相关论文: Quantifying the Bicoid morphogen gradient in livin…
Gene regulatory networks (GRNs) perform a wide range of biological functions. It is, however, often challenging to reveal their functioning mechanism with the conventional approach focusing on the network topological structure from a…
There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…
Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the…
The body plan of the fruit fly is determined by the expression of just a handful of genes. We show that the spatial patterns of expression for several of these genes scale precisely with the size of the embryo. Concretely, discrete…
Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a…
Organismal phenotypes emerge from a complex set of genotypic interactions. While technological advances in sequencing provide a quantitative description of an organism's genotype, characterization of an organism's physical phenotype lags…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
Biomolecular condensates form on timescales of seconds in cells upon environmental or compositional changes. Condensate formation is thus argued to act as a mechanism for sensing such changes and quickly initiating downstream processes,…
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
Embryonic development involves pattern formation characterized by the emergence of spatially localized domains characterized by distinct cell fates resulting from differential gene expression. The boundaries demarcating these domains are…
In the early stages of development, Drosophila melanogaster embryos possess very fast and well-coordinated cell cycles. In the cell cycle, CDK activity is essentially regulated by binding CDK and CycB to form an active complex and by…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
The rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic…
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…
The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic…
The mesoderm invagination of the Drosophila embryo is known as an archetypal morphogenic process. To explore the roles of the active cellular forces and the regulation of these forces, we developed an integrated vertex model that combines…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
Recent advances in Structure-based Drug Design (SBDD) have leveraged generative models for 3D molecular generation, predominantly evaluating model performance by binding affinity to target proteins. However, practical drug discovery…