Publications de Yu Lin | EPFL Graph Search

Fast ions in mode conversion heating (He-3)-H plasmas in JET

Fast ions were analysed in experiments focusing on fundamental He-3 minority and mode conversion (MC) in the ion cyclotron resonance range of frequencies (ICRF) in H plasmas and on second harmonic heating of He-3 ions at 2.65 T mimicking D-T plasma heating ...

2012

Minority and mode conversion heating in (He-3)-H JET plasmas

Mikhail Maslov, Yu Lin

Radio frequency (RF) heating experiments have recently been conducted in JET (He-3)-H plasmas. This type of plasmas will be used in ITER's non-activated operation phase. Whereas a companion paper in this same PPCF issue will discuss the RF heating scenario ...

2012

Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference

Yu Lin

The rapid accumulation of sequenced genomes offers the chance to resolve longstanding questions about the evolutionary histories, or phylogenies, of groups of organisms. The relatively rare occurrence of large-scale evolutionary events in a whole genome, e ...

EPFL2012

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Vaibhav Rajan, Yu Lin

Background: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have be ...

BioMed Central2012

Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion

Yu Lin, Mingfu Shao

Computing the edit distance between two genomes under certain operations is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. ...

Biomed Central Ltd2012

A Metric for Phylogenetic Trees Based on Matching

Bernard Moret, Vaibhav Rajan, Yu Lin

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 similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so f ...

2012

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Bernard Moret, Vaibhav Rajan, Yu Lin

TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, ...

Oxford University Press2012

A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes

Bernard Moret, Yu Lin

Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organiz ...

Mary Ann Liebert2011

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Vaibhav Rajan, Yu Lin

Springer Verlag2011

A metric for phylogenetic trees based on matching

Bernard Moret, Vaibhav Rajan, Yu Lin

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 similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so t ...

Springer Verlag2011

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Vaibhav Rajan, Yu Lin

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

2011

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes

Bernard Moret, Yu Lin

Springer-Verlag2010

Sorting signed permutations by inversions in O(nlogn) time

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli and Pevzner, who gave the first polynomial-time algorithm for sorting signed permutations by inv ...

2010

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Vaibhav Rajan, Yu Lin

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

Springer2010

Estimating true evolutionary distances under rearrangements, duplications, and losses

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

2010

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes

Bernard Moret, Yu Lin

Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organiz ...

Springer Verlag New York2010

Heuristics for the inversion median problem

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin, Wei Xu

2010

Hurdles and sorting by inversions: Combinatorial, statistical, and experimental results

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

2009

Sorting signed permutations by inversions in O(nlogn) time

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli and Pevzner, who gave the first polynomial-time algorithm for sorting signed permutations by inv ...

Springer2009

Estimating true evolutionary distances under the DCJ model

Bernard Moret, Yu Lin

2008