相关论文: Perfect Phylogeny Haplotyping is Complete for Logs…

Clustering genotypes based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of…

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…

Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…

Probabilistic Cell Decomposition (PCD) is a probabilistic path planning method combining the concepts of approximate cell decomposition with probabilistic sampling. It has been shown that the use of lazy evaluation techniques and supervised…

The Building Block Hypothesis (BBH) states that adaptive systems combine good partial solutions (so-called building blocks) to find increasingly better solutions. It is thought that Genetic Algorithms (GAs) implement the BBH. However, for…

We present an approach, called the "Shadow Method," for the identification of disease loci from dense genetic marker maps in complex, potentially incomplete pedigrees. "Shadow" is a simple method based on an analysis of the patterns of…

Genetic algorithms are modeled after the biological evolutionary processes that use natural selection to select the best species to survive. They are heuristics based and low cost to compute. Genetic algorithms use selection, crossover, and…

Mapping genotypes to phenotypes (G2P) is a fundamental goal in biology. So called PhyloG2P methods are a relatively new set of tools that leverage replicated evolution in phylogenetically independent lineages to identify genomic regions…

Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that…

The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper we take a few initial steps towards a description of this object, which may be…

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

In a distributed system, Task Assignment Problem (TAP) is a key factor for obtaining efficiency. TAP illustrates the appropriate allocation of tasks to the processor of each computer. In this problem, the proposed methods up to now try to…

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…

Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically…

Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…

Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…

We consider the problem of finding a Hamiltonian path with precedence constraints in the form of a partial order on the vertex set. This problem is known as Partially Ordered Hamiltonian Path Problem (POHPP). Here, we study the complexity…

Decreasing costs and new technologies have led to an increase in the amount of data available to plant breeding programs. High-throughput phenotyping (HTP) platforms routinely generate high-dimensional datasets of secondary features that…

We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…

Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…