Threading algorithms
(1) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. abstract (2) Protein fold recognition by prediction-based threading. abstract
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(1) Fold prediction by a hierarchy of sequence, threading, and modeling methods. abstract (2) Protein structure prediction by threading. Why it works and why it does not. abstract, paper
(1) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. abstract, paper (2) Protein Structure Comparison by Alignment of Distance Matrices. abstract, paper
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(1) A Unified Statistical Framework for Sequence Comparison and Structure Comparison. abstract, paper (2) Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. abstract, paper
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(1) Parser for protein folding units. abstract (2) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. abstract
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(1) Protein structural domain identification. abstract, paper (2) Protein domain decomposition using a graph-theoretic approach. abstract, paper
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(1) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. abstract, paper (2) Localizing proteins in the cell from their phylogenetic profiles. abstract, paper
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(1) Detecting protein function and protein-protein interactions from genome sequences. abstract, paper (2) Protein interaction maps for complete genomes based on gene fusion events. abstract, paper
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(1) A network of protein-protein interactions in yeast. abstract, paper (2) A fast method to predict protein interaction sites from sequences. abstract, paper (3) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. abstract, paper (4) A combined algorithm for genome-wide prediction of protein function. abstract, paper
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(1) Correlated mutations contain information about protein-protein interaction. abstract, paper (2) Coevolving Protein Residues: Maximum Likelihood Identification and Relationship to Structure. abstract, paper (3) Co-evolution of Proteins with their Interaction Partners. abstract, paper
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(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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