Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Using Constraint Programming and Local Search Methods to Solve Vehicle Routing Problems
CP '98 Proceedings of the 4th International Conference on Principles and Practice of Constraint Programming
A survey of very large-scale neighborhood search techniques
Discrete Applied Mathematics
Metaheuristics in combinatorial optimization: Overview and conceptual comparison
ACM Computing Surveys (CSUR)
Stochastic Local Search: Foundations & Applications
Stochastic Local Search: Foundations & Applications
The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotypes histories as pathways of recombinations
Bioinformatics
Information Processing Letters
Tabu Search for the Founder Sequence Reconstruction Problem: A Preliminary Study
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Tuning Metaheuristics: A Machine Learning Perspective
Tuning Metaheuristics: A Machine Learning Perspective
Hybrid Metaheuristics: An Emerging Approach to Optimization
Hybrid Metaheuristics: An Emerging Approach to Optimization
A randomized iterated greedy algorithm for the founder sequence reconstruction problem
LION'10 Proceedings of the 4th international conference on Learning and intelligent optimization
Minimum recombination histories by branch and bound
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Haplotype inference via hierarchical genotype parsing
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Improved algorithms for inferring the minimum mosaic of a set of recombinants
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Minimum mosaic inference of a set of recombinants
CATS '11 Proceedings of the Seventeenth Computing: The Australasian Theory Symposium - Volume 119
Hybrid metaheuristics in combinatorial optimization: a tutorial
TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
| Hi-index | 0.01 |
The reconstruction of founder genetic sequences of a population is a relevant issue in evolutionary biology research. The problem consists in finding a biologically plausible set of genetic sequences (founders), which can be recombined to obtain the genetic sequences of the individuals of a given population. The reconstruction of these sequences can be modelled as a combinatorial optimisation problem in which one has to find a set of genetic sequences such that the individuals of the population under study can be obtained by recombining founder sequences minimising the number of recombinations. This problem is called the founder sequence reconstruction problem. Solving this problem can contribute to research in understanding the origins of specific genotypic traits. In this paper, we present large neighbourhood search algorithms to tackle this problem. The proposed algorithms combine a stochastic local search with a branch-and-bound algorithm devoted to neighbourhood exploration. The developed algorithms are thoroughly evaluated on three different benchmark sets and they establish the new state of the art for realistic problem instances.