Related papers: Signal Manifestation Trade-offs in Incoherent Feed…
An incoherent feed-forward loop (IFFL) is a network motif known for its ability to accelerate responses and generate pulses. Though functions of IFFLs are well studied, most previous computational analysis of IFFLs used ordinary…
This note analyzes incoherent feedforward loops in signal processing and control. It studies the response properties of IFFL's to exponentially growing inputs, both for a standard version of the IFFL and for a variation in which the output…
Feed-forward dynamics, which is well-known to have several important implications in nonlinear dynamical systems, frequently occurs in gene expression motifs, and has been well explored experimentally and mathematically. However, dependency…
We present a theoretical formalism to study steady state information transmission in type 1 coherent feed-forward loop motif with an additive signal integration mechanism. Our construct allows a two-step cascade to be slowly transformed…
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we…
Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The…
In complex systems, the interplay between network structure and noise often leads to emergent phenomena. This study explores the effects of uneven coupling and asymmetric noise on the dynamics of feed-forward loop (FFL) motifs, essential…
The Forward-Forward Learning (FFL) algorithm is a recently proposed solution for training neural networks without needing memory-intensive backpropagation. During training, labels accompany input data, classifying them as positive or…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
Feedback is ubiquitous in both biological and engineered control systems. In biology, in addition to typical feedback between plant and controller, we observe feedback pathways within control systems, which we call internal feedback…
Networks are abundant in biological systems. Small sized over-represented network motifs have been discovered, and it has been suggested that these constitute functional building blocks. We ask whether larger dynamical network motifs exist…
Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large…
We study the monotonicity of the cumulative dose response (cDR) for a class of incoherent feedforward motifs (IFFM) systems with linear intermediate dynamics and nonlinear output dynamics. While the instantaneous dose response (DR) may be…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
Neural architectures in organisms support efficient and robust control that is beyond the capability of engineered architectures. Unraveling the function of such architectures is challenging; their components are highly diverse and…
In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops…
Fast feedforward networks (FFFs) are a class of neural networks that exploit the observation that different regions of the input space activate distinct subsets of neurons in wide networks. FFFs partition the input space into separate…
Feed-forward neural networks consist of a sequence of layers, in which each layer performs some processing on the information from the previous layer. A downside to this approach is that each layer (or module, as multiple modules can…
The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical…