Zobrazeno 1 - 10
of 147
pro vyhledávání: '"Huggins Peter"'
Publikováno v:
BMC Bioinformatics, Vol 13, Iss 1, p 210 (2012)
Abstract Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene tree
Externí odkaz:
https://doaj.org/article/ef8a225c8e834ff5930aefa8750ff2c3
Publikováno v:
Algorithms for Molecular Biology, Vol 3, Iss 1, p 5 (2008)
Abstract The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "optimal" when the algorithm outp
Externí odkaz:
https://doaj.org/article/499a2494a67c44e08a5ea9ae75c3bda8
We present an extension of sparse Canonical Correlation Analysis (CCA) designed for finding multiple-to-multiple linear correlations within a single set of variables. Unlike CCA, which finds correlations between two sets of data where the rows are ma
Externí odkaz:
http://arxiv.org/abs/1511.06419
Autor:
Huggins, Peter
We consider the classic problem of designing heaps. Standard binary heaps run faster in practice than Fibonacci heaps but have worse time guarantees. Here we present a new type of heap, a layered heap, that runs faster in practice than both standard
Externí odkaz:
http://arxiv.org/abs/1510.03367
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene transfers,
Externí odkaz:
http://arxiv.org/abs/1302.6422
Autor:
Arnaoudova, Elissaveta, Haws, David, Huggins, Peter, Jaromczyk, Jerzy W., Moore, Neil, Schardl, Chris, Yoshida, Ruriko
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing point esti
Externí odkaz:
http://arxiv.org/abs/1004.2101
Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet most reconstruction methods like ML do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution
Externí odkaz:
http://arxiv.org/abs/0911.0645
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of study in coph
Externí odkaz:
http://arxiv.org/abs/0809.1908
Autor:
Huggins, Peter, Yoshida, Ruriko
Optimal sequence alignments depend heavily on alignment scoring parameters. Given input sequences, {\em parametric alignment} is the well-studied problem that asks for all possible optimal alignment summaries as parameters vary, as well as the {\em o
Externí odkaz:
http://arxiv.org/abs/0809.1473
Autor:
Huggins, Peter, Pachter, Lior
Polyhedral geometry can be used to quantitatively assess the dependence of rankings on personal preference, and provides a tool for both students and universities to assess US News and World Report rankings.
Externí odkaz:
http://arxiv.org/abs/0805.1026