Related papers: Small RNAs Establish Delays and Temporal Threshold…
The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Despite growth being fundamental to all aspects of cell biology, we do not yet know its organizing principles in eukaryotic cells. Classic models derived from the bacteria E. coli posit that protein-synthesis rates are set by mass-action…
Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems…
While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that…
Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate…
The mechanisms underlying lifespan evolution in organisms have long been mysterious. However, recent studies have demonstrated that organisms evolutionarily gain noncoding RNAs (ncRNAs) that carry endogenous profound functions in higher…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
Across diverse biological systems -- ranging from neural networks to intracellular signaling and genetic regulatory networks -- the information about changes in the environment is frequently encoded in the full temporal dynamics of the…
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own…
A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in living cells. Previous statistical…
The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeutics through its ability to scale and multiplex. However, the emergence of loads on the key…
Micro RNAs (miRNA) are a type of non-coding RNA, which are involved in gene regulation and can be associated with diseases such as cancer, cardiovascular and neurological diseases. As such, identifying the entire genome of miRNA can be of…
Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…