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Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
The process controlling the diferentiation of stem, or progenitor, cells into one specific functional direction is called lineage specification. An important characteristic of this process is the multi-lineage priming, which requires the…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits: sets…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
We propose a novel dynamic image reconstruction method from PET listmode data that could be particularly suited to tracking single or small numbers of cells. In contrast to conventional PET reconstruction our method combines the information…
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…
Gradual transformation of the epidermal stem cells to corneocytes involves a chain of chronologically well-arranged events that mostly stimulated locally by their neighbors. Cell diversity that observed during the differentiation through…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
The task of learning patterns is typically associated with systems that update parameters on fixed architectures, such as neural networks, where learning proceeds through continuous optimization. Here, we demonstrate that pattern learning…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
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…
A recent technology breakthrough in spatial molecular profiling has enabled the comprehensive molecular characterizations of single cells while preserving spatial information. It provides new opportunities to delineate how cells from…
The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…