Timeline

Christophe Zimmer

Head of Structure

10 Apr 2024

publication

Deep learning-based detection of murine congenital heart defects from µCT scans

22 Nov 2023

event

Joint Microbiology and Computational Biology departments seminar: Yves Brun (University of Montreal, Canada) “Antimicrobial discovery by artificial intelligence-assisted high throughput microscopy” ; Wednesday 13 December @10.30am ; Agnes Ullman Amphitheater.

01 Jul 2023

publication

Deep learning in image-based phenotypic drug discovery.

30 Jun 2023

software

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

24 May 2023

event

Symposium – Artificial Intelligence in Biology and Health

11 Apr 2023

publication

Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.

08 Mar 2023

publication

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

21 Oct 2022

publication

ShareLoc – an open platform for sharing localization microscopy data.

25 Aug 2022

event

INCEPTION 2022 meeting: Integrative Biology, Social and Data Sciences to understand the Emergence of Diseases in Populations and in Individuals

23 Jun 2022

event

Conférence-Débat “Cerveaux et Intelligence Artificielle”

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.

25 Feb 2022

publication

Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging.

01 Jan 2022

publication

Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells.

06 Oct 2021

event

2021 Computational Biology Department Days

05 Oct 2021

publication

Listeriolysin S: A bacteriocin from Listeria monocytogenes that induces membrane permeabilization in a contact-dependent manner.

11 Jun 2021

news

An imaging and modeling approach to characterize the structure of DNA in human cells

03 Jun 2021

publication

Single-molecule localization microscopy

11 May 2021

publication

Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures.

04 Jan 2021

publication

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

28 Sep 2020

publication

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

21 Jul 2020

software

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

18 Jun 2020

publication

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder.

17 Jun 2020

project

CORONAFISH

10 May 2020

software

Imjoy – open access platform for deep learning methods

01 Dec 2019

publication

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

05 Mar 2019

publication

How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization

01 Dec 2018

publication

A computational framework to study sub-cellular RNA localization

07 Nov 2018

event

The 26th Pasteur-Weizmann symposium

07 Sep 2018

software

ZOLA-3D Zernike Optimized Localization approach

19 Jun 2018

publication

ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range

08 Jun 2018

publication

Chromatin mobility upon DNA damage: state of the art and remaining questions

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

23 Apr 2018

software

ANNA-PALM

16 Apr 2018

publication

Deep learning massively accelerates super-resolution localization microscopy

01 Jan 2018

publication

From dynamic chromatin architecture to DNA damage repair and back

01 Dec 2017

publication

GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells

15 Sep 2017

publication

Functional organization of cytoplasmic inclusion bodies in cells infected by respiratory syncytial virus.

10 Jul 2017

publication

Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast

01 Jul 2017

publication

Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway

12 Jun 2017

publication

Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme

03 May 2017

publication

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

01 Feb 2017

publication

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform.

28 Oct 2016

program_project

INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations

05 Sep 2016

publication

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

27 Jul 2016

publication

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

01 Jul 2016

project

Deep learning for biology

01 Feb 2016

publication

What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

13 Jan 2016

publication

Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast

05 Jan 2016

publication

Evidence for actin dual role in regulating chromosome organization and dynamics in yeast

11 Sep 2015

software

GRAAL: genome assembly from chromosome contact frequencies

11 Sep 2015

software

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

11 Sep 2015

software

QuickPALM: Reconstruction of PALM/STORM super-resolution microscopy images

11 Sep 2015

software

Nucloc: mapping gene territories in the yeast nucleus

06 Jun 2015

project

Pointillist nanoscopy

06 Jun 2015

project

Nuclear architecture and function

11 May 2015

team

Imaging and Modeling

06 Mar 2015

publication

Chromatin organization at the nuclear pore favours HIV replication.

01 Jan 2015

publication

In silico control of biomolecular processes.

17 Dec 2014

publication

High-quality genome (re)assembly using chromosomal contact data.

02 Dec 2014

team

Biological Image Analysis

01 Dec 2014

publication

A platform for rapid prototyping of synthetic gene networks in mammalian cells.

26 Jun 2014

publication

Transcription factors modulate c-Fos transcriptional bursts

07 Apr 2014

publication

Filling annotation gaps in yeast genomes using genome-wide contact maps.

01 Jan 2014

publication

FlAsH-PALM: super-resolution pointillist imaging with FlAsH-tetracysteine labeling.

01 Jan 2014

publication

Computational models of large-scale genome architecture

07 Oct 2013

publication

Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse

22 Aug 2013

publication

How to build a yeast nucleus

22 Jul 2013

publication

Systematic characterization of the conformation and dynamics of budding yeast chromosome XII

01 Jun 2013

publication

Species-specific impact of the autophagy machinery on Chikungunya virus infection.

05 May 2013

publication

Effect of nuclear architecture on the efficiency of double-strand break repair

01 Apr 2013

publication

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

15 Mar 2013

publication

Composition and abstraction of logical regulatory modules: application to multicellular systems.

01 Jan 2013

publication

STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification.

01 Nov 2012

publication

From microbes to numbers: extracting meaningful quantities from images

31 Oct 2012

publication

Single-molecule localization super-resolution microscopy: deeper and faster

30 Aug 2012

publication

A predictive computational model of the dynamic 3D interphase yeast nucleus

23 Apr 2012

publication

Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion

01 Mar 2011

publication

Principles of chromosomal organization: lessons from yeast

17 Jan 2011

publication

Super-resolution dynamic imaging of dendritic spines using a low-affinity photoconvertible actin probe

01 May 2010

publication

QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ

13 Jan 2010

publication

Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres

02 Nov 2008

publication

High-resolution statistical mapping reveals gene territories in live yeast

17 May 2008

publication

Improving single particle localization with an empirically calibrated Gaussian kernel

01 Jun 2006

publication

SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope

01 Apr 2006

publication

Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution

01 Feb 2006

publication

Human tumor necrosis factor is a chemoattractant for the parasite Entamoeba histolytica

01 Nov 2005

publication

Coupled parametric active contours

01 Sep 2005

publication

Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces

01 Jan 2005

publication

Myosin II and the Gal-GalNAc lectin play a crucial role in tissue invasion by Entamoeba histolytica

01 Jul 2004

publication

Imaging movement of malaria parasites during transmission by Anopheles mosquitoes

01 Jan 2003

publication

EhPAK, a member of the p21-activated kinase family, is involved in the control of Entamoeba histolytica migration and phagocytosis

01 Nov 2002

publication

Membrane-cytoskeleton interactions during the formation of the immunological synapse and subsequent T-cell activation

01 Oct 2002

publication

A little guide for advanced search:

Deep learning-based detection of murine congenital heart defects from µCT scans

Joint Microbiology and Computational Biology departments seminar: Yves Brun (University of Montreal, Canada) “Antimicrobial discovery by artificial intelligence-assisted high throughput microscopy” ; Wednesday 13 December @10.30am ; Agnes Ullman Amphitheater.

Deep learning in image-based phenotypic drug discovery.

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

Symposium – Artificial Intelligence in Biology and Health

Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.

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

ShareLoc – an open platform for sharing localization microscopy data.

INCEPTION 2022 meeting: Integrative Biology, Social and Data Sciences to understand the Emergence of Diseases in Populations and in Individuals

Conférence-Débat “Cerveaux et Intelligence Artificielle”

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

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

Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging.

Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells.

2021 Computational Biology Department Days

Listeriolysin S: A bacteriocin from Listeria monocytogenes that induces membrane permeabilization in a contact-dependent manner.

An imaging and modeling approach to characterize the structure of DNA in human cells

Single-molecule localization microscopy

Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures.

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

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

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder.

CORONAFISH

Imjoy – open access platform for deep learning methods

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

How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization

A computational framework to study sub-cellular RNA localization

The 26th Pasteur-Weizmann symposium

ZOLA-3D Zernike Optimized Localization approach

ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range

Chromatin mobility upon DNA damage: state of the art and remaining questions

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

ANNA-PALM

Deep learning massively accelerates super-resolution localization microscopy

From dynamic chromatin architecture to DNA damage repair and back

GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells

Functional organization of cytoplasmic inclusion bodies in cells infected by respiratory syncytial virus.

Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast

Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway

Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform.

INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations

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

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

Deep learning for biology

What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast

Evidence for actin dual role in regulating chromosome organization and dynamics in yeast

GRAAL: genome assembly from chromosome contact frequencies

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

QuickPALM: Reconstruction of PALM/STORM super-resolution microscopy images

Nucloc: mapping gene territories in the yeast nucleus

Pointillist nanoscopy

Nuclear architecture and function

Imaging and Modeling

Chromatin organization at the nuclear pore favours HIV replication.

In silico control of biomolecular processes.

High-quality genome (re)assembly using chromosomal contact data.

Biological Image Analysis

A platform for rapid prototyping of synthetic gene networks in mammalian cells.

Transcription factors modulate c-Fos transcriptional bursts

Filling annotation gaps in yeast genomes using genome-wide contact maps.

FlAsH-PALM: super-resolution pointillist imaging with FlAsH-tetracysteine labeling.

Computational models of large-scale genome architecture

Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse

How to build a yeast nucleus

Systematic characterization of the conformation and dynamics of budding yeast chromosome XII

Species-specific impact of the autophagy machinery on Chikungunya virus infection.

Effect of nuclear architecture on the efficiency of double-strand break repair

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

Composition and abstraction of logical regulatory modules: application to multicellular systems.

STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification.

From microbes to numbers: extracting meaningful quantities from images

Single-molecule localization super-resolution microscopy: deeper and faster

A predictive computational model of the dynamic 3D interphase yeast nucleus

Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion

Principles of chromosomal organization: lessons from yeast