A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks
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Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic ...
Copy number variations are genomic structural variants that are frequently associated with human diseases. Among these copy number variations, duplications of DNA segments are often assumed to lead to dosage effects by increasing the copy number of either ...
Gene regulatory networks control gene expression levels, and therefore play an essential role in mammalian development and function. Regulation of gene expression is the result of a complex interplay between DNA regulatory elements and their binding partne ...
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in huma ...
Regulation of gene expression is a carefully regulated phenomenon in the cell. “Reverse-engineering” algorithms try to reconstruct the regulatory interactions among genes from genome-scale measurements of gene expression profiles (microarrays). Mammalian c ...
Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here ...
The external control of Gene Regulatory Networks (GRNs) has received much attention in recent years. In this paper, we propose a novel algorithm for controlling partially observable GRNs coupling utility based state learning methods and Batch Mode Reinforc ...
How a complex animal can arise from a fertilized egg is one of the oldest and most fascinating questions of biology, the answer to which is encoded in the genome. Body shape and organ development, and their integration into a functional organism all depend ...
Motivation: Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide ...
Mycobacterium goes yeast: Target deconvolution of anti-tuberculosis drugs can be a very challenging task. Here we report a yeast 3-hybrid system that allows promising small molecules to be screened for protein targets of a pathogen in nontoxic yeast cells. ...
