(1) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. abstract (2) Optimization of a new score function for the detection of remote homologs. abstract
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(1) Twilight zone of protein sequence alignments abstract (2) Statistical alignment: computational properties, homology testing and goodness-of-fit abstract
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(1) Multiple Sequence Alignment Using Partial Order Graphs abstract, paper, figures (2) T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment. abstract
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(1) Searching the Protein Structure Databank with Weak Sequence Patterns and Structural Constraints. abstract
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(1) A homology identification method that combines protein sequence and structure information. abstract
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(1) Analysis and prediction of functional sub-types from protein sequence alignments. abstract, paper (2) A method to predict functional residues in proteins. abstract
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Introduction to Microarray Technology and Analysis
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(1) Comparison of methods for image analysis on cDNA microarray data. paper (2) Normalization for cDNA Microarray Data. paper
(1) Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations abstract, paper (2) Design and Analysis of Gene Expression Microarray Experiments. paper
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(1) Cluster analysis and display of genome-wide expression patterns. abstract, paper (2) Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. abstract, paper
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(1) Singular value decomposition for genome-wide expression data processing and modeling. abstract, paper (2) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. abstract, paper
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(1) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. abstract (2) Supervised harvesting of expression trees. abstract
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