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Book
Author Gusfield, Dan, author

Title Integer linear programming in computational and systems biology : an entry-level text and course / Dan Gusfield, University of California, Davis
Published Cambridge,United Kingdom ; New York, NY : Cambridge University Press, 2019

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Location Call no. Vol. Availability
 MELB  570.285 Gus/Ilp  AVAILABLE
Description 412 pages
Contents Machine generated contents note: Part I -- 1.A Flyover Introduction to Integer Unear Programming -- 1.1.Linear Programming (LP) and Its Use -- 1.2.Integer Linear Programming (LLP) -- 1.3.Expressibility of Integer Linear Formulations -- 2.Biological Networks, Graphs, and High-Density Subgraphs -- 2.1.Biological Graphs and Networks -- 2.2.The Maximum-Clique Problem and Its Solution Using ILP -- 2.3.Bounds and Gurobi Progress Reporting -- 3.Maximum Character Compatibility In Phylogenetlcs -- 3.1.Basic Definitions -- 3.2.Phylogenetic Trees -- 3.3.Perfect Phylogeny and Cancer -- 3.4.Character Removal in the Perfect-Phylogeny Model -- 3.5.Minimum Character Removal (MCR) in the Study of Cancer -- 4.Near Cliques, Dense Subgraphs, and Motifs In Biological Networks -- 4.1.Near Cliques -- 4.2.Inverting the Near-Clique Problem -- 4.3.A Short Interruption: Our First ILP Idioms -- 4.4.Return to Near Cliques -- 4.5.Finally: The Largest High-Density Subgraph Problem --
Contents note continued: 4.6.Motif Searching via Clique Finding -- 5.Convergent and Maximum Parsimony Problems in Phylogenetics -- 5.1.Phylogenetics via Maximum Parsimony -- 5.2.Improving the Practicality -- 5.3.Software -- 5.4.Concerted Convergent Evolution: Cliques Again! -- 5.5.Catching Infeasibility Errors Using An IIS in Gurobi -- 6.The RNA-Foldlng Problem -- 6.1.A Crude First Model of RNA Folding -- 6.2.More Complex Biological Enhancements -- 6.3.Fold Prediction Using a Known RNA Structure -- 7.Protein Problems Solved By Integer Programming -- 7.1.The Protein Side-Chain Positioning Problem -- 7.2.Protein Folding via the HP Model -- 7.3.Predicting Domain-Domain Interaction in Proteins -- 8.Tanglegrams and Coevolution -- 8.1.Introduction to Coevolution -- 8.2.Tree Drawings, Subtree Exchanges, and the Tanglegram Problem -- 8.3.Logic for Solving the Tanglegram Problem -- 8.4.An ILP Formulation -- 8.5.Software for the Tanglegram Problem --
Contents note continued: 8.6.The If-XOR Idiom for Binary Variables -- 9.Traveling Salesman Problems In Genomics -- 9.1.The Traveling Salesman Problem (TSP) in Genomics -- 9.2.The Traveling Salesman Problem (TSP) -- 9.3.TS Problems in DNA Sequencing and Assembly -- 9.4.Marker Ordering: A Different Fragment Layout Problem -- 9.5.Finding Signaling Pathways in Cervical Cancer -- 9.6.An ILP Solution to the TS Tour Problem on G' -- 9.7.Efficiency and Alternative Formulations -- 9.8.The Subtour-Elimination Approach to Solving TS Problems -- 9.9.Extended Modeling Exercises -- 10.Integer Programming In Molecular Sequence Analysis -- 10.1.The Importance of Sequence Analysis -- 10.2.The String Site-Removal Problem (SSRP) -- 10.3.Representative Sequences -- 10.4.The Longest Common-Subsequence (LCS) Problem -- 10.5.Optimal Pathogen and Species Barcoding -- 11.Metabolic Networks and Metabolic Engineering -- 11.1.Boolean Networks -- 11.2.Extending Boolean Networks, with ILP --
Contents note continued: 11.3.Fantasy Network Analysis -- 11.4.Time: The Final Frontier -- 12.ILP Idioms -- 12.1.General If-Then Idioms for Linear Functions with Binary Variables -- 12.2.General Only-If Idioms for Linear Functions and Binary Variables -- 12.3.Exploiting the Idioms -- 12.4.The Key to the Idioms -- Part II -- 13.Communities, Cuts, and High-Density Subgraphs -- 13.1.Community Detection in a Network -- 13.2.Cuts: Max, Min, and Multi -- 13.3.High-Density Subgraphs: A Refinement for Large, Sparse Graphs -- 14.Character Compatibility with Corrupted Data and Generalized Phylogenetic Models -- 14.1.Handling Missing and Corrupted Data in Character Compatibility Problems -- 14.2.Handling Both Missing and Corrupted Data -- 14.3.Back to the Artifact Problem in Pancreatic Cancer -- 14.4.An Extension of Perfect Phylogeny to Less Restricted Models -- 15.More Tanglegrams, More Trees, More ILPs -- 15.1.Minimizing Subtree Exchanges Within An Optimal Solution --
Contents note continued: 15.2.A Distance-Based Objective Function for Tanglegrams -- 15.3.An ILP Formulation -- 15.4.Rooted Subtree-Prune-and-Regraft (rSPR) Distance -- 16.Return to Steiner Trees and Maximum Parsimony -- 16.1.The Steiner-Tree Problem and Extensions -- 16.2.iPoint: Deducing Protein Pathways -- 16.3.Maximum Parsimony and Ductal Carcinoma Progression -- 17.Exploiting and Leveraging Protein Networks -- 17.1.Example 1: Exploiting PPI Networks to Find Disease-Related Proteins -- 17.2.Example 2: Leveraging PPI Knowledge Across Species -- 17.3.Example 3: Identifying Driver Genes in Cancer -- 18.More String and Sequence Problems Solved by ILP -- 18.1.The LCS Problem for Multiple Strings -- 18.2.Transforming Gene Order by Reversals -- 19.Maximum Likelihood Pedigree Reconstruction -- 19.1.Pedigrees -- 19.2.An ILP Formulation for the Maximum Likelihood Pedigree Reconstruction Problem -- 19.3.Inverse Genetics Problems -- 20.Two DNA Haplotyplng Problems -- 20.1.Introduction --
Contents note continued: 20.2.Haplotype Assembly: The Individual Variant of the HI Problem -- 20.3.The Population Variant of the HI Problem -- 20.4.Perfect Phylogeny Haplotyping -- 20.5.Software for the MP-PPH Haplotyping Problem -- 21.More Extended Exercises -- 21.1.Visualizing Hierarchical Clustering -- 21.2.Clustering to Predict In Vivo Toxicities from In Vitro Experiments -- 21.3.Bicliques and Biclustering in Biological Data -- 21.4.Combinatorial Drug Therapy -- 21.5.Return to the Cape of South Africa -- 21.6.Comparing Three-Dimensional Protein Structure with Contact Maps -- 21.7.Reconstructing Sibling Relations -- 22.What's Next? -- 23.Epilogue: Some Very Opinionated Comments for Advanced Readers -- 23.1.On the Power of Linearity and Linear Models -- 23.2.Why Is ILP in Computational Biology Different from Traditional ILP? -- 23.3.Black Boxes versus Clear Semantics and ILP
Bibliography Includes bibliographical references and index
Subject Computational biology -- Mathematical models
Systems biology -- Mathematical models
Linear programming
LC no. 2018061722
ISBN 9781108421768 (hardback : alk. paper)