Motivation: The promises of the post-genome era disease-related discoveries and advances have yet to be fully realized, with many opportunities for discovery hiding in the millions of biomedical papers published since. Public databases give access to data extracted from the literature by teams of experts, but their coverage is often limited and lags behind recent discoveries. We present a compu...

Protein-protein interfaces, which are regions of interaction between two protein molecules, contain the information regarding patterns of interacting functional groups. Recognition of such patterns is useful both for prediction of binding partners and for the development of drugs that can interfere with the formation of the protein-protein complex. Here we present a novel method, Interface-to-I...

Because of the importance of proteinprotein interaction (PPI) extraction from text, many corpora have been proposed with slightly differing definitions of proteins and PPI. Since no single corpus is large enough to saturate a machine learning system, it is necessary to learn from multiple different corpora. In this paper, we propose a solution to this challenge. We designed a rich feature vecto...

In this chapter a survey on the main graph-based clustering techniques proposed in the literature to mine proteinprotein interaction networks (PINs) is presented. The detection of putative protein complexes is an important research problem in systems biology. In fact it may help in understanding the mechanisms regulating cell life, in deriving conservations across species, in predicting the bio...

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently, efforts have been devoted during recent years to develop computational approaches to predict the interactions utilizing various sources of information. Ther...

We have investigated the osmotic pressure dependence of the association between ferric cytochrome P450cam and putidaredoxin (Pdx) to gain an insight into the role of water molecules in the P450cam-reduced Pdx complexation amenable to physiological electron transfer. The association constant was evaluated from the electron transfer rates from reduced Pdx to P450cam. The natural logarithm of the ...

The introduction of high-throughput gene expression profiling technologies (DNA microarrays) in molecular biology and their expected applications to the clinic have allowed the design of predictive signatures linked to a particular clinical condition or patient outcome in a given clinical setting. However, it has been shown that such signatures are prone to several problems: (i) they are heavil...

In this paper, we propose an abstract interpretation-based framework for reducing the state space of stochastic semantics for proteinprotein interaction networks. Our approach consists in quotienting the state space of networks. Yet interestingly, we do not apply the widelyused strong lumpability criterion which imposes that two equivalent states behave similarly with respect to the quotient, b...

The majority of biological functions of any living being are related to ProteinProtein Interactions (PPI). PPI discoveries are reported in form of research publications whose volume grows day after day. Consequently, automatic PPI information extraction systems are a pressing need for biologists. In this paper we are mainly concerned with the named entity detection module of PPIES (the PPI Info...

Cadherins are calcium-dependent, cell surface glycoproteins involved in cell-cell adhesion. To function in cell-cell adhesion, the transmembrane cadherin molecule must be associated with the cytoskeleton via cytoplasmic proteins known as catenins. Three catenins, α-catenin, β-catenin and γ-catenin (also known as plakoglobin), have been identified. β-catenin or plakoglobin is associated directly...