Jens Lagergren

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The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. 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(More)
We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such(More)
MOTIVATION The identification of regulatory control regions within genomes is a major challenge. Studies have demonstrated that regulating regions can be described as locally dense clusters or modules of cis-acting transcription factor binding sites (TFBS). For well-described biological contexts, it is possible to train predictive algorithms to discern(More)
MOTIVATION Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many(More)
Gene tree and species tree reconstruction, orthology analysis and reconciliation, are problems important in multigenome-based comparative genomics and biology in general. In the present paper, we advance the frontier of these areas in several respects and provide important computational tools. First, exact algorithms are given for several probabilistic(More)
We study the Max k-Cut problem and its dual, the Abstract-1 Min k-Partition problem. In the Min k-Partition problem, given a graph G = (V, E) and positive edge weights, we want to find an edge set of minimum weight whose removal makes G k-colorable. For the Max k-Cut problem we show that, if P 6= NP, no polynomial time approximation algorithm can achieve a(More)