Estelle Chaix

Estelle Chaix
Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail | ANSES · Department of Risk Assessment

PhD
Scientific Coordinator - Food risk assessment

About

30
Publications
4,030
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
412
Citations
Introduction
Estelle Chaix currently works at the French Agency for Food, Environmental and Occupational Health & Safety. Estelle does research in Microbiology, Food Science, Text-Mining and Ontologies.
Additional affiliations
March 2019 - present
Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail
Position
  • Expertise coordinator
January 2015 - February 2019
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • PostDoc Position
Description
  • Manual and automatic annotation of Molecular Biology papers (specifically on seed development in Arabidopsis thaliana and biodiversity and microbial phenotype), guided by a knowledge model and ontologies.
September 2011 - August 2014
Université de Montpellier
Position
  • PhD Student
Description
  • Characterization and modeling of gas transfer (O2 / CO2) in the system packaging / food related microbial growth reactions (predictive microbiology)

Publications

Publications (30)
Article
A mechanistic model coupling O2 and CO2 mass transfer (namely diffusion and solubilisation in the food itself and permeation through the packaging material) to microbial growth models was developed aiming at predicting the shelf life of modified atmosphere packaging (MAP) systems. It was experimentally validated on a non-respiring food by investiga...
Conference Paper
Full-text available
This paper presents the SeeDev Task of the BioNLP Shared Task 2016. The purpose of the SeeDev Task is the extraction from scientific articles of the descriptions of genetic and molecular mechanisms involved in seed development of the model plant, Arabidopsis thaliana. The SeeDev task consists in the extraction of many different event types that inv...
Conference Paper
Full-text available
This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (biotopes and geographical places) of bacteria from PubMed abstracts and the characterization of bacteria and their associated habitats with respect to reference knowled...
Article
Full-text available
Information on food microbial diversity is scattered across millions of scientific papers. Researchers need tools to assist their bibliographic search in such large collections. Text mining and knowledge engineering methods are useful to automatically and efficiently find relevant information in Life Science. This work describes how the Alvis text...
Preprint
Full-text available
Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-valu...
Preprint
The dramatic increase in the amount of microbe descriptions in databases, reports and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis. Recent text mining methods offer powerful ways to...
Article
Full-text available
Brevetoxins (BTXs) are marine biotoxins responsible for neurotoxic shellfish poisoning (NSP) after ingestion of contaminated shellfish. NSP is characterized by neurological, gastrointesti-nal and/or cardiovascular symptoms. The main known producer of BTXs is the dinoflagellate Kare-nia brevis, but other microalgae are also suspected to synthesize B...
Technical Report
En France, de nombreuses toxines non réglementées sont suivies dans le cadre du réseau de veille d’émergence des biotoxines marines dans les coquillages (EMERGTOX) dont le comité de pilotage est présidé par la DGAL et inclut la DGS, la Direction des pêches maritimes et de l'aquaculture (DPMA), Santé publique France, l’Anses, l’Ifremer et la Dire...
Article
Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-valu...
Preprint
Full-text available
Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitation at large-scale. It is very c...
Book
Full-text available
Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitation at large-scale. It is very c...
Conference Paper
Full-text available
To ensure the usefulness of a bioinformatics service, analysis of user needs is an essential step. Furthermore, if the service anticipates the identified needs, acceptance by the user is easier. The aim of this work is to provide an overview of the requirements of a microbial diversity research community for ontology-based text-mining applications....
Presentation
Full-text available
Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant inf...
Article
Full-text available
This data article contains values of oxygen and carbon dioxide solubility and diffusivity measured in various model and real food products. These data are stored in a public repository structured by ontology. These data can be retrieved through the @Web tool, a user-friendly interface to capitalise and query data. The @Web tool is accessible online...
Article
Predicting microbial safety of fresh products in modified atmosphere packaging implies to take into account the dynamic of O2, CO2 and N2 exchanges in the system and its effect on microbial growth. In this paper a mechanistic model coupling gas transfer and predictive microbiology was validated using dedicated challenge-tests performed on poultry m...
Article
Based on the measurement of local oxygen partial pressure kinetic, a non-invasive methodology was proposed to assess O2 diffusivity (DO2) in liquid, viscous and solid matrices. This new method was compared with a previous invasive method, developed by the same group, based on the same principle. The new method has proven to be essential to measure...
Article
A cheap and easy to handle methodology was adapted to achieve the measurement of CO2 diffusivity within solid food matrices. This methodology was tested on real food products with different composition (cooked ham, butter and processed cheese). Local distribution profiles, measured using a customized chemical titration, permitted in the same time...
Presentation
Full-text available
Information Extraction Challenge Gene Regulation Network in Arabidopsis thaliana (GRNA)
Poster
Full-text available
A comprehensive understanding of the molecular network underlying seed development regulations remains a major scientific challenge with important potential impact for fundamental research, agriculture and industry. Seed development requires the coordinated growth of different tissues that involves complex genetics and environmental regulations. Mo...
Article
The performances of Modified Atmosphere Packaging (MAP) for perishable foodstuffs depend mainly on food composition, on the initial microbiological qualities, on the nature of the packaging and on gaz contents. The expected shelf life will be limited by the bacterial development and the evolution of organoleptic properties. The solubility of the ga...
Poster
Full-text available
Seed is the main vector for breeding and production of annual field crops, and the accumulation of seed storage compounds (sugars, lipids, proteins) is of primary importance for food, feed and industrial uses. Seed development requires the coordinated growth of different tissues and involves complex genetics and environmental regulations. A compreh...
Article
Coupling gas transfer with predictive microbiology is essential to rationally design modified atmosphere packaging (MAP) strategies to ensure and guarantee food safety. Nowadays, these strategies are generally empirically built and over-sized since packaging material with high barrier properties is often chosen by default even if such a high level...
Thesis
Packaging is a key player on reducing food losses. In Modified Atmosphere Packaging (MAP) of fresh produce, the gaseous composition of the headspace is chosen in order to prevent microorganism growth (usually low O2 and high CO2 concentrations are chosen). This work aimed at initiating and developing a generalised approach permitting to study and q...
Article
Oxygen and carbon dioxide solubility and diffusivity are 2 key parameters to understand gas transfer in food matrices. Knowledge of these parameters could help to predict gas concentration in modified atmosphere packaging and, consequently, to predict shelf-life of the product through the development of appropriate mathematical models. The aim of t...
Conference Paper
Full-text available
Modified Atmosphere Packaging (MAP) relies on modification of the atmosphere inside the package in order to extend food shelf life by reducing oxidation and microbial degradation rate. In the peculiar case of inert products (e.g. meat- or fish-based food products) MAP is achieved by the interplay of two processes: (1) the transfer of gases through...
Conference Paper
Full-text available
Carbon dioxide is the most important gas in Modified Atmosphere Packaging (MAP) systems, usually intentionally added for its bacteriostatic properties for increasing shelf life of non-respiring fresh products. For example, CO2 level between 20 to 30% are usually used for MAP of meat product. In such case of high CO2 headspace concentration, a CO2 t...

Network

Cited By

Projects

Projects (5)
Project
The main goal of this project is to gain insights on the circulation of SARS-CoV-2 in meat processing plants in order to provide preventive or risk mitigation measures for workers and consumers.
Project
The domain of text-mining for biology (BioNLP) develops automatic methods to assist the analysis of knowledge expressed in natural language scientific articles. The formal description of biotopes and their properties is an essential step for the study of interactions between the organisms and their environment.