*Current perceptions that poplars have high levels of nucleotide variation, large effective population sizes, and rapid decay of linkage disequilibrium are based primarily on studies from one poplar species, Populus tremula. *We analysed 590 gene fragments (average length 565 bp) from each of 15 individuals from different populations from throughout the range of Populus balsamifera. *Nucleotide...

We uniquely characterize two members of the Q-Clustering family in an axiomatic framework. We introduce properties that use known tree constructions for the purpose of characterization. To characterize the Max-Sum clustering algorithm, we use the Gomory-Hu construction, and to characterize Single-Linkage, we use the Maximum Spanning Tree. Although at first glance it seems these properties are ‘...

A graph-based clustering method is proposed to cluster protein sequences into families, which automatically improves clusters of the conventional single linkage clustering method. Our approach formulates sequence clustering problem as a kind of graph partitioning problem in a weighted linkage graph, which vertices correspond to sequences, edges correspond to higher similarities than given thres...

Gene set enrichment analysis (GSEA) is typically based on tests derived from the KolmogorovSmirnov, which is underpowered and a need for simpler methods has been identified.[2] The wgsea package contains functions for conducting GSEA using a Wilcoxon test to test for differences in the distribution of p values between SNPs within the gene set under test and a control set of SNPs. The mean of th...

Knowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lanc...

Repetitive sequences make up a major part of eukaryotic genomes. We have developed an approach for the de novo identification and classification of repeat sequence families that is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Our extensions use multiple alignment information to define the boundaries of individual ...

This study develops the framework for an abusive-billing detection system that can potentially be used for examining claims of Medicare home health agencies, skilled nursing facilities, hospital outpatient facilities and hospice facilities. This system, which utilizes Medicare claims and other data, is comprised of two components: (1) a single-linkage clustering algorithm that defines market ar...

Although many biotechnological advancements have been made in the past decade, there has been very limited success in unraveling the genetic component of complex traits. Heavily invested research has been initiated based on etiological models of unrealistic simplicity and conducted under poor experimental designs, on data sets of insufficient size, leading to an overestimation of the effect siz...

Single-nucleotide polymorphism (SNP) genotypes were recently examined in an 890-kb region flanking the human gene CYP2D6. Single-marker and haplotype-based analyses identified, with genomewide significance (P < 10-7), a 403-kb interval displaying strong linkage disequilibrium (LD) with predicted poor-metabolizer phenotype. However, the width of this interval makes the location of causal variant...

Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. In this study the accuracy of predicting breeding values is compared for four different models including a large number of markers, at different marker densities for traits with heritabilities of 50 and 10%. The models estimated the effe...