkai, D. Notterman, K. Gish, S. Ybarra, D. Mack, A. Levine, Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon cancer tissues probed by oligonucleotide arrays, In: Cell Biology, 96:6745-6750, 1999

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An EM Algorithm for Joint Feature Selection and - Classifier Design Balaji (Correct)

Bagged Ensembles of Support Vector Machines for Gene.. - Valentini, Muselli.. (Correct)

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U. Alon et al. Broad patterns of gene expressions revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. PNAS, 96:6745--6750, 1999.

Data Mining - Challenges, Models, Methods and Algorithms - Hegland (2003) (Correct)

Feature Selection for Support Vector Machines by Means .. - Fröhlich, Chapelle.. (2002) (Correct)

Functional Bioinformatics of Microarray Data: From .. - Moreau, De Smet.. (2002) (2 citations) (Correct)

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U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine, Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays, Proc. Natl. Acad. Sci. USA 96 (1999), 67456750.

Genomic Signal Processing: The Salient Issues - Dougherty, al. (2004) (Correct)

Experiments with Random Projections for Machine Learning - Fradkin, Madigan (2003) (1 citation) (Correct)

Cancer Recognition with Bagged Ensembles of Support.. - Valentini, Muselli.. (2003) (Correct)

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U. Alon et al. Broad patterns of gene expressions revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96 (1999) 6745--6750.

Advances in Cluster Analysis of Microarray Data - Sheng, Moreau, De Smet.. (Correct)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96:6745--6750, 1999.

Unsupervised Clustering of Bioinformatics Data - Tasoulis, Plagianakos, Vrahatis (2004) (Correct)

The Walking Cluster Algorithm - De Smet, Marchal, Thijs, Mathys, De.. (Correct)

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U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96:67456750, 1999.

Joint Classifier and Feature Optimization for Comprehensive.. - Krishnapuram, al. (Correct)

Visualized Classification of Multiple Sample Types - Li Zhang And (Correct)

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Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D, and Levine, A. J.g. Broad Patterns of Gene Expression Revealed by Clustering Analysis of Tumor and Normal Colon Tissues Probed by Oligonucleotide Array. Proc. Natl. Acad. Sci. USA,Vol. 96(12):6745-6750, June 1999.

Fast Feature Selection from Microarray Expression Data via.. - Gentile (2003) (Correct)

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Alon, U., et al. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon cancer tissues probed by oligonucleotide arrays. Cell Biol., 96, 6745-- 6750.

Bagged Ensembles of Support Vector Machines for Gene.. - Valentini, Muselli.. (Correct)

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U. Alon et al. Broad patterns of gene expressions revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. PNAS, 96:6745--6750, 1999.

Finding Predictive Gene Groups from Microarray Data - Dettling, Bühlmann (Correct)

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U. Alon, N. Barkai, D. Notterdam, K. Gish, S. Ybarra, D. Mack, A. Levine, Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays, Proceedings of the National Academy of Science 96 (1999) 6745-6750.

Self-Organizing Latent Lattice Models for Temporal Gene.. - Zhang, Chi (2003) (Correct)

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Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D., and Levine, A.J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences, 96, 6745-6750.

Practical Approaches to Analyzing Results of Microarray.. - Kaminski, Friedman (Correct)

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Alon, U., N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine. 1999. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96:6745--6750.

Extracting Conserved Gene Expression Motifs From Gene.. - Murali, Kasif (2003) (4 citations) (Correct)

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U Alon, N Barkai, D A Notterman, K Gish, S Ybarra, D Mack, and A J Levine. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A, 96(12):6745--50, 1999.

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