Mathematical programming in computational biology: an annotated bibliography

DOI10.3390/A1020100MaRDI QIDQ1662439zbMATH OpenOpenAlexFDO

Authors Giuseppe Lancia

Publication date 20 August 2018

Published in Algorithms (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3390/a1020100

zbMATH Keywords

bioinformaticscomputational biologyhaplotypinginteger programminglinear programmingmathematical programmingprotein structuressequencing

Mathematics Subject Classification ID

General reference works (handbooks, dictionaries, bibliographies, etc.) pertaining to operations research and mathematical programming (90-00) Applications of mathematical programming (90C90) Software, source code, etc. for problems pertaining to biology (92-04) Computational methods for problems pertaining to biology (92-08)

Review text

Summary: The field of computational biology has experienced a tremendous growth in the past 15 years. In this bibliography, we survey some of the most significant contributions that were made to the field and which employ mathematical programming techniques, while giving a broad overview of application areas of modern computational molecular biology. The areas include sequence analysis, microarrays, protein structure and function, haplotyping and evolutionary distances.

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Cites work

• A branch-and-cut algorithm for multiple sequence alignment
• A Compact Mathematical Programming Formulation for DNA Motif Finding
• A constraint-based approach to fast and exact structure prediction in three-dimensional protein models
• A polyhedral approach to sequence alignment problems
• A polynomial case of the parsimony haplotyping problem
• A semidefinite programming approach to side chain positioning with new rounding strategies
• Algorithms and Computation
• An Effective Heuristic Algorithm for the Traveling-Salesman Problem
• An optimization approach to the problem of protein structure prediction
• Approximation algorithms for the test cover problem
• Combinatorial Pattern Matching
• Compact optimization can outperform separation: a case study in structural proteomics
• Computational Science – ICCS 2005
• Exact algorithms for minimum routing cost trees
• Genetic Design of Drugs Without Side-Effects
• Haplotyping populations by pure parsimony: complexity of exact and approximation algorithms
• scientific article; zbMATH DE number 1003281 (Why is no real title available?)
• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• scientific article; zbMATH DE number 1301595 (Why is no real title available?)
• scientific article; zbMATH DE number 1301598 (Why is no real title available?)
• scientific article; zbMATH DE number 1305456 (Why is no real title available?)
• scientific article; zbMATH DE number 1775449 (Why is no real title available?)
• Integer linear programming approaches for non-unique probe selection
• Large-scale linear programming techniques for the design of protein folding potentials
• Multiple sequence alignment as a facility-location problem
• On the closest string and substring problems
• On the primer selection problem in polymerase chain reaction experiments
• Optimal Protein Structure Alignment Using Maximum Cliques
• Optimal solutions for the closest-string problem via integer programming
• Physical mapping of chromosomes: A combinatorial problem in molecular biology
• Protein threading by linear programming: theoretical analysis and computational results
• Protein threading: from mathematical models to parallel implementations
• Rearrangement of DNA fragments: a branch-and-cut algorithm.
• Side Chain-Positioning as an Integer Programming Problem
• Simple and Fast Inverse Alignment
• Simultaneous classification and relevant feature identification in high-dimensional spaces: Application to molecular profiling data
• Sorting permutations by reversals through branch-and-price
• The reversal median problem

Cited in

(11)

• A bibliography on computational molecular biology and genetics
• A bibliography for the development of an intelligent mathematical programming system
• Analysis method and algorithm design of biological sequence problem based on generalized k-mer vector
• Solving the maximum edge-weight clique problem in sparse graphs with compact formulations
• Opportunities for combinatorial optimization in computational biology
• Integer Linear Programming in Computational Biology
• scientific article; zbMATH DE number 1121823 (Why is no real title available?)
• scientific article; zbMATH DE number 1368928 (Why is no real title available?)
• Computational molecular biology
• Integer Linear Programming in Computational and Systems Biology
• An integer programming approach to DNA sequence assembly

Describes a project that uses

Uses Software

• RAPTOR
• Concorde

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