Publications related to CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Related publications (30)

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Moritz Hofer

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

EPFL2024

Metabolically enhanced CAR T cells efficiently clear solid tumors in mice

Li Tang

Chimeric antigen receptor (CAR) T cells in the solid tumor microenvironment enter a partially dysfunctional state called T cell exhaustion. Interleukin (IL)-10-producing CAR T cells retain their metabolic fitness, resist T cell exhaustion and display unpre ...

Nature Portfolio2024

Ru(II)-Arene Complexes of Curcumin and Bisdesmethoxycurcumin Metabolites

Paul Joseph Dyson, Farzaneh Fadaei Tirani, Mouna Hadiji

Curcuminoids and their complexes continue to attract attention in medicinal chemistry, but little attention has been given to their metabolic derivatives. Here, the first examples of (arene)Ru(II) complexes with curcuminoid metabolites, tetrahydrocurcumin ...

Amer Chemical Soc2024

Characterization of the gut-bone marrow axis through bile acid signaling

Alejandro Alonso Calleja

Communication between the intestine and other organs such as the lungs, brain or bones is mediated by several metabolites, like short-chain fatty acids or bile acids, that relay information about nutritional and microbiota status. Bile acids are endogenous ...

EPFL2024

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Chen Zhang

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

EPFL2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Martin Weigert

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

Bioengineering functional organoid models across scales

Tania Hübscher

The last two decades have seen the development of organoid models for many different tissues and organs. Organoids are three-dimensional organ-mimetics derived from stem or progenitor cells comprising various specialized cell types, resembling the architec ...

EPFL2024

In vivo polydopamine coating of Rhodobacter sphaeroides for enhanced electron transfer

Ardemis Anoush Boghossian, Melania Reggente

Recent advances in coupling light-harvesting microorganisms with electronic components have led to a new generation of biohybrid devices based on microbial photocatalysts. These devices are limited by the poorly conductive interface between phototrophs and ...

2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Nanoindentation hardness and modulus of Al2O3-SiO2-CaO and MnO-SiO2-FeO inclusions in iron

Eva Luisa Vogt, Jonathan Aristya Setyadji, Andreas Mortensen, Léa Deillon, Alejandra Inés Slagter, David Hernandez Escobar

Dataset corresponding to the following manuscript: Slagter, A., Setyadji, J.A., Vogt, E.L. et al. Nanoindentation Hardness and Modulus of Al2O3–SiO2–CaO and MnO–SiO2–FeO Inclusions in Iron. Metall Mater Trans A (2024). https://doi.org/10.1007/s11661-024-0 ...

Zenodo2024

Reducing uncertainties in response predictions of earthquake-damaged masonry buildings using data from image-based inspection

Ian Smith, Katrin Beyer, Bryan German Pantoja Rosero, Mathias Christian Haindl Carvallo

Image information about the state of a building after an earthquake, which can be collected without endangering the post-earthquake reconnaissance activities, can be used to reduce uncertainties in response predictions for future seismic events. This paper ...

Springer2024

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

Pauline Ambre Melenec, Andrea Ablasser, Jonathan Jean-Pierre Ricci, Baptiste Claude André Guey, Chong Liu, Pengbiao Xu, Ying Liu, Lingyun Li

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

Nature Portfolio2024

Single-cell analysis of the interactions between Mycobacterium tuberculosis and macrophages

Ophélie Rutschmann

Mycobacterium Tuberculosis is a highly effective pathogen infecting nearly a third of the world's population. An M. tuberculosis infection starts when droplets containing bacteria enter an individual's lungs. The first host cells to contact the bacteria ar ...

EPFL2024

Exploration and modulation of mechanical cues for enhanced cancer immunotherapy

Armand Kurum

The advent of immunotherapy, such as immune checkpoint blockade (ICB) and adoptive transfer of cytotoxic lymphocytes, has transformed the clinical care of cancer. However, a significant proportion of patients are resistant to immunotherapy or experience re ...

EPFL2024

Distinct ultrastructural phenotypes of glial and neuronal alpha-synuclein inclusions in multiple system atrophy

Henning Paul-Julius Stahlberg, Marta Di Fabrizio, Amanda Jennifer Lewis, Domenic Burger

Multiple System Atrophy is characterized pathologically by the accumulation of alpha-synuclein (aSyn) into glial cytoplasmic inclusions (GCIs). The mechanism underlying the formation of GCIs is not well understood. In this study, correlative light and elec ...

2024

Dataset for '3D printing of customizable transient bioelectronics and sensors'

Danick Briand, Nicolas Francis Fumeaux

This data set contains the data collected during the FNS project Green Piezo (Grant no. 179064) in association with the recent publication entitled “3D printing of customizable transient bioelectronics and sensors”. This work aims to study and demonstrate ...

Zenodo2024

Data set for control of Ge island coalescence for the formation of nanowires on silicon

Anna Fontcuberta i Morral, Alok Rudra, Santhanu Panikar Ramanandan, Joel René Sapera

This document contains all the data and the details of the analysis used in the manuscript titled " Control of Ge island coalescence for the formation of nanowires on silicon." https://doi.org/10.1039/D3NH00573A ...

EPFL Infoscience2024

Data and scripts for the RaFSIP scheme

Athanasios Nenes, Paraskevi Georgakaki

This repository contains microphysics routines, scripts, and processed data from the Weather Research and Forecasting (WRF) model simulations presented in the paper "RaFSIP: Parameterizing ice multiplication in models using a machine learning approach", by ...

Zenodo2024