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Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
In multiprocessor systems, one of the main factors of systems' performance is task scheduling. The well the task be distributed among the processors the well be the performance. Again finding the optimal solution of scheduling the tasks…
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…
We consider a problem of multi-product scheduling in production. Each product can be produced by a family of alternative multi-machine technologies. Multi-machine technologies require more than one machine at the same time. A sequence…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
A number of coordinated behaviors have been proposed for achieving specific tasks for multi-robot systems. However, since most applications require more than one such behavior, one needs to be able to compose together sequences of behaviors…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
A coupled map is suggested to investigate various spatial or temporal designs in biology: Several cells (or tissues) in an organ are considered as connected to each other in terms of some molecular diffusions or electrical potential…
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to…
Systems neuroscience relies on two complementary views of neural data, characterized by single neuron tuning curves and analysis of population activity. These two perspectives combine elegantly in neural latent variable models that…
Neurons can display highly variable dynamics. While such variability presumably supports the wide range of behaviors generated by the organism, their gene expressions are relatively stable in the adult brain. This suggests that neuronal…
Biological foundation models have shown strong performance in single-cell representation learning by applying transformer architectures directly to gene-expression matrices. However, these approaches predominantly operate in static settings…
Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on…
We demonstrate that the information contained in the spike occurrence times of a population of neurons can be broken up into a series of terms, each of which reflect something about potential coding mechanisms. This is possible in the…
In kernel methods, temporal information on the data is commonly included by using time-delayed embeddings as inputs. Recently, an alternative formulation was proposed by defining a gamma-filter explicitly in a reproducing kernel Hilbert…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
A classical approach to design controllers for interconnected systems is to assume that the different subsystems operate at different time scales, then design simpler controllers within each time scale, and finally certify stability of the…
We investigate the potential of bio-inspired evolutionary algorithms for designing quantum circuits with specific goals, focusing on two particular tasks. The first one is motivated by the ideas of Artificial Life that are used to reproduce…