Related papers: An equilibrium model for ribosome competition
The work is devoted to the analysis of cell population dynamics where cells make a choice between differentiation and apoptosis. This choice is based on the values of intracellular proteins whose concentrations are described by a system of…
Many applications of RCTs involve the presence of multiple treatment administrators -- from field experiments to online advertising -- that compete for the subjects' attention. In the face of competition, estimating a causal effect becomes…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…
How does competition in markets for information affect the creation and division of surplus? We study this question in a search environment in which an agent searches sequentially for a high-quality good and learns about the quality of…
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…
In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
Analysis of multivariate data sets from e.g. microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of…
Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, non-reproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this paper,…
Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
We consider the problem of regulating by means of external control inputs the ratio of two cell populations. Specifically, we assume that these two cellular populations are composed of cells belonging to the same strain which embeds some…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…
A striking limitation of human cognition is our inability to execute some tasks simultaneously. Recent work suggests that such limitations can arise from a fundamental tradeoff in network architectures that is driven by the sharing of…
Winners-take-all situations introduce an incentive for agents to diversify their behavior, since doing so will result in splitting an eventual price with fewer people. At the same time, when the payoff of a process depends on a parameter…
Imbalanced classification problems are extremely common in natural language processing and are solved using a variety of resampling and filtering techniques, which often involve making decisions on how to select training data or decide…
Translation is a crucial step in gene expression. During translation, macromolecules called ribosomes "read" the mRNA strand in a sequential manner and produce a corresponding protein. Translation is known to consume most of the cell's…