Compressive genomics

Compressive genomics for protein databases

MOTIVATION The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search. Acceleration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homolo...

From Compressive Clustering to Compressive Learning

It is often useful to fit a probability model to a data collection, in order to concisely represent the data, to feed learning algorithms that work on densities, to extract features or, simply, to uncover underlying structures. A particularly popular probability model is the Gaussian Mixture Model (GMM). Among many other applications, GMM form a central tool to build time-frequency models of au...

Genomics update Wine Genomics

Comparative genomics of human stem cell factor (SCF)

Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCB...

Compressive beamforming.

Sound source localization with sensor arrays involves the estimation of the direction-of-arrival (DOA) from a limited number of observations. Compressive sensing (CS) solves such underdetermined problems achieving sparsity, thus improved resolution, and can be solved efficiently with convex optimization. The DOA estimation problem is formulated in the CS framework and it is shown that CS has su...