Related papers: Towards Application of the RBNK Model
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
Network of packages with regulatory interactions (dependences and conflicts) from Debian GNU/Linux operating system is compiled and used as analogy of a gene regulatory network. Using a trace-back algorithm we assembly networks from the…
Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This…
In several domains such as linguistics, molecular biology or social sciences, holistic effects are hardly well-defined by modeling with single units, but more and more studies tend to understand macro structures with the help of meaningful…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
We developed a simulator to quantify the effect of changes in environmental parameters on plant growth in precision farming. Our approach combines the processing of plant images with deep convolutional neural networks (CNN), growth curve…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
High-throughput pheno-, geno-, and envirotyping allows characterization of plant genotypes and the trials they are evaluated in, producing different types of data. These different data modalities can be integrated into statistical or…
Pollinators play a crucial role for plant reproduction, either in natural ecosystem or in human-modified landscape. Global change drivers,including climate change or land use modifications, can alter the plant-pollinator interactions. To…
Quantum and quantum-inspired machine learning has emerged as a promising and challenging research field due to the increased popularity of quantum computing, especially with near-term devices. Theoretical contributions point toward…
It is tempting to think that machines are less prone to unfairness and prejudice. However, machine learning approaches compute their outputs based on data. While biases can enter at any stage of the development pipeline, models are…
In this paper we present two modifications of traditional $NK$ fitness landscapes, the $\theta NK$ and $HNK$ models, and explore these modifications via accessibility and ruggedness. The $\theta NK$ model introduces a parameter $\theta$ to…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
The idea of a collective intelligence behind the complex natural structures built by organisms suggests that the organization of social networks is selected so as to optimize problem-solving competence at the group-level. Here we study the…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Complex networks are frequently employed to model physical or virtual complex systems. When certain entities exist across multiple systems simultaneously, unveiling their corresponding relationships across the networks becomes crucial. This…