Timeline

David Bikard

Head of Structure

22 Oct 2024

publication

Delivery of functional Cas:DNA nucleoprotein complexes into recipient bacteria through a type IV secretion system.

07 Aug 2024

publication

A virally-encoded tRNA neutralizes the PARIS antiviral defence system.

01 Aug 2024

publication

In situ targeted base editing of bacteria in the mouse gut.

24 Jun 2024

event

Seminar Joe Bondy-Denomy “A bacteriophage that evades immune nucleases by pretending to be a eukaryote”

27 May 2024

event

Microbiology dpt seminar: Vincent Libis (Elis lab, Paris, France) : “Scalable discovery of microbial secondary metabolites through synthetic biology” ; Friday 7 June @ 11:30am ; Auditorium François Jacob.

07 May 2024

publication

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.

25 Apr 2024

publication

Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity.

04 Mar 2024

event

Symposium ATC-IA – Artificial Intelligence in Biology and Health – Edition 2024

01 Mar 2024

event

Dpt of Computational Biology & SPAIS joint seminar – ATC-AI : Inferring and Characterizing Cellular and Neural Dynamics with Geometric and Topological Deep Learning

12 Jan 2024

publication

Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems.

01 Nov 2023

publication

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.

01 Jun 2023

publication

Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies.

25 Apr 2023

program_project

Artificial Intelligence at the Institut Pasteur

17 Mar 2023

publication

Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity.

11 May 2022

publication

Phages and their satellites encode hotspots of antiviral systems.

21 Mar 2022

news

Congratulation to David Bikard for being awarded an ERC Consolidator Granthttps://www.imt.fr/wp-content/uploads/2015/02/201501_ERC.jpg

18 Mar 2022

tool

Find our plasmids and strains on Addgene

17 Mar 2022

project

ERC CoG: In situ genetic perturbation of gut bacteria with engineered phage vectors and CRISPR

02 Feb 2022

project

Impact of chromosomal integrons on bacterial life and evolution (Chromintevol)

15 Sep 2021

publication

High‑throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome

23 Jun 2021

event

Seminar Dept Microbiology “Tacking control of Salmonella evolution”, Médéric Diard

12 Jun 2021

publication

Improving sequence-based modeling of protein families using secondary structure quality assessment.

17 May 2021

event

CRISPR 2021 – Virtual meeting

13 Apr 2021

publication

Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane, promoting fitness upon envelope stress.

01 Mar 2021

publication

The impact of genetic diversity on gene essentiality within the Escherichia coli species.

26 Feb 2021

publication

Generating functional protein variants with variational autoencoders.

07 Dec 2020

event

Microbiology DPT Work in Progress “Understanding the sequence determinants of guide RNAs for the activity of dCas9 in bacteria”, Alicia Calvo-Villamañán

01 Jul 2020

publication

Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement

30 Apr 2020

publication

On-target activity predictions enable improved CRISPR-dCas9 screens in bacteria

24 Jan 2020

publication

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

06 Jan 2020

publication

Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects

30 Sep 2019

event

Microbiology seminar: “CRISPR-Cas: acquired immunity in prokaryotes”

01 Aug 2019

publication

Gene silencing with CRISPRi in bacteria and optimization of dCas9 expression levels

26 Jul 2019

tool

crispr.pasteur.fr

13 May 2019

publication

Editing the microbiome the CRISPR way

13 May 2019

publication

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

20 Feb 2019

event

130 Years of Institut Pasteur: Celebrating Science

07 Nov 2018

publication

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

15 May 2018

publication

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

08 Mar 2018

publication

Tuning dCas9’s ability to block transcription enables robust, noiseless knockdown of bacterial genes

12 Dec 2017

publication

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

27 Nov 2017

project

ERC starting grant – CRISPAIR: Study of the interplay between CRISPR interference and DNA repair pathways towards the development of novel CRISPR tools

15 Aug 2017

publication

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

01 Jun 2017

publication

Using CRISPR-Cas systems as antimicrobials

28 Mar 2017

publication

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance.

10 Mar 2017

event

From phage defense to biotechnological tools: CRISPR and more

14 Feb 2017

software

PhageTerm

05 Jan 2017

publication

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response

23 Sep 2016

project

Prophage elements as a significant source of genetic diversity among epidemic C. difficile 027 strains

17 Sep 2016

publication

A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages

08 Apr 2016

publication

Consequences of Cas9 cleavage in the chromosome of Escherichia coli

27 Jul 2015

publication

Adapting to new threats: the generation of memory by CRISPR-Cas immune systems

02 Jul 2015

project

Studying and fighting pathogenic bacteria with the help of CRISPR

11 May 2015

team

Synthetic Biology

11 May 2015

team

Bacterial Genome Plasticity

18 Feb 2015

publication

Cas9 specifies functional viral targets during CRISPR-Cas adaptation

05 Oct 2014

publication

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

31 Aug 2014

publication

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

01 Feb 2014

publication

The integron integrase efficiently prevents the melting effect of Escherichia coli single-stranded DNA-binding protein on folded attC sites.

01 Nov 2013

publication

Control of gene expression by CRISPR-Cas systems

12 Jun 2013

publication

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

29 Jan 2013

publication

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

01 Jan 2013

publication

Shuffling of DNA cassettes in a synthetic integron

16 Aug 2012

publication

CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection

11 Nov 2011

publication

Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages

09 Jun 2010

publication

The synthetic integron: an in vivo genetic shuffling device

01 May 2008

publication

A little guide for advanced search:

Delivery of functional Cas:DNA nucleoprotein complexes into recipient bacteria through a type IV secretion system.

A virally-encoded tRNA neutralizes the PARIS antiviral defence system.

In situ targeted base editing of bacteria in the mouse gut.

Seminar Joe Bondy-Denomy “A bacteriophage that evades immune nucleases by pretending to be a eukaryote”

Microbiology dpt seminar: Vincent Libis (Elis lab, Paris, France) : “Scalable discovery of microbial secondary metabolites through synthetic biology” ; Friday 7 June @ 11:30am ; Auditorium François Jacob.

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans.

Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity.

Symposium ATC-IA – Artificial Intelligence in Biology and Health – Edition 2024

Dpt of Computational Biology & SPAIS joint seminar – ATC-AI : Inferring and Characterizing Cellular and Neural Dynamics with Geometric and Topological Deep Learning

Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems.

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.

Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies.

Artificial Intelligence at the Institut Pasteur

Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity.

Phages and their satellites encode hotspots of antiviral systems.

Congratulation to David Bikard for being awarded an ERC Consolidator Granthttps://www.imt.fr/wp-content/uploads/2015/02/201501_ERC.jpg

Find our plasmids and strains on Addgene

ERC CoG: In situ genetic perturbation of gut bacteria with engineered phage vectors and CRISPR

Impact of chromosomal integrons on bacterial life and evolution (Chromintevol)

High‑throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome

Seminar Dept Microbiology “Tacking control of Salmonella evolution”, Médéric Diard

Improving sequence-based modeling of protein families using secondary structure quality assessment.

CRISPR 2021 – Virtual meeting

Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane, promoting fitness upon envelope stress.

The impact of genetic diversity on gene essentiality within the Escherichia coli species.

Generating functional protein variants with variational autoencoders.

Microbiology DPT Work in Progress “Understanding the sequence determinants of guide RNAs for the activity of dCas9 in bacteria”, Alicia Calvo-Villamañán

Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement

On-target activity predictions enable improved CRISPR-dCas9 screens in bacteria

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects

Microbiology seminar: “CRISPR-Cas: acquired immunity in prokaryotes”

Gene silencing with CRISPRi in bacteria and optimization of dCas9 expression levels

crispr.pasteur.fr

Editing the microbiome the CRISPR way

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

130 Years of Institut Pasteur: Celebrating Science

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

Tuning dCas9’s ability to block transcription enables robust, noiseless knockdown of bacterial genes

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

ERC starting grant – CRISPAIR: Study of the interplay between CRISPR interference and DNA repair pathways towards the development of novel CRISPR tools

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

Using CRISPR-Cas systems as antimicrobials

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance.

From phage defense to biotechnological tools: CRISPR and more

PhageTerm

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response

Prophage elements as a significant source of genetic diversity among epidemic C. difficile 027 strains

A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages

Consequences of Cas9 cleavage in the chromosome of Escherichia coli

Adapting to new threats: the generation of memory by CRISPR-Cas immune systems

Studying and fighting pathogenic bacteria with the help of CRISPR

Synthetic Biology

Bacterial Genome Plasticity

Cas9 specifies functional viral targets during CRISPR-Cas adaptation

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

The integron integrase efficiently prevents the melting effect of Escherichia coli single-stranded DNA-binding protein on folded attC sites.

Control of gene expression by CRISPR-Cas systems

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

Shuffling of DNA cassettes in a synthetic integron

CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection

Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages

The synthetic integron: an in vivo genetic shuffling device

[First French team success during iGEM synthetic biology competition]