Related papers: Analog computation with transcriptional networks
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Analog quantum computation is an attractive paradigm for the simulation of time-dependent quantum systems. Programmable analog quantum computers have been realized in hardware using a variety of physical principles, including neutral-atom…
Most chemical processes, such as distillation, absorption, extraction, and catalytic reactions, are extremely complex processes that are affected by multiple factors. The relationships between their input variables and output variables are…
Biological neural networks are often modeled as systems of coupled, nonlinear, ordinary or partial differential equations. The number of differential equations used to model a network increases with the size of the network and the level of…
Tracers provide users with useful information about program executions. In this article, we propose a ``tracer driver''. From a single tracer, it provides a powerful front-end enabling multiple dynamic analysis tools to be easily…
Relative to digital computation, analog computation has been neglected in the philosophical literature. To the extent that attention has been paid to analog computation, it has been misunderstood. The received view -- that analog…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
Predictive coding (PC) networks are a biologically interesting class of neural networks. Their layered hierarchy mimics the reciprocal connectivity pattern observed in the mammalian cortex, and they can be trained using local learning rules…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
We study social networks and focus on covert (also known as hidden) networks, such as terrorist or criminal networks. Their structures, memberships and activities are illegal. Thus, data about covert networks is often incomplete and…
At present, technological subsystems are usually hard-coded to produce a consumer product with a certain performance, and efficiency, which is defined either by the factory settings, or determined by the technologist's view on the mode,…
The energy efficiency of analog forms of computing makes it one of the most promising candidates to deploy resource-hungry machine learning tasks on resource-constrained system such as mobile or embedded devices. However, it is well known…
Analogical reasoning has been a principal focus of various waves of AI research. Analogy is particularly challenging for machines because it requires relational structures to be represented such that they can be flexibly applied across…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
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…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…