Networks are a fundamental and flexible way of representing various complex systems. Many domains such as communication, citation, procurement, biology, social media, transportation can be modeled set entities their relationships. Temporal networks specialization general where every relationship occurs at discrete time. The temporal evolution is important to understand the structure We present ...

Specificity of mammalian gene regulatory regions is achieved to a large extent through the combinatorial binding of sets of transcription factors to distinct binding sites, discrete combinations of which are often referred to as regulatory modules. Identification and subsequent characterization of gene regulatory modules will be a key step in assembling transcriptional regulatory networks from ...

Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Most motif finding algorithms perform well in finding over-represented substrings in a small collection of sequences. This requires some prior knowledge about the functional relations among genes in a study in order to select a good collection of promoters. Microarray gene profiling...

The analysis of network motifs, patterns of local interconnections with potential functional properties, has applications in many fields of science. Network motif analysis is particularly important for the exploration of biological networks. The distribution and multiple occurrences of motifs in a network, complicated by different concepts for the determination of motif frequency, create variou...

DNA regulatory motifs reflect the direct transcriptional interactions between regulators and their target genes and contain important information regarding transcriptional networks. In silico motif detection strategies search for DNA patterns that are present more frequently in a set of related sequences than in a set of unrelated sequences. Related sequences could be genes that are coexpressed...

Motif Finding is one of the important tasks in gene regulation which is essential in understanding biological cell functions. Based on Tompa et al. study, the performance of current motif finders is not satisfactory. A number of ensemble methods has been proposed to enhance the results. Existing ensemble methods overall performance is better than stand-alone motif finders. A recent ensemble met...