Publications by Vaibhav Rajan | EPFL Graph Search

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments

Oxford University Press2013

Bootstrapping phylogenies inferred from rearrangement data

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

Reconstruction of Large-Scale Phylogenies : Advances in Algorithms and Statistical Methods

Vaibhav Rajan

The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput se ...

EPFL2012

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

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

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

Estimating true evolutionary distances under rearrangements, duplications, and losses

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

2010

Heuristics for the inversion median problem

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

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

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

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

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

2009

Hurdles hardly have to be heeded

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

Springer2008