Related papers: Pure Parsimony Xor Haplotyping
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
Haplotyping is the bioinformatics problem of predicting likely haplotypes based on given genotypes. It can be approached using Gusfield's perfect phylogeny haplotyping (PPH) method for which polynomial and linear time algorithms exist.…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
Let $\mathbf{K}$ be a field of characteristic zero with $\overline{\mathbf{K}}$ its algebraic closure. Given a sequence of polynomials $\mathbf{g} = (g_1, \ldots, g_s) \in \mathbf{K}[x_1, \ldots , x_n]^s$ and a polynomial matrix $\mathbf{F}…
Nowadays hybrid evolutionary algorithms, i.e, heuristic search algorithms combining several mutation operators some of which are meant to implement stochastically a well known technique designed for the specific problem in question while…
In the counting Graph Homomorphism problem (#GraphHom) the question is: Given graphs G,H, find the number of homomorphisms from G to H. This problem is generally #P-complete, moreover, Cygan et al. proved that unless the ETH is false there…
Given a graph G, we investigate the question of determining the parity of the number of homomorphisms from G to some other fixed graph H. We conjecture that this problem exhibits a complexity dichotomy, such that all parity graph…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
Polynomial system solving has seen major progress in both theory and practice over the past decade. A landmark achievement was addressing Smale's 17th problem, establishing average-case polynomial-time algorithms for computing approximate…
We reveal a complexity chasm, separating the trinomial and tetranomial cases, for solving univariate sparse polynomial equations over certain local fields. First, for any fixed field $K\in\{\mathbb{Q}_2,\mathbb{Q}_3,\mathbb{Q}_5,\ldots\}$,…
For several computational problems in homotopy theory, we obtain algorithms with running time polynomial in the input size. In particular, for every fixed k>1, there is a polynomial-time algorithm that, for a 1-connected topological space X…
The Minimum-Recombinant Haplotype Configuration problem (MRHC) has been highly successful in providing a sound combinatorial formulation for the important problem of genotype phasing on pedigrees. Despite several algorithmic advances and…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
The classical work of (Arora et al., 1999) provides a scheme that gives, for any $\epsilon>0$, a polynomial time $1-\epsilon$ approximation algorithm for dense instances of a family of $\mathcal{NP}$-hard problems, such as Max-CUT and…