Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Node-and edge-deletion NP-complete problems
STOC '78 Proceedings of the tenth annual ACM symposium on Theory of computing
On the complexity of the Maximum Subgraph Problem
STOC '78 Proceedings of the tenth annual ACM symposium on Theory of computing
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
Journal of Computer and System Sciences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
FAW '08 Proceedings of the 2nd annual international workshop on Frontiers in Algorithmics
A Practical Exact Algorithm for the Individual Haplotyping Problem MEC/GI
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
On the Approximability of Some Haplotyping Problems
AAIM '09 Proceedings of the 5th International Conference on Algorithmic Aspects in Information and Management
A practical parameterised algorithm for the individual haplotyping problem mlf†
Mathematical Structures in Computer Science
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
HAPLOFREQ: estimating haplotype frequencies efficiently
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
New results for the Longest Haplotype Reconstruction problem
Discrete Applied Mathematics
Solving VLSI design and DNA sequencing problems using bipartization of graphs
Computational Optimization and Applications
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
Journal of Biomedical Informatics
Semi-supervised clustering algorithm for haplotype assembly problem based on MEC model
International Journal of Data Mining and Bioinformatics
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
A heuristic algorithm for haplotype reconstruction from aligned weighted SNP fragments
International Journal of Bioinformatics Research and Applications
Parameterised algorithms of the individual haplotyping problem with gaps
International Journal of Bioinformatics Research and Applications
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Single nucleotide polymorphisms (SNPs) are the most frequent form of human genetic variation. They are of fundamental importance for a variety of applications including medical diagnostic and drug design. They also provide the highest-resolution genomic fingerprint for tracking disease genes. This paper is devoted to algorithmic problems related to computational SNPs validation based on genome assembly of diploid organisms. In diploid genomes, there are two copies of each chromosome. A description of the SNPs sequence information from one of the two chromosomes is called SNPs haplotype. The basic problem addressed here is the Haplotyping, i.e., given a set of SNPs prospects inferred from the assembly alignment of a genomic region of a chromosome, find the maximally consistent pair of SNPs haplotypes by removing data "errors" related to DNA sequencing errors, repeats, and paralogous recruitment. In this paper, we introduce several versions of the problem from a computational point of view. We show that the general SNPs Haplotyping Problem is NP-hard for mate-pairs assembly data, and design polynomial time algorithms for fragment assembly data.We give a network-flow based polynomial algorithm for the Minimum Fragment Removal Problem, and we show that the Minimum SNPs Removal problem amounts to finding the largest independent set in a weakly triangulated graph.