Timeline

Thomas Cokelaer

Research Engineer

27 Mar 2024

publication

Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump.

20 Dec 2023

publication

Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis.

30 Jun 2023

publication

Reprohackathons: promoting reproducibility in bioinformatics through training.

05 Apr 2023

publication

SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

23 Mar 2023

publication

Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity.

11 Nov 2022

publication

Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis

28 Jun 2022

publication

SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination.

01 Mar 2022

publication

Experimental evolution links post-transcriptional regulation to Leishmania fitness gain.

26 Jan 2022

publication

Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry.

03 Jan 2022

publication

JC Polyomavirus whole genome sequencing at the single molecule level reveals emerging neurotropic populations in Progressive Multifocal Leucoencephalopathy

13 Dec 2021

publication

Investigating the role of the carbon storage regulator A (CsrA) Leptospira spp.

24 Aug 2021

course

Analyse de données reproductible

09 Aug 2021

publication

Attenuation of clinical and immunological outcomes during SARS-CoV-2 infection by ivermectin.

29 Jul 2021

news

Ivermectin alleviates COVID-19 symptoms in an animal model

01 Jul 2021

publication

Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad.

18 Jun 2021

news

COVID-19: discovery of the mechanisms of short- and long-term anosmia

02 Jun 2021

publication

COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters.

05 Jan 2021

publication

Broad spectrum compounds targeting early stages of RABV infection

31 Jul 2020

project

Oncobiomics – THE (heterogenity tumor ecosystem)

11 Feb 2020

tool

sequana_coverage standalone application

19 Aug 2019

publication

Compatibility of 5-ethynyl-2’F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers

02 Aug 2019

team

Biomics – Dry-Lab

24 Jun 2019

event

Core4Life Paris 2019 (joint Curie-Pasteur)

24 Oct 2018

publication

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.

27 Sep 2018

tool

Bioconda

06 Sep 2018

publication

Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models

20 Aug 2018

publication

High Acquisition Rate of ESBL-Producing Enterobacteriaceae among French Military Personnel on Mission Abroad, without Evidence of Inter-Individual Transmission.

19 Jul 2018

course

Scientific Programming in Python

19 Jul 2018

project

Bioconvert

02 Jul 2018

publication

Bioconda: sustainable and comprehensive software distribution for the life sciences

26 Jun 2018

software

Sequanix: a dynamic graphical interface for Snakemake workflows

19 Jan 2018

publication

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

24 Nov 2017

publication

GDSCTools for Mining Pharmacogenomic Interactions in Cancer.

27 Oct 2017

software

Spectral Analysis in Python

31 Mar 2017

publication

Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models

22 Nov 2016

software

Sequana: a set of flexible NGS pipelines

12 Aug 2016

publication

Efficient randomization of biological networks while preserving functional characterization of individual nodes

06 Jul 2016

publication

A Landscape of Pharmacogenomic Interactions in Cancer

24 Jun 2016

software

BioServices: a common Python package to access biological Web Services programmatically

23 Jun 2016

software

DREAMTools

23 Jun 2016

software

GDSCTools: drug discovery

22 Feb 2016

publication

Inferring causal molecular networks: empirical assessment through a community-based effort

09 Oct 2015

publication

DREAMTools: a Python package for scoring collaborative challenges

26 Jun 2015

team

Bioinformatics and Biostatistics HUB

18 Mar 2015

team

Biomics

25 Jan 2015

publication

Cooperative development of logical modelling standards and tools with CoLoMoTo

09 Dec 2014

publication

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

01 Jun 2014

publication

A community effort to assess and improve drug sensitivity prediction algorithms

10 May 2014

publication

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

07 Feb 2014

publication

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

10 Dec 2013

publication

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

23 Sep 2013

publication

BioServices: a common Python package to access biological Web Services programmatically

12 Jul 2013

publication

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

27 Jan 2013

publication

Evaluation of methods for modeling transcription factor sequence specificity

18 Oct 2012

publication

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

30 May 2012

publication

L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language

20 Aug 2009

publication

An upper limit on the stochastic gravitational-wave background of cosmological origin

20 Mar 2009

publication

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

21 Nov 2008

publication

Search for gravitational-wave bursts from soft gamma repeaters

22 Nov 2005

publication

Upper limits on a stochastic background of gravitational waves

12 May 2005

publication

A little guide for advanced search:

Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump.

Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis.

Reprohackathons: promoting reproducibility in bioinformatics through training.

SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity.

Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis

SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination.

Experimental evolution links post-transcriptional regulation to Leishmania fitness gain.

Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry.

JC Polyomavirus whole genome sequencing at the single molecule level reveals emerging neurotropic populations in Progressive Multifocal Leucoencephalopathy

Investigating the role of the carbon storage regulator A (CsrA) Leptospira spp.

Analyse de données reproductible

Attenuation of clinical and immunological outcomes during SARS-CoV-2 infection by ivermectin.

Ivermectin alleviates COVID-19 symptoms in an animal model

Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad.

COVID-19: discovery of the mechanisms of short- and long-term anosmia

COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters.

Broad spectrum compounds targeting early stages of RABV infection

Oncobiomics – THE (heterogenity tumor ecosystem)

sequana_coverage standalone application

Compatibility of 5-ethynyl-2’F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers

Biomics – Dry-Lab

Core4Life Paris 2019 (joint Curie-Pasteur)

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection.

Bioconda

Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models

High Acquisition Rate of ESBL-Producing Enterobacteriaceae among French Military Personnel on Mission Abroad, without Evidence of Inter-Individual Transmission.

Scientific Programming in Python

Bioconvert

Bioconda: sustainable and comprehensive software distribution for the life sciences

Sequanix: a dynamic graphical interface for Snakemake workflows

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

GDSCTools for Mining Pharmacogenomic Interactions in Cancer.

Spectral Analysis in Python

Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models

Sequana: a set of flexible NGS pipelines

Efficient randomization of biological networks while preserving functional characterization of individual nodes

A Landscape of Pharmacogenomic Interactions in Cancer

BioServices: a common Python package to access biological Web Services programmatically

DREAMTools

GDSCTools: drug discovery

Inferring causal molecular networks: empirical assessment through a community-based effort

DREAMTools: a Python package for scoring collaborative challenges

Bioinformatics and Biostatistics HUB

Biomics

Cooperative development of logical modelling standards and tools with CoLoMoTo

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

A community effort to assess and improve drug sensitivity prediction algorithms

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

BioServices: a common Python package to access biological Web Services programmatically

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Evaluation of methods for modeling transcription factor sequence specificity

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language

An upper limit on the stochastic gravitational-wave background of cosmological origin

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

Search for gravitational-wave bursts from soft gamma repeaters

Upper limits on a stochastic background of gravitational waves

Limits on gravitational-wave emission from selected pulsars using LIGO data