In protein-protein interaction (PPI) networks, functional similarity is often inferred based on
the function of directly interacting proteins, or more generally, some notion of interaction …

Motivation: The exponential growth of protein sequence databases has increasingly made
the fundamental question of searching for homologs a computational bottleneck. The amount …

Many datasets exhibit a well-defined structure that can be exploited to design faster search
tools, but it is not always clear when such acceleration is possible. Here, we introduce a …

… Prat, Y., Fromer, M., Linial, N. and Linial, M. Recovering key biological constituents
through sparse representation of gene expression. Bioinformatics 5 (2011), 655–661 …

Motivation: One of the most successful methods to date for recognizing protein sequences
that are evolutionarily related has been profile hidden Markov models (HMMs). However, …

With the ease of gene sequencing and the technology available to study and manipulate
non-model organisms, the extension of the methodological toolbox required to translate our …

Background The quality of multiple protein structure alignments are usually computed and
assessed based on geometric functions of the coordinates of the backbone atoms from the …

Vertebrates have evolved three paralogs, termed LUC7L, LUC7L2, and LUC7L3, of the
essential yeast U1 small nuclear RNA (snRNA)-associated splicing factor Luc7p. We …

Anomaly and outlier detection is a long-standing problem in machine learning. In some
cases, anomaly detection is easy, such as when data are drawn from well-characterized …

We introduce MRFy, a tool for protein remote homology detection that captures beta-strand
dependencies in the Markov random field. Over a set of 11 SCOP beta-structural …