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Organs and organelles represent core biological systems in mammals, but the diversity in protein composition remains unclear. Here, we combine subcellular fractionation with exhaustive tandem mass spectrometry-based shotgun sequencing to examine the protein content of four major organellar compartments (cytosol, membranes [microsomes], mitochondria, and(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)
MOTIVATION We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems. RESULTS This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries(More)
Many computational problems in biology involve parameters for which a small range of values cover important applications. We argue that for many problems in this setting, parameterized computational complexity rather than NP-completeness is the appropriate tool for studying apparent intractability. At issue in the theory of parameterized complexity is(More)
Two natural kinds of problems about " structured collections of symbols " can be generally referred to as the LARGEST COMMON SUBOBJECT and the SMALLEST COMMON SUPEROBJECT problems, which we consider here as the dual problems of interest. For the case of rooted binary trees where the symbols occur as leaf-labels and a subobject is defined by label-respecting(More)
A bipartite graph is biplanar if the vertices can be placed on two parallel lines (layers) in the plane such that there are no edge crossings when edges are drawn as line segments between the layers. In this paper we study the 2-LAYER PLANARIZATION problem: Can k edges be deleted from a given graph G so that the remaining graph is biplanar? This problem is(More)
The tumour stroma is believed to contribute to some of the most malignant characteristics of epithelial tumours. However, signalling between stromal and tumour cells is complex and remains poorly understood. Here we show that the genetic inactivation of Pten in stromal fibroblasts of mouse mammary glands accelerated the initiation, progression and malignant(More)