Jens Lagergren

TL;DR: This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers).

TL;DR: This paper develops MCMC algorithms for the gene sequence evolution model that, given gene sequence data, allows for orthology analysis, reconciliation analysis, and gene tree reconstruction, w.r.t. a species tree reconstruction that balances a likely/unlikely reconciliation and a likely-unlikely gene tree.

TL;DR: Within this model, an activity parameter is identified that measures the number of genes that are allowed to be simultaneously active in the genome of a taxa and it is shown that finding the most parsimonious scenario that reconciles the disagreeing gene trees with the species tree is doable in polynomial time.

Abstract: We consider the problem of constructing a species tree given a number of gene trees. In the frameworks introduced by Goodman et al. [3], Page [10], and Guigo, Muchnik, and Smith [5] this is formulated as an optimization problem; namely, that of finding the species tree requiring the minimum number of duplications and/ or losses in order to explain the gene trees.In this paper, we introduce the WIDTH k DUPLICATION-LOSS and WIDTH k DUPLICATION problems. A gene tree has width k w.r.t. a species tree, if the species tree can be reconciled with the gene tree using at most k simultaneously active copies of the gene along its branches. We explain w.r.t. to the underlying biological model, why this width is typically very small in comparison to the total number of duplications and losses. We show polynomial time algorithms for finding optimal species trees having bounded width w.r.t. at least one of the input gene trees. Furthermore, we present the first algorithm for input gene trees that are unrooted. Lastly, we apply our algorithms to a dataset from [5] and show a species tree requiring significantly fewer duplications and fewer duplications/losses than the trees given in the original paper.

TL;DR: The genomic analyses of the primary tumors and metastatic lesions from 99 samples obtained from 20 patients with breast cancer provide genomic evidence for a role of ALN metastasis in seeding distant organ metastasis and elucidate the evolving mutational landscape during cancer progression.