203 research outputs found
Response to comment on "Human-specific gain of function in a developmental enhancer"
Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive selection. We reinforce our previous conclusion by analyzing hypothesized BGC
events genomewide and assessing the effect of recombination rates on human-accelerated conserved noncoding sequence ascertainment. We also provide evidence that AT → GC substitution bias can coexist with positive selection
Viral quasispecies inference from 454 pyrosequencing
10.1186/1471-2105-14-355BMC Bioinformatics141-BBMI
Improved Lower Bounds for Constant GC-Content DNA Codes
The design of large libraries of oligonucleotides having constant GC-content
and satisfying Hamming distance constraints between oligonucleotides and their
Watson-Crick complements is important in reducing hybridization errors in DNA
computing, DNA microarray technologies, and molecular bar coding. Various
techniques have been studied for the construction of such oligonucleotide
libraries, ranging from algorithmic constructions via stochastic local search
to theoretical constructions via coding theory. We introduce a new stochastic
local search method which yields improvements up to more than one third of the
benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide
libraries when n <= 14. We also found several optimal libraries by computing
maximum cliques on certain graphs.Comment: 4 page
A Survey of Combinatorial Methods for Phylogenetic Networks
The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation
Insertion Magnets
Chapter 3 in High-Luminosity Large Hadron Collider (HL-LHC) : Preliminary
Design Report. The Large Hadron Collider (LHC) is one of the largest scientific
instruments ever built. Since opening up a new energy frontier for exploration
in 2010, it has gathered a global user community of about 7,000 scientists
working in fundamental particle physics and the physics of hadronic matter at
extreme temperature and density. To sustain and extend its discovery potential,
the LHC will need a major upgrade in the 2020s. This will increase its
luminosity (rate of collisions) by a factor of five beyond the original design
value and the integrated luminosity (total collisions created) by a factor ten.
The LHC is already a highly complex and exquisitely optimised machine so this
upgrade must be carefully conceived and will require about ten years to
implement. The new configuration, known as High Luminosity LHC (HL-LHC), will
rely on a number of key innovations that push accelerator technology beyond its
present limits. Among these are cutting-edge 11-12 tesla superconducting
magnets, compact superconducting cavities for beam rotation with ultra-precise
phase control, new technology and physical processes for beam collimation and
300 metre-long high-power superconducting links with negligible energy
dissipation. The present document describes the technologies and components
that will be used to realise the project and is intended to serve as the basis
for the detailed engineering design of HL-LHC.Comment: 19 pages, Chapter 3 in High-Luminosity Large Hadron Collider (HL-LHC)
: Preliminary Design Repor
Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree
Introduction: A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events might occur. Hence, it is of great challenge to infer the containing species tree from a set of gene trees. One common approach to this inference problem is through gene tree and species tree reconciliation. Results: In this paper, we generalize the traditional least common ancestor (LCA) reconciliation to define a reconciliation between a gene tree and species tree under the tree homomorphism framework. We then study the structural properties of the space of all reconciliations between a gene tree and a species tree in terms of the gene duplication, gene loss or deep coalescence costs. As application, we show that the LCA reconciliation is the unique one that has the minimum deep coalescence cost, provide a novel characterization of the reconciliations with the optimal duplication cost, and present efficient algorithms for enumerating (nearly-)optimal reconciliations with respect to each cost. Conclusions: This work provides a new graph-theoretic framework for studying gene tree and species tree reconciliations
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