The concept of multiple graph alignment has recently been introduced as a novel method for the structural analysis of biomolecules. Using inexact, approximate graph-matching techniques, this method enables the robust identification of approximately conserved patterns in biologically related structures. In particular, ...

Motivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor binding sites in promoter regions of potential transcription factor target genes. It is typically approached by position weight matrix-based motif ...

Today, RNA is well known to perform important regulatory and catalytic function due to its distinguished structure. Consequently, state-of-the-art RNA multiple alignment algorithms consider structure as well as sequence information. However, existing tools neglect the important aspect of locality. Notably, locality in ...

Apomixis is a reproductive phenomenon that occurs in flowering plants. It allows a plant to produce asexual seeds, with its same genetic constitution. The existence of a genetic basis for apomixis is crushing, but the molecular mechanisms are unclear. The search for the “master apomixis gene” had led to the isolation of ...

Alignments are part of the most important data type in the field of comparative genomics. They can be abstracted to a character matrix derived from aligned sequences. A variety of biological questions forces the researcher to inspect these alignments. Our tool, called COMPOSALIGN, was developed to sonify large scale ...

Structural alignments of proteins are used to identify structural similarities. These similarities can indicate homology or a common or similar function. Several, mostly heuristic methods are available to compute structural alignments. In this paper, we present a novel algorithm that uses methods from combinatorial ...

Genome annotation relies to a large extent on the recognition of homologs to already known genes. The starting point for such protocols is a collection of known sequences from one or more species, from which a model is constructed – either automatically or manually – that encodes the defining features of a single gene ...

It is often challenging to reconstruct accurately a complete dynamic biological network due to the scarcity of data collected in cost-effective experiments. This paper addresses the possibility of comparatively identifying qualitative interaction shifts between two dynamical networks from comparative time course data. ...

The analysis of RNA folding landscapes yields insights into the kinetic folding behavior not available from classical structure prediction methods. This is especially important for multi-stable RNAs whose function is related to structural changes, as in the case of riboswitches. However, exact methods such as barrier ...

A wealth of time series of microarray measurements have become available over recent years. Several two-sample tests for detecting differential gene expression in these time series have been defined, but they can only answer the question whether a gene is differentially expressed across the whole time series, not in which ...