Related papers: Transcription and noise in negative feedback loops
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task, examples include ecosystems, financial markets, complex diseases, etc. In this paper, we…
We introduce a neural auto-encoder that transforms the musical dynamic in recordings of singing voice via changes in voice level. Since most recordings of singing voice are not annotated with voice level we propose a means to estimate the…
In supervised classification tasks, models are trained to predict a label for each data point. In real-world datasets, these labels are often noisy due to annotation errors. While the impact of label noise on the performance of deep…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Inhibition is considered to shape neural activity, and broaden its pattern repertoire. In the sensory organs, where the anatomy of neural circuits is highly structured, lateral inhibition sharpens contrast among stimulus properties. The…
The transduction process that occurs in the inner ear of the auditory system is a complex mechanism which requires a non-linear dynamical description. In addition to this, the stochastic phenomena that naturally arise in the inner ear…
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct…
Gene transcription is a stochastic process that involves thousands of reactions. The first set of these reactions, which happen near a gene promoter, are considered to be the most important in the context of stochastic noise. The most…
Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…
We present studies of quantum interference in a noise power spectrum in the system of two quantum dots (2QD) in a T-geometry. Performing the spectral decomposition we are able to separate local currents and distinguish between the intra-…
A central challenge in computational modeling of dynamic biological systems is parameter inference from experimental time course measurements. However, one would not only like to infer kinetic parameters but also study their variability…
Vibrational resonance focuses on the resonance behavior of a nonlinear system when it is subjected to both a weak low-frequency characteristic signal and a high-frequency auxiliary signal. A traditional Duffing system has a fixed natural…
Fractional killing in response to drugs is a hallmark of non-genetic cellular heterogeneity. Yet how individual lineages evade drug treatment, as observed in bacteria and cancer cells, is not quantitatively understood. We analyse a…
The effect of electron-phonon coupling on the current noise in a molecular junction is investigated within a simple model. The model comprises a 1-level bridge representing a molecular level that connects between two free electron…
Neurons in the nervous system are submitted to distinct sources of noise, such as ionic-channel and synaptic noise, which introduces variability in their responses to repeated presentations of identical stimuli. This motivates the use of…
Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more…