Related papers: Target search on DNA by interacting molecules: Fir…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational…
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Personalized cancer treatments based on the molecular profile of a patient's tumor are an emerging and exciting class of treatments in oncology. As genomic tumor profiling is becoming more common, targeted treatments to specific molecular…
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of disease subtypes. Analyses of these data are becoming ever more…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…