Related papers: Quantifying the Bicoid morphogen gradient in livin…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
Proper vertebrae formation relies on a tissue-wide oscillator called the segmentation clock. Individual cellular oscillators in the presomitic mesoderm are modulated by intercellular coupling and external signals, leading to the propagation…
Biological cells estimate concentration gradients of signaling molecules with a precision that is limited not only by sensing noise, but additionally by the cell's own stochastic motion. We ask for the theoretical limits of gradient…
A hallmark of biological tissues, viewed as complex cellular materials, is the active generation of mechanical stresses by cellular processes, such as cell divisions. Each cellular event generates a force dipole that deforms the surrounding…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
In this paper, we investigate a practical yet challenging task: On-the-fly Category Discovery (OCD). This task focuses on the online identification of newly arriving stream data that may belong to both known and unknown categories,…
Establishing sharp and correctly positioned boundaries in spatial gene expression patterns is a central task, both in developmental and synthetic biology. We consider situations where a global morphogen gradient provides positional…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
In the French flag problem, initially uncolored cells on a grid must differentiate to become blue, white or red. The goal is for the cells to color the grid as a French flag, i.e., a three-colored triband, in a distributed manner. To solve…
We derive a controlled generation objective within the framework of Variational Flow Matching (VFM), which casts flow matching as a variational inference problem. We demonstrate that controlled generation can be implemented two ways: (1) by…
Classifier-Free Guidance (CFG) is widely used to improve conditional fidelity in diffusion models, but its impact on sampling dynamics remains poorly understood. Prior studies, often restricted to unimodal conditional distributions or…
The cell nucleus is enveloped by a complex membrane, whose wrinkling has been implicated in disease and cellular aging. The biophysical dynamics and spectral evolution of nuclear wrinkling during multicellular development remain poorly…
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct…
Transcription factor concentrations provide signals to cells that allow them to regulate gene expression to make correct cell fate decisions. Calculations for noise bounds in gene regulation suggest that clustering or cooperative binding of…
Genes are often regulated in living cells by proteins called transcription factors (TFs) that bind directly to short segments of DNA in close proximity to specific genes. These binding sites have a conserved nucleotide appearance, which is…
We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric…
Here we present the first method for tracking each leg of a fruit fly behaving spontaneously upon a trackball, in real time. Legs were tracked with infrared-fluorescent dye invisible to the fly, and compatible with two-photon microscopy and…
Single-particle cryo-electron microscopy (cryo-EM) has become a cornerstone of structural biology, enabling near-atomic resolution analysis of macromolecules through advanced computational methods. However, the development of cryo-EM…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…