Related papers: Two-exponential models of gene expression patterns…
In multicellular organisms, patterns of gene expression are established in response to gradients of signaling molecules. During fly development in early Drosophila embryos, the Bicoid (Bcd) morphogen gradient is established within the first…
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in {\it Drosophila melanogaster} embryos is well documented and studied. There are still…
The predetermination, formation and maintenance of the primary morphogenetic gradient (bicoid gradient) of the early Drosophila embryo involves many interrelated processes. Here we focus on a system-biological analysis of the processes of…
We propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of \textit{Drosophila}. In this model, we consider that \textit{bicoid} mRNA…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…
Diffusion models have become a central tool in deep generative modeling, but standard formulations rely on a single network and a single diffusion schedule to transform a simple prior, typically a standard normal distribution, into the…
Recently, the attention-enhanced multi-layer encoder, such as Transformer, has been extensively studied in Machine Reading Comprehension (MRC). To predict the answer, it is common practice to employ a predictor to draw information only from…
During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to…
We propose a novel approach to denoising diffusion magnetic resonance images (dMRI) using convolutional neural networks, that exploits the benefits of data acquired at multiple b-values to offset the need for many redundant observations.…
During embryonic development, a spatial pattern is formed in which proportions are established precisely. As an early pattern formation step in Drosophila embryos, an anterior-posterior gradient of Bicoid (Bcd) induces hunchback (hb)…
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…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy molecular process, is regulated to…
This article focuses on covariance estimation for multi-study data. Popular approaches employ factor-analytic terms with shared and study-specific loadings that decompose the variance into (i) a shared low-rank component, (ii)…
We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA…
Diffusion models have gained attention for their ability to represent complex distributions and incorporate uncertainty, making them ideal for robust predictions in the presence of noisy or incomplete data. In this study, we develop and…
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…
Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise…
Uncertainty quantification is critical in scientific inverse problems to distinguish identifiable parameters from those that remain ambiguous given available measurements. The Conditional Diffusion Model-based Inverse Problem Solver (CDI)…