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Data-Intensive Modelling and Simulation in Life Sciences and Socio-economical and Physical Sciences

coordinated work of the ‘‘modelling’’ working groups WG3 and WG4 across the first two years of the Action. Andrea Bracciali and Elisabeth Larsson, guest editors of this volume and chairs of WG3 and WG4

PWHATSHAP: efficient haplotyping for future generation sequencing

Background Haplotype phasing is an important problem in the analysis of genomics information. Given a set of DNA fragments of an individual, it consists of determining which one of the possible alleles (alternative forms of a gene) each fragment comes from. Haplotype information is relevant to gene regulation, epigenetics, genome-wide association studies, evolutionary and...

Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy

Background Several diseases, many of which nowadays pandemic, consist of multifactorial pathologies. Paradigmatic examples come from the immune response to pathogens, in which cases the effects of different infections combine together, yielding complex mutual feedback, often a positive one that boosts infection progression in a scenario that can easily become lethal. HIV is one...

On deducing causality in metabolic networks

Background Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks. One of the relevant problems in this context is the comprehension of causality dependencies amongst the molecules involved in the metabolic process. Results We...

Stochastic models for the in silico simulation of synaptic processes

Background Research in life sciences is benefiting from a large availability of formal description techniques and analysis methodologies. These allow both the phenomena investigated to be precisely modeled and virtual experiments to be performed in silico. Such experiments may result in easier, faster, and satisfying approximations of their in vitro/vivo counterparts. A promising...