Integer Linear Programming in Computational Biology

DOI10.1007/978-3-642-03456-5_14MaRDI QIDQ3644723zbMATH OpenOpenAlexWikidataFDO

Authors Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Knut Reinert, Hans-Peter Lenhof

Publication date 12 November 2009

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-642-03456-5_14

Mathematics Subject Classification ID

Linear programming (90C05) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Integer programming (90C10) Computational methods for problems pertaining to biology (92-08)

Recommendations

• Integer Linear Programming in Computational and Systems Biology
• Computational molecular biology
• Comparing integer linear programming to SAT-solving for hard problems in computational and systems biology
• Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data
• Integer quadratic programming models in computational biology

Cites work

• scientific article; zbMATH DE number 1003281 (Why is no real title available?)
• scientific article; zbMATH DE number 714531 (Why is no real title available?)
• A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
• A Lagrangian relaxation approach for the multiple sequence alignment problem
• A branch-and-cut algorithm for multiple sequence alignment
• A semidefinite programming approach to side chain positioning with new rounding strategies
• Algorithms and Computation
• An exact mathematical programming approach to multiple RNA sequence-structure alignment
• Efficient methods for multiple sequence alignment with guaranteed error bounds
• Exact Solution of the Quadratic Knapsack Problem
• Exact algorithms for minimum routing cost trees
• Integer linear programming approaches for non-unique probe selection
• Mathematical programming in computational biology: an annotated bibliography
• Protein threading by linear programming: theoretical analysis and computational results
• Protein threading: from mathematical models to parallel implementations
• Side Chain-Positioning as an Integer Programming Problem
• Simple and Fast Inverse Alignment

Cited in

(7)

• Computational molecular biology
• Comparing integer linear programming to SAT-solving for hard problems in computational and systems biology
• Integer linear programming approaches for non-unique probe selection
• Integer quadratic programming models in computational biology
• An integer programming approach to DNA sequence assembly
• Integer Linear Programming in Computational and Systems Biology
• Mathematical programming in computational biology: an annotated bibliography

Describes a project that uses

Uses Software

• T-coffee
• RAPTOR
• Knapsack

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