Search Results - "Moret, Bernard M.E."

How many bootstrap replicates are necessary? by Pattengale, Nicholas D, Alipour, Masoud, Bininda-Emonds, Olaf R P, Moret, Bernard M E, Stamatakis, Alexandros

“…Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from…”
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Sequence-Based Synteny Analysis of Multiple Large Genomes by Doerr, Daniel, Moret, Bernard M E

“…Current methods for synteny analysis provide only limited support to study large genomes at the sequence level. In this chapter, we describe a pipeline based…”
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Estimating true evolutionary distances under the DCJ model by Lin, Yu, Moret, Bernard M.E.

“…Motivation: Modern techniques can yield the ordering and strandedness of genes on each chromosome of a genome; such data already exists for hundreds of…”
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A Metric for Phylogenetic Trees Based on Matching by Yu Lin, Rajan, V., Moret, B. M. E.

“…Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of…”
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A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes by Lin, Yu, Moret, Bernard M E

“…Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over…”
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Efficiently computing the Robinson-Foulds metric by Pattengale, Nicholas D, Gottlieb, Eric J, Moret, Bernard M E

“…The Robinson-Foulds (RF) metric is the measure most widely used in comparing phylogenetic trees; it can be computed in linear time using Day's algorithm. When…”
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A Transcript Perspective on Evolution by Christinat, Yann, Moret, Bernard M. E.

“…Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes, yet its evolution is poorly…”
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Scaling up accurate phylogenetic reconstruction from gene-order data by Tang, Jijun, Moret, Bernard M.E.

“…Motivation: Phylogenetic reconstruction from gene-order data has attracted increasing attention from both biologists and computer scientists over the last few…”
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Refining Regulatory Networks through Phylogenetic Transfer of Information by Xiuwei Zhang, Moret, B. M. E.

“…The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to…”
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Sorting signed permutations by inversions in O(nlogn) time by Swenson, Krister M, Rajan, Vaibhav, Lin, Yu, Moret, Bernard M E

“…The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli…”
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Refining transcriptional regulatory networks using network evolutionary models and gene histories by Zhang, Xiuwei, Moret, Bernard M E

“…Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper…”
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Hurdles and sorting by inversions: combinatorial, statistical, and experimental results by Swenson, Krister M, Lin, Yu, Rajan, Vaibhav, Moret, Bernard M E

“…As data about genomic architecture accumulates, genomic rearrangements have attracted increasing attention. One of the main rearrangement mechanisms,…”
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Evaluating synteny for improved comparative studies by Ghiurcuta, Cristina G, Moret, Bernard M E

“…Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early…”
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Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining by St. John, Katherine, Warnow, Tandy, Moret, Bernard M.E, Vawter, Lisa

“…We present the results of a large-scale experimental study of quartet-based methods (quartet cleaning and puzzling) for phylogeny reconstruction. Our…”
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An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes by Shao, Mingfu, Lin, Yu, Moret, Bernard M E

“…Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis…”
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Comparing genomes with rearrangements and segmental duplications by Shao, Mingfu, Moret, Bernard M E

“…Large-scale evolutionary events such as genomic rearrange.ments and segmental duplications form an important part of the evolution of genomes and are widely…”
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On Computing Breakpoint Distances for Genomes with Duplicate Genes by Shao, Mingfu, Moret, Bernard M E

“…A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or…”
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New approaches for reconstructing phylogenies from gene order data by Moret, Bernard M.E., Wang, Li-San, Warnow, Tandy, Wyman, Stacia K.

“…We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Our mathematical techniques include new polynomial-time methods…”
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Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes by Lin, Yu, Hu, Fei, Tang, Jijun, Moret, Bernard M E

“…The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements,…”
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Probabilistic partitioning methods to find significant patterns in ChIP-Seq data by Nair, Nishanth Ulhas, Kumar, Sunil, Moret, Bernard M E, Bucher, Philipp

“…We have witnessed an enormous increase in ChIP-Seq data for histone modifications in the past few years. Discovering significant patterns in these data is an…”
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