Related papers: Cutting an alignment with Ockham's razor
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…
One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
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 reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…
We consider the problem of detecting multiple changepoints in large data sets. Our focus is on applications where the number of changepoints will increase as we collect more data: for example in genetics as we analyse larger regions of the…
The linearly constrained matrix rank minimization problem is widely applicable in many fields such as control, signal processing and system identification. The tightest convex relaxation of this problem is the linearly constrained nuclear…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
We introduce a novel variant of cutting production planning problems named Integrated Cutting and Packing Heterogeneous Precast Beams Multiperiod Production Planning (ICP-HPBMPP). We propose an integer linear programming model for the…
Given a threshold $L$ and a set $\mathcal{R} = \{R_1, \ldots, R_m\}$ of $m$ haplotype sequences, each having length $n$, the minimum segmentation problem for founder reconstruction is to partition the sequences into disjoint segments…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute…
We study the problem of image alignment for panoramic stitching. Unlike most existing approaches that are feature-based, our algorithm works on pixels directly, and accounts for errors across the whole images globally. Technically, we…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
A frame is a generalization of a basis of a vector space to a redundant overspanning set whose vectors are linearly dependent. Frames find applications in signal processing and quantum information theory. We present a genetic algorithm that…