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This paper focuses on Beta-binders, a language of processes with typed interaction sites which has been recently introduced to represent biological entities. Here the syntax and semantics of Beta-binders are enriched to achieve a stochastic version of it, in order to obtain quantitative measures on biological phenomena. The relevance of quantitative(More)
The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological(More)
A stochastic extension of COWS is presented. First the formalism is given an operational semantics leading to finitely branching transition systems. Then its syntax and semantics are enriched along the lines of Markovian extensions of process calculi. This allows addressing quantitative reasoning about the behaviour of the specified web services. For(More)
Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. Such studies often present with computationally challenging burdens that hinder genome-wide investigations across large datasets that are now becoming(More)
The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and(More)
Genomic instability is a fundamental feature of human cancer often resulting from impaired genome maintenance. In prostate cancer, structural genomic rearrangements are a common mechanism driving tumorigenesis. However, somatic alterations predisposing to chromosomal rearrangements in prostate cancer remain largely undefined. Here, we show that SPOP, the(More)
The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. et al. 2014. " Unraveling the clonal hierarchy of somatic genomic aberrations. " Genome Biology 15 (8): 439. Abstract Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal(More)
Biological systems are characterised by a large number of interacting entities whose dynamics is described by a number of reaction equations. Mathematical methods for modelling biological systems are mostly based on a centralised solution approach: the modelled system is described as a whole and the solution technique, normally the integration of a system(More)
IMPORTANCE Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer. OBJECTIVE To understand how(More)
Data protection legislation requires personal data to be collected and processed only for lawful and legitimate purposes. Unfortunately, existing protection mechanisms are not appropriate for purpose control: they only prevent unauthorized actions from occurring and do not guarantee that the data are actually used for the intended purpose. In this paper, we(More)