Related papers: Designing sequential transcription logic: a simple…
Epigenetic cell memory, the inheritance of gene expression patterns across subsequent cell divisions, is a critical property of multi-cellular organisms. In recent work [10], a subset of the authors observed in a simulation study how the…
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a…
Selective attention allows to process stimuli which are behaviorally relevant, while attenuating distracting information. However, it is an open question what mechanisms implement selective routing, and how they are engaged in dependence on…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
Training data is always finite, making it unclear how to generalise to unseen situations. But, animals do generalise, wielding Occam's razor to select a parsimonious explanation of their observations. How they do this is called their…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
We report the experimental verification of noise-enhanced logic behaviour in an electronic analog of a synthetic genetic network, composed of two repressors and two constitutive promoters. We observe good agreement between circuit…
Processing sequential inputs is a fundamental brain function, underlying tasks such as sensory perception, language, and motor control. A challenge in sequence processing is to represent not only the order of events, but also their precise…
Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Neural networks often struggle with catastrophic forgetting when learning sequences of tasks or data streams, unlike humans who can continuously learn and consolidate new concepts even in the absence of explicit cues. Online…
Temporal gates play a significant role in modern recurrent-based neural encoders, enabling fine-grained control over recursive compositional operations over time. In recurrent models such as the long short-term memory (LSTM), temporal gates…
Little is known theoretically about the associative memory capabilities of neural networks in which information is encoded not only in the mean firing rate but also in the timing of firings. Particularly, in the case that the fraction of…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
Recent studies have reported that T cells can integrate signals between interrupted encounters with Antigen Presenting Cells (APCs) in such a way that the process of signal integration exhibits a form of memory. Here, we carry out a…
Our goal is to $\textit{efficiently}$ discover a compact set of temporal logic rules to explain irregular events of interest. We introduce a neural-symbolic rule induction framework within the temporal point process model. The negative…
For practical construction of complex synthetic genetic networks able to perform elaborate functions it is important to have a pool of relatively simple "bio-bricks" with different functionality which can be compounded together. To…
Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide…
How intracellular and extracellular signals are integrated by transcription factors is essential for understanding complex cellular patterns at the population level. In this Letter, by using a synthetic genetic oscillator coupled to a…