Publications by Yu Lin | EPFL Graph Search

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Recent achievements in studies of the effects of ICRF (Ion Cyclotron Range of Frequencies) power on the SOL (Scrape-Off Layer) and PWI (Plasma Wall Interactions) in ASDEX Upgrade (AUG), Alcator C-Mod, and JET-ILW are reviewed. Capabilities to diagnose and ...

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 ...

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 ...

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 ...

The significant degradation of reconstructed image resolution and the presence of apparent artifacts can result from sub-millimetric misalignment of scanner configuration in highspatial resolution positron emission tomography (PET) systems. Therefore, ensu ...

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 ...

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 ...

Background: In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant r ...

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...

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 ...

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, ...

We study the problem of sorting genomes under an evolutionary model that includes genomic rearrangements and segmental duplications. We propose an iterative algorithm to improve any initial evolutionary trajectory between two genomes in terms of parsimony. ...

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. ...

Yu Lin

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Impact of ICRF on the scrape-off layer and on plasma wall interactions: From present experiments to fusion reactor

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

A Metric for Phylogenetic Trees Based on Matching

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

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

Inverse Rendering for PET Scanner Calibration

A metric for phylogenetic trees based on matching

Sorting signed permutations by inversions in O(nlogn) time

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

A maximum-likelihood approach for building cell-type trees by lifting

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

Study of cell differentiation by phylogenetic analysis using histone modification data

Bootstrapping phylogenies inferred from rearrangement data

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

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

Sorting genomes with rearrangements and segmental duplications through trajectory graphs

Heuristics for the inversion median problem

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

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

Estimating true evolutionary distances under rearrangements, duplications, and losses