Related papers: Biological logics are restricted
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs, which suppress gene expression by selectively binding to the 3-noncoding region of specific message RNAs through base-pairing. Given the diversity and abundance of miRNA targets, miRNAs…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central…
Systems biology studies the structure and behavior of complex gene regulatory networks. One of its aims is to develop a quantitative understanding of the modular components that constitute such networks. The self-regulating gene is a type…
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…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
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…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Biological systems rely on robust internal information processing: Survival depends on highly reproducible dynamics of regulatory processes. Biological information processing elements, however, are intrinsically noisy (genetic switches,…
For 20 years the beautiful structure in the grid cell code has presented an attractive puzzle: what computation do these representations subserve, and why does it manifest so curiously in neurons. The first question quickly attracted an…
A method of discovering how neurons are connected to process information is presented here: Design a simple logic circuit that can perform a single, biologically advantageous function. Engineering concepts can be helpful in choosing the…