Mathematical programming in computational biology: an annotated bibliography
DOI10.3390/A1020100zbMATH Open1461.90001OpenAlexW2048620321MaRDI QIDQ1662439FDOQ1662439
Authors: 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
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linear programmingmathematical programminginteger programmingcomputational biologybioinformaticssequencinghaplotypingprotein structures
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) General reference works (handbooks, dictionaries, bibliographies, etc.) pertaining to operations research and mathematical programming (90-00)
Cites Work
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- Approximation algorithms for the test cover problem
- A semidefinite programming approach to side chain positioning with new rounding strategies
- Optimal solutions for the closest-string problem via integer programming
- On the closest string and substring problems
- Genetic Design of Drugs Without Side-Effects
- An Effective Heuristic Algorithm for the Traveling-Salesman Problem
- A polyhedral approach to sequence alignment problems
- Large-scale linear programming techniques for the design of protein folding potentials
- The reversal median problem
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- Exact algorithms for minimum routing cost trees
- A polynomial case of the parsimony haplotyping problem
- Haplotyping populations by pure parsimony: complexity of exact and approximation algorithms
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- Title not available (Why is that?)
- Side Chain-Positioning as an Integer Programming Problem
- Algorithms and Computation
- Optimal Protein Structure Alignment Using Maximum Cliques
- Title not available (Why is that?)
- Protein threading: from mathematical models to parallel implementations
- A constraint-based approach to fast and exact structure prediction in three-dimensional protein models
- A Compact Mathematical Programming Formulation for DNA Motif Finding
- An optimization approach to the problem of protein structure prediction
- Multiple sequence alignment as a facility-location problem
- Sorting permutations by reversals through branch-and-price
- Integer linear programming approaches for non-unique probe selection
- Simultaneous classification and relevant feature identification in high-dimensional spaces: Application to molecular profiling data
- A branch-and-cut algorithm for multiple sequence alignment
- Physical mapping of chromosomes: A combinatorial problem in molecular biology
- On the primer selection problem in polymerase chain reaction experiments
- Compact optimization can outperform separation: a case study in structural proteomics
- Protein threading by linear programming: theoretical analysis and computational results
- Simple and Fast Inverse Alignment
- Title not available (Why is that?)
- Computational Science – ICCS 2005
- Combinatorial Pattern Matching
- Rearrangement of DNA fragments: a branch-and-cut algorithm.
Cited In (9)
- Solving the maximum edge-weight clique problem in sparse graphs with compact formulations
- Computational molecular biology
- Opportunities for combinatorial optimization in computational biology
- Integer Linear Programming in Computational Biology
- Analysis method and algorithm design of biological sequence problem based on generalized k-mer vector
- An integer programming approach to DNA sequence assembly
- A bibliography on computational molecular biology and genetics
- A bibliography for the development of an intelligent mathematical programming system
- Integer Linear Programming in Computational and Systems Biology
Uses Software
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