Publications by Krister Swenson

Uncovering hidden phylogenetic consensus in large datasets

Bernard Moret, Alexandros Stamatakis, Krister Swenson

Institute of Electrical and Electronics Engineers2011

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

The Metropolized Partial Importance Sampling MCMC mixes slowly on minimal reversal rearrangement paths

Krister Swenson

Markov chain Monte Carlo has been the standard technique for inferring the posterior distribution of genome rearrangement scenarios under a Bayesian approach. We present here a negative result on the rate of convergence of the generally used Markov chains. ...

2010

Uncovering hidden phylogenetic consensus

Bernard Moret, Krister Swenson

Springer2010

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

Inversion-based genomic signatures

Bernard Moret, Krister Swenson

Background: Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While modest successes have been reported fo ...

2009

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

Maximum independent sets of commuting and noninterfering inversions

Bernard Moret, Krister Swenson

Background: Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard to approximate. Yet median-based ap ...

2009

Evolution of whole genomes through inversions : models and algorithms for duplicates, ancestors, and edit scenarios

Krister Swenson

Advances in sequencing technology are yielding DNA sequence data at an alarming rate – a rate reminiscent of Moore's law. Biologists' abilities to analyze this data, however, have not kept pace. On the other hand, the discrete and mechanical nature of the ...

EPFL2009

Hurdles hardly have to be heeded

Bernard Moret, Vaibhav Rajan, Krister Swenson, Yu Lin

Springer2008

Phylogenetic reconstruction from complete gene orders of whole genomes

Bernard Moret, Krister Swenson

Imperial College Press2008