Related papers: Epigenetic Tracking: Towards a Project for an Arti…
A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…
A systematic analysis of the cell behavior requires automated approaches for cell segmentation and tracking. While deep learning has been successfully applied for the task of cell segmentation, there are few approaches for simultaneous cell…
A central challenge in modeling neurodegenerative diseases is connecting cellular-level mechanisms to tissue-level pathology, in particular to determine whether pathology is driven primarily by cell-autonomous triggers or by propagation…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Recent advances in deep learning led to novel generative modeling techniques that achieve unprecedented quality in generated samples and performance in learning complex distributions in imaging data. These new models in medical image…
The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in…
We present Bionic Tracking, a novel method for solving biological cell tracking problems with eye tracking in virtual reality using commodity hardware. Using gaze data, and especially smooth pursuit eye movements, we are able to track cells…
In this article, I advance the idea that physics plays a central role in cell differentiation and makes fundamental contributions to morphogenesis, revealing the totipotent nature of the zygote. Totipotency is a persistent mechanical memory…
There is growing consensus among neuroscientists that neural circuits critical for survival are the result of genomic decompression processes. We introduce SynaptoGen, a novel computational framework--member of the Connectome Models…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Neoteny, also spelled Paedomorphosis, can be defined in biological terms as the retention by an organism of juvenile or even larval traits into later life. In some species, all morphological development is retarded; the organism is…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
Epigenetics is most often reduced to chromatin marking in the current literature, whereas this notion was initially defined in a more general context. This restricted view ignores that epigenetic memories are in fact more robustly ensured…
Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid…