Publications

In this article, we present a computational multiscale model for the characterization of subcellular proteins. The model is encoded inside a simulation tool that builds coarse-grained (CG) force fields from atomistic simulations. Equilibrium molecular dynamics simulations on an all-atom model of the actin filament are performed. Then, using the statistical distribution of the distances between pairs of selected groups of atoms at the output of the MD simulations, the force field is parameterized using the Boltzmann inversion approach. This CG force field is further used to characterize the dynamics of the protein via Brownian dynamics simulations. This combination of methods into a single computational tool flow enables the simulation of actin filaments with length up to 400 nm, extending the time and length scales compared to state-of-the-art approaches. Moreover, the proposed multiscale modeling approach allows to investigate the relationship between atomistic structure and changes on the overall dynamics and mechanics of the filament and can be easily (i) extended to the characterization of other subcellular structures and (ii) used to investigate the cellular effects of molecular alterations due to pathological conditions.

The common paradigm employed for object detection is the sliding window (SW) search. This approach generates grid-distributed patches, at all possible positions and sizes, which are evaluated by a binary classifier: the trade-off between computational burden and detection accuracy is the real critical point of sliding windows; several methods have been proposed to speed up the search such as adding complementary features. We propose a paradigm that differs from any previous approach, since it casts object detection into a statistical-based search using a Monte Carlo sampling for estimating the likelihood density function with Gaussian kernels. The estimation relies on a multi-stage strategy where the proposal distribution is progressively refined by taking into account the feedback of the classifiers. The method can be easily plugged in a Bayesian-recursive framework to exploit the temporal coherency of the target objects in videos. Several tests on pedestrian and face detection, both on images and videos, with different types of classifiers (cascade of boosted classifiers, soft cascades and SVM) and features (covariance matrices, Haar-like features, integral channel features and histogram of oriented gradients) demonstrate that the proposed method provides higher detection rates and accuracy as well as a lower computational burden w.r.t. sliding window detection.

The aim of this work was to design and implement a new bioinformatics software which is able to identify the protein peptides from the peaks which arise from in-source or MS/MS fragmentation. The oligopeptide fraction was extracted from Fontina cheese at different ages of ripening and subsequently analyzed by LC/MS/MS. On the resulting total ion chromatograms, the peptides were identified by a method based both on the in-source fragmentation detectable with a single-quadrupole mass analyzer and by a new software which was developed. This software performs an in-silico digestion of the major milk proteins, it calculates all the possible peptide fragments which are generated by the loss of the first N- or C-terminal amino acids, and finally, it matches the experimental ion chromatogram with the in-silico which generated theoretical spectrum to identify the exact amino-acid protein sequence of the unknown oligopeptide. With this tool, the useful insights into the proteolytic processes which occur during Fontina cheese aging are obtained, which leads to a better knowledge about the functional features of the proteolysis end product.

Nearly two decades have passed since the publication of the first study reporting the discovery of microRNAs (miRNAs). The key role of miRNAs in post-transcriptional gene regulation led to the performance of an increasing number of studies focusing on origins, mechanisms of action and functionality of miRNAs. In order to associate each miRNA to a specific functionality it is essential to unveil the rules that govern miRNA action. Despite the fact that there has been significant improvement exposing structural characteristics of the miRNA-mRNA interaction, the entire physical mechanism is not yet fully understood. In this respect, the development of computational algorithms for miRNA target prediction becomes increasingly important. This manuscript summarizes the research done on miRNA target prediction. It describes the experimental data currently available and used in the field and presents three lines of computational approaches for target prediction. Finally, the authors put forward a number of considerations regarding current challenges and future directions.

In this paper we present a novel algorithm to synthesize an optimal decision tree from OR-decision tables, an extension of standard decision tables, complete with the formal proof of optimality and computational cost analysis. As many problems which require to recognize particular patterns can be modeled with this formalism, we select two common binary image processing algorithms, namely connected components labeling and thinning, to show how these can be represented with decision tables, and the benets of their implementation as optimal decision trees in terms of reduced memory accesses. Experiments are reported, to show the computational time improvements over state of the art implementations.

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environment.

The recognition of people orientation in single images is still an open issue in several real cases, when the image resolution is poor, body parts cannot be distinguished and localized or motion cannot be exploited. However, the estimation of a person orientation, even an approximated one, could be very useful to improve people tracking and re-identification systems, or to provide a coarse alignment of body models on the input images. In these situations, holistic features seem to be more effective and faster than model based 3D reconstructions. In this paper we propose to describe the people appearance with multi-level HoG feature sets and to classify their orientation using an array of Extremely Randomized Trees classifiers trained on quantized directions. The outputs of the classifiers are then integrated into a global continuous probability density function using a Mixture of Approximated Wrapped Gaussian distributions. Experiments on the TUD Multiview Pedestrians, the Sarc3D, and the 3DPeS datasets confirm the efficacy of the method and the improvement with respect to state of the art approaches.

This paper presents an innovative approach for detecting and localizing duplicate objects in pick-and-place applications under extreme conditions of occlusion, where standard appearance-based approaches are likely to be ineffective. The approach exploits SIFT keypoint extraction and mean shift clustering to partition the correspondences between the object model and the image onto different potential object instances with real-time performance. Then, the hypotheses of the object shape are validated by a projection with a fast Euclidean transform of some delimiting points onto the current image. Moreover, in order to improve the detection in the case of reflective or transparent objects, multiple object models (of both the same and different faces of the object) are used and fused together. Many measures of efficacy and efficiency are provided on random disposals of heavily-occluded objects, with a specific focus on real-time processing. Experimental results on different and challenging kinds of objects are reported. © 2012 Elsevier B.V. All rights reserved.