Timeline

Florian Muller

Group Leader

06 Jul 2024

publication

A point cloud segmentation framework for image-based spatial transcriptomics.

10 Apr 2024

software

Comseg – Cell segmentation for spatial transcriptomics data

13 Feb 2024

publication

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

30 Jun 2023

tool

smiFISH : a cheap and versatile smFISH approach

30 Jun 2023

project

autoFISH : a modular toolbox for sequential FISH experiments

30 Jun 2023

software

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

27 Jun 2023

team

Quantitative RNA imaging

28 Apr 2023

publication

An interactive murine single-cell atlas of the lung responses to radiation injury.

08 Mar 2023

publication

A specific molecular signature in SARS-CoV-2-infected kidney biopsies.

14 Feb 2023

publication

PointFISH: Learning Point Cloud Representations for RNA Localization Patterns

01 Jan 2023

publication

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

24 Oct 2022

publication

HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging.

01 Jun 2022

publication

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

01 Apr 2022

publication

Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH.

24 Jan 2022

publication

piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development.

01 Dec 2021

publication

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions.

01 Aug 2021

publication

Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants.

23 Jul 2021

publication

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting.

08 Apr 2021

publication

Spatial transcriptomics for respiratory research and medicine.

04 Mar 2021

publication

Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos.

01 Mar 2021

publication

A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport.

04 Jan 2021

publication

Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages.

19 Nov 2020

publication

Functional compensation precedes recovery of tissue mass following acute liver injury.

28 Sep 2020

publication

A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting.

15 Jun 2020

publication

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

18 May 2020

publication

Remodeling of the Core Leads HIV-1 Preintegration Complex into the Nucleus of Human Lymphocytes.

01 Dec 2019

publication

ImJoy: an open-source computational platform for the deep learning era

11 Jul 2019

publication

A Deep Learning Approach To Identify MRNA Localization Patterns

15 Apr 2019

publication

Co-translational assembly of mammalian nuclear multisubunit complexes

07 Mar 2019

publication

The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells

01 Dec 2018

publication

A computational framework to study sub-cellular RNA localization

02 Aug 2018

publication

A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges

29 May 2018

publication

Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence

17 Aug 2017

team

Photonic BioImaging (UTechS PBI)

10 Oct 2016

publication

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

05 Sep 2016

publication

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

05 Sep 2016

publication

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

26 Aug 2016

publication

Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin

27 Jul 2016

publication

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

07 Apr 2016

publication

Divergent Binding and Transactivation by Two Related Steroid Receptors at the Same Response Element

11 Sep 2015

software

FISH-quant: automatically counting transcripts in RNA-FISH images

18 Aug 2014

publication

Distinctly different dynamics and kinetics of two steroid receptors at the same response elements in living cells

26 Jun 2014

publication

Transcription factors modulate c-Fos transcriptional bursts

06 Mar 2014

publication

PRC1 components exhibit different binding kinetics in Polycomb bodies

19 Nov 2013

publication

Stable assembly of HIV-1 export complexes occurs cotranscriptionally

11 Sep 2013

publication

Quantifying transcription factor kinetics: at work or at play?

01 Aug 2013

publication

Convergence of chromatin binding estimates in live cells

01 Jul 2013

publication

Defective cerebellar control of cortical plasticity in writer’s cramp

13 Jun 2013

publication

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP

01 Apr 2013

publication

FISH-quant: automatic counting of transcripts in 3D FISH images

09 Dec 2012

publication

Fast multicolor 3D imaging using aberration-corrected multifocus microscopy

11 Apr 2012

publication

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function

03 Apr 2012

publication

Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis

01 Jan 2012

publication

Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching

14 Nov 2010

publication

Three-dimensional cellular ultrastructure resolved by X-ray microscopy

01 Nov 2010

publication

Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates

21 Apr 2010

publication

FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

11 Mar 2010

publication

Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis

02 Sep 2008

publication

Regulation of TATA-binding protein dynamics in living yeast cells

07 Apr 2008

publication

Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression

16 Jan 2008

publication

Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching

05 May 2006

publication

A little guide for advanced search:

A point cloud segmentation framework for image-based spatial transcriptomics.

Comseg – Cell segmentation for spatial transcriptomics data

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

smiFISH : a cheap and versatile smFISH approach

autoFISH : a modular toolbox for sequential FISH experiments

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

Quantitative RNA imaging

An interactive murine single-cell atlas of the lung responses to radiation injury.

A specific molecular signature in SARS-CoV-2-infected kidney biopsies.

PointFISH: Learning Point Cloud Representations for RNA Localization Patterns

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

HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging.

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

Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH.

piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development.

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions.

Live single-cell transcriptional dynamics via RNA labelling during the phosphate response in plants.

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting.

Spatial transcriptomics for respiratory research and medicine.

Germline inherited small RNAs facilitate the clearance of untranslated maternal mRNAs in C. elegans embryos.

A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport.

Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages.

Functional compensation precedes recovery of tissue mass following acute liver injury.

A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting.

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

Remodeling of the Core Leads HIV-1 Preintegration Complex into the Nucleus of Human Lymphocytes.

ImJoy: an open-source computational platform for the deep learning era

A Deep Learning Approach To Identify MRNA Localization Patterns

Co-translational assembly of mammalian nuclear multisubunit complexes

The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells

A computational framework to study sub-cellular RNA localization

A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges

Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence

Photonic BioImaging (UTechS PBI)

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

Divergent Binding and Transactivation by Two Related Steroid Receptors at the Same Response Element

FISH-quant: automatically counting transcripts in RNA-FISH images

Distinctly different dynamics and kinetics of two steroid receptors at the same response elements in living cells

Transcription factors modulate c-Fos transcriptional bursts

PRC1 components exhibit different binding kinetics in Polycomb bodies

Stable assembly of HIV-1 export complexes occurs cotranscriptionally

Quantifying transcription factor kinetics: at work or at play?

Convergence of chromatin binding estimates in live cells

Defective cerebellar control of cortical plasticity in writer’s cramp

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP

FISH-quant: automatic counting of transcripts in 3D FISH images

Fast multicolor 3D imaging using aberration-corrected multifocus microscopy

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function

Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis

Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching

Three-dimensional cellular ultrastructure resolved by X-ray microscopy

Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates

FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis

Regulation of TATA-binding protein dynamics in living yeast cells

Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression

Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching

Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching