Chromatin is important for the regulation of transcription and other functions, yet the
diversity of chromatin composition and the distribution along chromosomes are still poorly …

In vertebrates, densely methylated DNA is associated with inactive transcription. Actors in
this process include proteins of the MBD family that can recognize methylated CpGs and …

How cells adopt different identities has long fascinated biologists. Signal transduction in
response to environmental cues results in the activation of transcription factors that determine …

Chromosomal architecture is known to influence gene expression, yet its role in controlling
cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem …

The human genome is segmented into topologically associating domains (TADs), but the role
of this conserved organization during transient changes in gene expression is not known. …

The sequence of a genome is insufficient to understand all genomic processes carried out
in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is …

Motivation: The increasing throughput of sequencing technologies offers new applications
and challenges for computational biology. In many of those applications, sequencing errors …

DNA methylation is an essential epigenetic mark in mammals that has to be re-established
after each round of DNA replication. The protein UHRF1 is essential for this process; it has …

The main obstacle to curing HIV is the presence of latent proviruses in the bodies of infected
patients. The partial success of reactivation therapies suggests that the genomic context of …

HIV-1 recurrently targets active genes and integrates in the proximity of the nuclear pore
compartment in CD4 + T cells. However, the genomic features of these genes and the relevance …