Algorithms in Bioinformatics Book

	Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spaces	1
	Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Design	10
	Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problem	29
	Methods for Inferring Block-Wise Ancestral History from Haploid Sequences	44
	Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks	60
	Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometry	68
	Improved Approximation Algorithms for NMR Spectral Peak Assignment	82
	Efficient Methods for Inferring Tandem Duplication History	97
	Genome Rearrangement Phylogeny Using Weighbor	112
	Segment Match Refinement and Applications	126
	Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation	140
	Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics	157
	FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structures	172
	Efficient Unbound Docking of Rigid Molecules	185
	A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variants	201
	A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding	210
	Comparative Methods for Gene Structure Prediction in Homologous Sequences	220
	MultiProt - A Multiple Protein Structural Alignment Algorithm	235
	A Hybrid Scoring Function for Protein Multiple Alignment	251
	Functional Consequences in Metabolic Pathways from Phylogenetic Profiles	263
	Finding Founder Sequences from a Set of Recombinants	277
	Estimating the Deviation from a Molecular Clock	287
	Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesis	300
	Approximating the Expected Number of Inversions Given the Number of Breakpoints	316
	Invited Lecture - Accelerating Smith-Waterman Searches	331
	Sequence-Length Requirements for Phylogenetic Methods	343
	Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle	357
	NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks	375
	On the Control of Hybridization Noise in DNA Sequencing-by-Hybridization	392
	Restricting SBH Ambiguity via Restriction Enzymes	404
	Invited Lecture - Molecule as Computation: Towards an Abstraction of Biomolecular Systems	418
	Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search	419
	Rapid Large-Scale Oligonucleotide Selection for Microarrays	434
	Border Length Minimization in DNA Array Design	435
	The Enhanced Suffix Array and Its Applications to Genome Analysis	449
	The Algorithmic of Gene Teams	464
	Combinatorial Use of Short Probes for Differential Gene Expression Profiling	477
	Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome	491
	K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data	506
	Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data	521
	Modified Mincut Supertrees	537
	Author Index	553