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Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...
Pioneer transcription factors (PTF) are a subset of transcription factors with nucleosome-binding properties allowing them to bind specific sequences in condensed chromatin. Although the biological functions of PTFs including target genes and epigenetic ch ...
Modern large-scale data platforms manage colossal amount of data, generated by the ever-increasing number of concurrent users. Geo-replicated and sharded key-value data stores play a central role when building such platforms. As the strongest consistency m ...
Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depen ...
Effector proteins are recruited to chromatin via transient interactions between their reader domains and histone post-translational modification (PTM) patterns. These interactions form signaling pathways that control gene expression or repression and which ...
Caenorhabditiselegans (C. elegans) has gained importance as a model for studying host-microbiota interactions and bacterial infections related to human pathogens. Assessing the fate of ingested bacteria in the worm's intestine is therefore of great interes ...
Rod-shaped bacteria frequently localize proteins to one or both cellpoles in order to regulate processes such as chromosome replication or polar organ-elle development. However, the roles of polar factors in responses to extracellularstimuli have been gene ...
We consider the problem of making apps fault-tolerant through replication, when apps operate at the microsecond scale, as in finance, embedded computing, and microservices apps. These apps need a replication scheme that also operates at the microsecond sca ...
Binding of mammalian transcription factors (TFs) to regulatory regions is hindered by chromatin compaction and DNA methylation of their binding sites. Nevertheless, pioneer transcription factors (PFs), a distinct class of TFs, have the ability to access nu ...
One of the reasons for the lengthy tuberculosis (TB) treatment is the difficulty to treat the nonmultiplying mycobacterial subpopulation. In order to assess the ability of (new) TB drugs to target this subpopulation, we need to incorporate dormancy models ...
