SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation

Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques have motivated the development of a large number of bioinformatics methods for the detection of regulatory motifs. The regulatory process is extremely complex and individual computational algorithm...

Computational methods for transcriptional regulation.

How is the information from a thousand gene-expression arrays, the location of more than two hundred regulatory factors, and nine sequenced genomes to be integrated into a global view of the regulatory network in budding yeast? Computational methods that fit incomplete noisy data provide the outlines of regulatory pathways, but the errors are not quantified. In the fly, embryonic patterning has...

Computational tools for studying gene regulation in the 3-dimensional genome

Determining the 3-dimensional structure of the genome and its impact on gene expression has been a long-standing question in cell biology. Recent development in mapping technologies for chromatin interactions has led to a rapid increase in this kind of interaction data, revealing a hierarchical organization of the 3D genome, from large compartments spanning multiple chromosomes, to mega-base-si...

Computational Tools for a Novel Transcriptional Profiling Method

In this thesis we provide computational tools for the planning of VTTTRAC experiments. VTT-TRAC is a novel method for measuring expression levels of genes. Monitoring gene expression by measuring the amounts of transcribed mRNAs (transcriptional profiling) has become an important experimental method in molecular biology. This has been due to rapid advance in the high-throughput measurement tech...

Atypical transcriptional regulation and function of a new toxin-antitoxin-like module in Bradyrhizobium japonicum Miclea