相关论文: Perfect Phylogeny Haplotyping is Complete for Logs…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
Exploration of task mappings plays a crucial role in achieving high performance in heterogeneous multi-processor system-on-chip (MPSoC) platforms. The problem of optimally mapping a set of tasks onto a set of given heterogeneous processors…
In both population genetics and forensic genetics it is important to know how haplotypes are distributed in a population. Simulation of population dynamics helps facilitating research on the distribution of haplotypes. In forensic genetics,…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
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…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
The flawless functioning of a protein is essentially linked to its own three-dimensional structure. Therefore, the prediction of a protein structure from its amino acid sequence is a fundamental problem in many fields that draws researchers…
The decision problem of perfect matchings in uniform hypergraphs is famously an NP-complete problem. It has been shown by Keevash--Knox--Mycroft [STOC, 2013] that for every $\varepsilon>0$, such decision problem restricted to $k$-uniform…
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 process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century there have been remarkable advances in the development of theory for this diversification, and the theory's success…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…
The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without…
Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either…
A perfect matching in an undirected graph $G=(V,E)$ is a set of vertex disjoint edges from $E$ that include all vertices in $V$. The perfect matching problem is to decide if $G$ has such a matching. Recently Rothvo{\ss} proved the striking…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Classification in the dissimilarity space has become a very active research area since it provides a possibility to learn from data given in the form of pairwise non-metric dissimilarities, which otherwise would be difficult to cope with.…