Learn More
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)
R c 1997 The Massachusetts Institute of Technology. Subscribers are licensed to use journal articles in a variety of ways, limited only as required to insure fair attribution to authors and the journal, and to prohibit use in a competing commercial product. See the journal's World Wide Web site for further details. The Chicago Journal of Theoretical(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)
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)
Identification of functional transcription factor binding sites in genomic sequences is notoriously difficult. The critical problem is the low specificity of predictions, which directly reflects the low target specificity of DNA binding proteins. To overcome the noise produced in predictions of individual binding sites, a new generation of algorithms(More)
A collection of T 1 , T 2 ,. .. , T k of unrooted, leaf labelled (phylogenetic) trees, all with different leaf sets, is said to be compatible if there exists a tree T such that each tree T i can be obtained from T by deleting leaves and contracting edges. Determining compatibility is NP-hard, and the fastest algorithm to date has worst case complexity of(More)
Cancer can be a result of accumulation of different types of genetic mutations such as copy number aberrations. The data from tumors are cross-sectional and do not contain the temporal order of the genetic events. Finding the order in which the genetic events have occurred and progression pathways are of vital importance in understanding the disease. In(More)