Florian Mueller

Engineered dual-gastruloid model for foregut-pharyngeal mesoderm co-development

This paper introduces a dual-gastruloid model to study the co-development of foregut-pharyngeal mesoderm in mice, showing the role of Foxa2 in Tbx1 expression.

MYC and MAX drive the reactivation of the genome after mitosis

This study identifies MYC and MAX as critical for post-mitotic genome reactivation in pluripotent mouse embryonic stem cells, showing MAX's role in bookmarking and MYC recruitment.

RNA2seg: a generalist model for cell segmentation in image-based spatial transcriptomics

RNA2seg is a cell segmentation model for spatial transcriptomics trained on MERFISH and CosMx data, showing superior performance in zero-shot and few-shot settings.

A Deep Learning approach for time-consistent cell cycle phase prediction from microscopy data

The paper predicts cell cycle phases from microscopy data using a variational auto-encoder with auxiliary tasks, and provides a new annotated dataset.

autoFISH - a modular toolbox for sequential smFISH experiments

autoFISH provides a modular toolbox for automated smFISH experiments, including equipment plans, software, protocols, and analysis workflows validated on cell lines and tissues.

A point cloud segmentation framework for image-based spatial transcriptomics

This paper introduces ComSeg, a segmentation algorithm for image-based spatial transcriptomics that outperforms existing methods in cell type calling and handles complex tissue structures.

A DIY guide for image-based spatial transcriptomic: TLS as a case example

The paper provides a DIY guide for image-based spatial transcriptomics using TLS as an example, covering experimental design, wet lab methods, and analysis.

U-FISH: a universal deep learning approach for accurate FISH spot detection across diverse datasets

U-FISH improves FISH spot detection accuracy and generalization using a deep learning approach with a U-Net model and a large annotated dataset.

pyHiM, a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging

pyHiM provides a modular, open-source software package for analyzing spatial genomics data from multiplexed DNA-FISH imaging, enabling chromatin trace reconstruction and data validation.

Mitotic bookmarking redundancy by nuclear receptors mediates robust post-mitotic reactivation of the pluripotency network.

The paper shows that redundancy among nuclear receptor bookmarking factors ensures robust reactivation of pluripotency genes after mitosis.

Excessive self-grooming, gene dysregulation and imbalance between the striosome and matrix compartments in the striatum of Shank3 mutant mice

This study identifies gene dysregulation and striosome-matrix imbalance in Shank3 mutant mice, linking these changes to behavioral abnormalities associated with autism.

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting

The paper uses single molecule imaging to study HIV-1 promoter pausing and finds that stochastic pausing leads to transcriptional bursting in latent cells.

FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis

FISH-quant v2 is a modular tool for analyzing smFISH images, enabling detection, segmentation, quantification, and visualization of RNA localization at the single-cell level.

Germline inherited small RNAs clear untranslated maternal mRNAs in C. elegans embryos

This study shows that C. elegans embryos use inherited small RNAs to cleave and remove maternal mRNAs through the catalytic activity of Argonaute CSR-1.

mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage

The paper shows that mRNA localization to P granules in C. elegans embryos is linked to translational repression, not just a downstream effect.

Co-translation drives the assembly of mammalian nuclear multisubunit complexes

The paper shows that mammalian nuclear transcription complexes assemble co-translationally, with dimerization domains dictating the assembly pathway.

The molecular logic of Nanog-induced self-renewal

This study shows how Nanog uses different mechanisms to enhance embryonic stem cell self-renewal by rewiring pluripotency networks and blocking differentiation through histone modification.