Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis

Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces. Statistical inference methods detecting residue-residue coevolution have recently triggered considerable progress in using sequence data for quaternary protein structure prediction; they require, however, large joint alignments of homologous protein pairs known to interact. The generation of such alignments is a complex computational task on its own; application of coevolutionary modeling has in turn been restricted to proteins without paralogs, or to bacterial systems with the corresponding coding genes being co-localized in operons. Here we show that the Direct-Coupling Analysis of residue coevolution can be extended to connect the different scales, and simultaneously to match interacting paralogs, to identify inter-protein residue-residue contacts and to discriminate interacting from noninteracting families in a multiprotein system. Our results extend the potential applications of coevolutionary analysis far beyond cases treatable so far.Comment: Main Text 19 pages Supp. Inf. 16 page

Accurate 3D maps from depth images and motion sensors via nonlinear Kalman filtering

This paper investigates the use of depth images as localisation sensors for 3D map building. The localisation information is derived from the 3D data thanks to the ICP (Iterative Closest Point) algorithm. The covariance of the ICP, and thus of the localization error, is analysed, and described by a Fisher Information Matrix. It is advocated this error can be much reduced if the data is fused with measurements from other motion sensors, or even with prior knowledge on the motion. The data fusion is performed by a recently introduced specific extended Kalman filter, the so-called Invariant EKF, and is directly based on the estimated covariance of the ICP. The resulting filter is very natural, and is proved to possess strong properties. Experiments with a Kinect sensor and a three-axis gyroscope prove clear improvement in the accuracy of the localization, and thus in the accuracy of the built 3D map.Comment: Submitted to IROS 2012. 8 page

Probabilistic Cross-Identification of Astronomical Sources

We present a general probabilistic formalism for cross-identifying astronomical point sources in multiple observations. Our Bayesian approach, symmetric in all observations, is the foundation of a unified framework for object matching, where not only spatial information, but physical properties, such as colors, redshift and luminosity, can also be considered in a natural way. We provide a practical recipe to implement an efficient recursive algorithm to evaluate the Bayes factor over a set of catalogs with known circular errors in positions. This new methodology is crucial for studies leveraging the synergy of today's multi-wavelength observations and to enter the time-domain science of the upcoming survey telescopes.Comment: Accepted for publication in the Astrophysical Journal, 8 pages, 1 figure, emulateapj w/ apjfont