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The determination of transcriptional regulatory networks is key to the understanding of biological systems. However, the experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while current ...
In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are c ...
The enrichment culture SL2 dechlorinating tetrachloroethene (PCE) to ethene with strong trichloroethene (TCE) accumulation prior to cis-1,2-dichloroethene (cis-DCE) formation was analyzed for the presence of organohalide respiring bacteria and reductive de ...
Motivation: Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate bench ...
Chromatin immunoprecipitation experiments followed by ultra-high-throughput sequencing (ChIP-seq) is becoming the method of choice to identify transcription factor binding sites in prokaryotes and eukaryotes in vivo. Here, we review the computational steps ...
The majority of diseases in the retina are caused by genetic mutations affecting the development and function of photoreceptor cells. The transcriptional networks directing these processes are regulated by genes such as nuclear hormone receptors. The nucle ...
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression. The first miRNA was discovered less than 20 years ago in the context of studying Caenorabditis elegans development. The discovery of the second miR ...
Activity-dependent changes in gene expression are implicated in the pathogenesis of Huntington's disease (Gambazzi et al., 2010; Spektor et al., 2002; Luthi-Carter et al., 2000). One of the most important facets of transcriptional dysfunction in HD appears ...
Virtually every cell in our body tracks daily time using an endogenous mechanism called the circadian clock, which has a period of about 24 hours. This timing system offers a selective advantage by enabling organisms to anticipate periodic changes in envir ...
The number of transgenic mouse lines expressing Cre in either type of pigment cells (melanocytes and retinal pigment epithelium, RPE) is limited, and the available lines do not always offer sufficient specificity. In this study, we addressed this issue and ...