Jean Ollion

Jean Ollion
Sorbonne Université | UPMC · Laboratoire Jean Perrin - FRE 3231

About

16
Publications
2,202
Reads
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697
Citations
Citations since 2016
8 Research Items
647 Citations
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2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
Introduction
I am now working as an independent researcher, providing data analysis expertise to scientists. My knowledge and experience in biology facilitate a deep understanding of the scientific problematic and technical stakes behind the data. I also maintain a research activity, and recently developed an original bio-image processing method involving deep learning.
Additional affiliations
June 2019 - present
SABILab
Position
  • entrepreneur
Description
  • I am now working as an independent researcher, providing data analysis expertise to scientists. My knowledge and experience in biology facilitate a deep understanding of the scientific problematic and technical stakes behind the data.
June 2015 - May 2019
Sorbonne Université
Position
  • PostDoc Position
Description
  • Real-time single cell study of mutation dynamics in E. Coli bacteria, using the mother machine. I did both experimental work as well as image processing, and developed BACMMAN a software for high-throughput processing of mother machine data.
Education
September 2010 - February 2014
Muséum National d'Histoire Naturelle / Sorbonne Université
Field of study
  • Cellular biology
September 2009 - June 2010
Sorbonne Université
Field of study
  • Cellular and molecular biology
September 2006 - June 2010
École Polytechnique
Field of study
  • Informatics / Mathematics / Physics / Specialization in Biology

Publications

Publications (16)
Article
Mutation rates and effects in single cells Understanding the dynamics of mutations and the distribution of fitness effects is critical for most evolutionary models. Robert et al. used a single-cell technology to visualize the accumulation of new mutations. The method identifies DNA sequences with mispaired bases and small insertions or deletions ca...
Article
Full-text available
The cell nucleus is a highly organized structure, playing an important role in gene regulation. Understanding the mechanisms that sustain this organization is therefore essential for understanding genome function. Centromeric regions (CR) of chromosomes have been known for years to adopt specific nuclear positioning patterns, but the significance o...
Article
Full-text available
Motivation: The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limite...
Preprint
Full-text available
We propose a novel self-supervised image blind denoising approach in which two neural networks jointly predict the clean signal and infer the noise distribution. Assuming that the noisy observations are independent conditionally to the signal, the networks can be jointly trained without clean training data. Therefore, our approach is particularly r...
Chapter
The mother machine is a popular microfluidic device that allows long-term time-lapse imaging of thousands of cells in parallel by microscopy. It has become a valuable tool for single-cell level quantitative analysis and characterization of many cellular processes such as gene expression and regulation, mutagenesis or response to antibiotics. The au...
Preprint
Full-text available
The mother machine is a popular microfluidic device that allows long-term time-lapse imaging of thousands of cells in parallel by microscopy. It has become a valuable tool for single-cell level quantitative analysis and characterization of many cellular processes such as gene expression and regulation, mutagenesis or response to antibiotics. The au...
Article
Mutations are the driving force of evolution and the source of important pathologies. The characterization of the dynamics and effects of mutations on fitness is therefore central to our understanding of evolution and to human health. This protocol describes how to implement two methods that we recently developed: mutation visualization (MV) and mi...
Article
The analysis of bacteria at the single-cell level is essential to characterization of processes in which cellular heterogeneity plays an important role. BACMMAN (bacteria mother machine analysis) is a software allowing fast and reliable automated image analysis of high-throughput 2D or 3D time-series images from experiments using the 'mother machin...
Article
The cell nucleus is a highly organized cellular organelle that contains the genome. An important step to understand the relationships between genome positioning and genome functions is to extract quantitative data from three-dimensional (3D) fluorescence imaging. However, such approaches are limited by the requirement for processing and analyzing l...
Article
Full-text available
The cell nucleus is a highly organized structure, playing an important role in gene regulation. Understanding the underlying mechanisms is therefore essential for understanding genome function. Numerous studies conducted in mouse cells have shown that centromeric regions (RC) of chromosomes play a role in nuclear organization. The spatial organizat...
Thesis
Full-text available
The cell nucleus is a highly organized structure, playing an important role in gene regulation. Understanding the underlying mechanisms is therefore essential for understanding genome function. Numerous studies conducted in mouse cells have shown that centromeric regions (RC) of chromosomes play a role in nuclear organization. The spatial organizat...
Conference Paper
Full-text available
The study of nuclear architecture has become a very important field of cellular biology. When studied with an imaging approach, a limiting step is the automatic processing and quantification of the images. Here we present TANGO (Tools for Analysis of Nuclear Genome Organization), an ImageJ plug-in for high-throughput quantitative analysis of 3D flu...

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