Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. Overrepresentation of convergent occurrences of motifs in proteins with a common attribute (such as similar subcellular location or a shared interaction partner) provides a feasible means to discover novel occurrences computationally. The SLiMDisc (Short, Linear Motif Di...

Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information av...

Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http:...

The research work presented in this paper tackles the personal information overload phenomenon. Our purpose is to offer a set of interactive visualization techniques allowing one’s personal digital memory to be organized and overviewed. This system will provide easy browsing, guiding towards the wanted piece of information and allow a free exploration of the personal information space. Three ma...

We present the new THOT toolkit for fullyautomatic and interactive statistical machine translation (SMT). Initial public versions of THOT date back to 2005 and did only include estimation of phrase-based models. By contrast, the new version offers several new features that had not been previously incorporated. The key innovations provided by the toolkit are computeraided translation, including ...

A new method for electronic publishing of articles with text linked to its interactive three dimensional content is described. The method is based on a single document containing a variety of objects such as formatted text, multiple three dimensional molecular objects, textured shapes and surfaces, data tables and graphs, chemical spreadsheets, alignments, etc. The 3D article can then be publis...

The vast majority of lichenicolous fungi are relatively host-specific, nonvirulent ascomycetes and heterobasidiomycetes. A few known lichenicolous homobasidiomycetes (mushroom-forming fungi) generally exhibit broad host ecologies and in some cases, high virulence. Many produce conspicuous sclerotia or bulbils, thought to be adaptive in dispersal and survival. To more clearly understand the evol...

According to balance theory (Heider, 1958), when two coworkers develop different levels of leader-member exchange (LMX) relationships with their supervisor, a triadic relational imbalance will arise among the three parties that may result in hostile sentiments and poor social interactions between them. This study examines the consequences and psychological processes of (dis)similar levels of LM...