Mathematical programming in computational biology: an annotated bibliography

DOI10.3390/a1020100zbMath1461.90001OpenAlexW2048620321MaRDI QIDQ1662439

Giuseppe Lancia

Publication date: 20 August 2018

Published in: Algorithms (Search for Journal in Brave)

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

zbMATH Keywords

linear programminginteger programmingsequencingmathematical programmingbioinformaticscomputational biologyhaplotypingprotein structures

Mathematics Subject Classification ID

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

Related Items (4)

An integer programming approach to DNA sequence assembly ⋮ Solving the maximum edge-weight clique problem in sparse graphs with compact formulations ⋮ Analysis method and algorithm design of biological sequence problem based on generalized k-mer vector ⋮ Integer Linear Programming in Computational Biology

Uses Software

• Concorde
• RAPTOR

Cites Work

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• A constraint-based approach to fast and exact structure prediction in three-dimensional protein models
• Integer linear programming approaches for non-unique probe selection
• Simultaneous classification and relevant feature identification in high-dimensional spaces: Application to molecular profiling data
• Approximation algorithms for the test cover problem
• A polyhedral approach to sequence alignment problems
• Compact optimization can outperform separation: a case study in structural proteomics
• Large-scale linear programming techniques for the design of protein folding potentials
• An optimization approach to the problem of protein structure prediction
• Protein threading by linear programming: theoretical analysis and computational results
• Physical mapping of chromosomes: A combinatorial problem in molecular biology
• A polynomial case of the parsimony haplotyping problem
• A branch-and-cut algorithm for multiple sequence alignment
• Sorting Permutations by Reversals Through Branch-and-Price
• The Reversal Median Problem
• Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
• A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies
• Protein Threading: From Mathematical Models to Parallel Implementations
• Optimal Solutions for the Closest-String Problem via Integer Programming
• Multiple Sequence Alignment as a Facility-Location Problem
• On the closest string and substring problems
• Simple and Fast Inverse Alignment
• Genetic Design of Drugs Without Side-Effects
• Exact algorithms for minimum routing cost trees
• Side Chain-Positioning as an Integer Programming Problem
• A Compact Mathematical Programming Formulation for DNA Motif Finding
• Optimal Protein Structure Alignment Using Maximum Cliques
• An Effective Heuristic Algorithm for the Traveling-Salesman Problem
• Computational Science – ICCS 2005
• Algorithms and Computation
• Combinatorial Pattern Matching
• Rearrangement of DNA fragments: a branch-and-cut algorithm.
• On the primer selection problem in polymerase chain reaction experiments

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