Related papers: Precise spatial scaling in the early fly embryo
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
Within developing embryos, tissues flow and reorganize dramatically on timescales as short as minutes. This includes epithelial tissues, which often narrow and elongate in convergent extension movements due to anisotropies in external…
When trained on large-scale object classification datasets, certain artificial neural network models begin to approximate core object recognition behaviors and neural response patterns in the primate brain. While recent machine learning…
We propose an unsupervised deep learning method for atlas based registration to achieve segmentation and spatial alignment of the embryonic brain in a single framework. Our approach consists of two sequential networks with a specifically…
To study how a zygote develops into an embryo with different tissues, large-scale 4D confocal movies of C. elegans embryos have been produced recently by experimental biologists. However, the lack of principled statistical methods for the…
During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of…
Motivation: Spatial pattern formation of the primary anterior-posterior morphogenetic gradient of the transcription factor Bicoid (Bcd) has been studied experimentally and computationally for many years. Bcd specifies positional information…
We use dynamical models that include bulk rotation, velocity dispersion anisotropy and both stars and dark matter to explore the conditions that give rise to the early-type galaxy scaling relations referred to as the Fundamental Plane (FP)…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Most animals possess the ability to actuate a vast diversity of movements, ostensibly constrained only by morphology and physics. In practice, however, a frequent assumption in behavioral science is that most of an animal's activities can…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
We investigate the formation of stripe patterns that appear on the surface of a dry granular system as the container is deformed very slowly. In an experimental study using nearly mono-disperse glass beads, we found that many faults develop…
Mechanical strain and stress play a major role in biological processes such as wound healing or morphogenesis. To assess this role quantitatively, fixed or live images of tissues are acquired at a cellular precision in large fields of…
The collection of wild larvae seed as a source of raw material is a major sub industry of shellfish aquaculture. To predict when, where and in what quantities wild seed will be available, it is necessary to track the appearance and growth…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
We ask the question "when will natural selection on a gene in a spatially structured population cause a detectable trace in the patterns of genetic variation observed in the contemporary population?". We focus on the situation in which…