Related papers: Bayesian detection of embryonic gene expression on…
Cancer progression is an evolutionary process that is driven by mutation and selection in a population of tumor cells. We discuss mathematical models of cancer progression, starting from traditional multistage theory. Each stage is…
The developmental process of embryos follows a monotonic order. An embryo can progressively cleave from one cell to multiple cells and finally transform to morula and blastocyst. For time-lapse videos of embryos, most existing developmental…
During embryonic development, differentiating cells respond via gene expression to positional cues from morphogen gradients. While gene expression is often highly erratic, embryonic development is precise. We show by theory and simulations…
Live-cell microscopy allows to go beyond measuring average features of cellular populations to observe, quantify and explain biological heterogeneity. Deep Learning-based instance segmentation and cell tracking form the gold standard…
3D microscopy is key in the investigation of diverse biological systems, and the ever increasing availability of large datasets demands automatic cell identification methods that not only are accurate, but also can imply the uncertainty in…
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…
Motivated by examples from genetic association studies, this paper considers the model selection problem in a general complex linear model system and in a Bayesian framework. We discuss formulating model selection problems and incorporating…
Computational models provide crucial insights into complex biological processes such as cancer evolution, but their mechanistic nature often makes them nonlinear and parameter-rich, complicating calibration. We systematically evaluate…
Diffusion models have recently driven significant breakthroughs in generative modeling. While state-of-the-art models produce high-quality samples on average, individual samples can still be low quality. Detecting such samples without human…
In genomic applications, there is often interest in identifying genes whose time-course expression trajectories exhibit periodic oscillations with a period of approximately 24 hours. Such genes are usually referred to as circadian, and…
Automatic analyses and comparisons of different stages of embryonic development largely depend on a highly accurate spatiotemporal alignment of the investigated data sets. In this contribution, we assess multiple approaches for automatic…
In this paper, we present a novel approach to accelerate the Bayesian inference process, focusing specifically on the nested sampling algorithms. Bayesian inference plays a crucial role in cosmological parameter estimation, providing a…
Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements -…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
We consider the situation where a temporal process is composed of contiguous segments with differing slopes and replicated noise-corrupted time series measurements are observed. The unknown mean of the data generating process is modelled as…
Bulk tissue RNA sequencing of heterogeneous samples provides averaged gene expression profiles, obscuring cell type-specific dynamics. To address this, we present a probabilistic hierarchical Bayesian model that deconvolves bulk RNA-seq…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
Infertility is a major global health issue, and while in-vitro fertilization has improved treatment outcomes, embryo selection remains a critical bottleneck. Time-lapse imaging enables continuous, non-invasive monitoring of embryo…
Cell division timing is critical for cell fate specification and morphogenesis during embryogenesis. How division timings are regulated among cells during development is poorly understood. Here we focus on the comparison of asynchrony of…
Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point…