Christophe Trefois

Christophe Trefois
University of Luxembourg · Luxembourg Centre for Systems Biomedicine (LCSB)

Doctor of Philosophy

About

44
Publications
14,659
Reads
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671
Citations
Citations since 2016
29 Research Items
620 Citations
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
Education
September 2006 - September 2008
École Polytechnique Fédérale de Lausanne
Field of study
  • Communication Systems

Publications

Publications (44)
Article
Full-text available
The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's disease (PD) and other neurodegenerative...
Article
Full-text available
Ecosystems and biological systems are known to be inherently complex and to exhibit nonlinear dynamics. Diseases such as microbiome dysregulation or depression can be seen as complex systems as well and were shown to exhibit patterns of nonlinearity in their response to perturbations. These nonlinearities can be revealed by a sudden shift in system...
Article
Full-text available
Objective Mitochondrial dysfunction is a hallmark of idiopathic Parkinson's disease (IPD), which has been reported not to be restricted to striatal neurons. However, studies that analyzed mitochondrial function at the level of selected enzymatic activities in peripheral tissues have produced conflicting data. We considered the electron transport ch...
Conference Paper
Full-text available
Automated clump decomposition is essential for single cell based analysis of fluorescent microscopy images. This paper presents a new method for automatically splitting clumps of cell nuclei in fluorescence microscopy images. Nuclei are first segmented using histogram concavity analysis. Clumps of nuclei are detected by fitting an ellipse to the se...
Article
Full-text available
Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused by a complex interplay of genetic and environmental factors. Information on various aspects of PD pathogenesis is rapidly increasing and needs to be efficiently organized, so that the resulting data is available for exploration and analysis. Here we introduce...
Article
Metabolic models are typically characterized by a large number of parameters. Traditionally, metabolic control analysis is applied to differential equation-based models to investigate the sensitivity of predictions to parameters. A corresponding theory for constraint-based models is lacking, due to their formulation as optimization problems. Here,...
Article
Full-text available
COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report...
Preprint
Full-text available
COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report...
Article
Full-text available
Omics experiments are ubiquitous in biological studies, leading to a deluge of data. However, it is still challenging to connect changes in these data to changes in cell functions because of complex interdependencies between genes, proteins, and metabolites. Here, we present a framework allowing researchers to infer how metabolic functions change o...
Article
Full-text available
Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. PredictProtein was the first Internet server for protein predictions. It pioneered combining evolutionar...
Article
Full-text available
Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly...
Preprint
Full-text available
Since 1992 PredictProtein ( https://predictprotein.org ) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. PredictProtein was the first Internet server for protein predictions. It pioneered combining evolution...
Preprint
Full-text available
Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly...
Article
Full-text available
Background The amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow the easy generation of data with hundreds of millions of single-cell data points with >40 parameters, originating from thousands of individual samples. The analysis of that amoun...
Preprint
Full-text available
Background: The amount of data generated in large clinical and phenotyping studies that use single-cell cytometry is constantly growing. Recent technological advances allow to easily generate data with hundreds of millions of single-cell data points with more than 40 parameters, originating from thousands of individual samples. The analysis of that...
Poster
Full-text available
For processing massive flow and mass cytometry datasets, we have implemented a modern, extremely scalable and flexible version of the popular FlowSOM tool, called GigaSOM.jl. GigaSOM.jl simplifies the use of the commonly available compute infrastructure, and allows almost-interactive processing datasets that comprise thousands of individual samples...
Poster
Full-text available
Over the past years, websites have become prevalent in communicating science and promoting research related content. All of these websites have traditionally been separate entities commonly managed by several people, and based on content management systems (such as Wordpress, Drupal, or Joomla, which are notoriously known for weak security). A recu...
Preprint
Full-text available
Large-scale omics experiments have become standard in biological studies, leading to a deluge of data. However, researchers still face the challenge of connecting changes in the omics data to changes in cell functions, due to the complex interdependencies between genes, proteins and metabolites. Here we present a novel framework that begins to over...
Article
Full-text available
Background The new European legislation on data protection, namely, the General Data Protection Regulation (GDPR), has introduced comprehensive requirements for the documentation about the processing of personal data as well as informing the data subjects of its use. GDPR’s accountability principle requires institutions, projects, and data hubs to...
Presentation
Full-text available
The NETTAB 2018 conference programme can be found here: http://www.igst.it/nettab/2018/programme/scientific-programme
Chapter
Within life-science research the upcoming EU General Data Protection Regulation has a significant operational impact on organisations that use and exchange controlled-access Human Data. One implication of the GDPR is data bookkeeping. In this poster we describe a software tool, the Data Information System (DAISY), designed to record data protection...
Article
Full-text available
Background Translational research platforms share the aim to promote a deeper understanding of stored data by providing visualization and analysis tools for data exploration and hypothesis generation. However, such tools are usually platform-bound and are not easily reusable by other systems. Furthermore, they rarely address access restriction issu...
Article
Full-text available
Motivation: Automatically testing changes to code is an essential feature of continuous integration. For open-source code, without licensed dependencies, a variety of continuous integration services exist. The COnstraint-Based Reconstruction and Analysis (COBRA) Toolbox is a suite of open-source code for computational modelling with dependencies on...
Article
Full-text available
The immortalized and proliferative cell line SH-SY5Y is one of the most commonly used cell lines in neuroscience and neuroblastoma research. However, undifferentiated SH-SY5Y cells share few properties with mature neurons. In this study, we present an optimized neuronal differentiation protocol for SH-SY5Y that requires only two work steps and 6 da...
Article
Cell lines are widely used in translational biomedical research to study the genetic basis of diseases. A major approach for experimental disease modeling are genetic perturbation experiments that aim to trigger selected cellular disease states. In this type of experiments it is crucial to ensure that the targeted disease-related genes and pathways...
Article
Full-text available
Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused by a complex interplay of genetic and environmental factors. Information on various aspects of PD pathogenesis is rapidly increasing and needs to be efficiently organized, so that the resulting data is available for exploration and analysis. Here we introduce...
Article
Full-text available
Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular p...
Article
Full-text available
Abstract Although very developed in many sectors (databases, filesystems), access control schemes are still somewhat elusive when it comes to wireless sensor net- works. However, it is clear that many WSN systems—such as healthcare and automotive ones—need a controlled access to data that sensor nodes produce, given its high sensitivity. Enforcing...
Article
Full-text available
Wireless sensors are small devices that are able to gather, process and deliver information from a physical environment to an external system. By doing so, they open new applications in different domains, such as healthcare, traffc control, defense and agriculture. The integration of Wireless Sensor Networks (WSN) with Business Applications (BA) ra...
Conference Paper
Full-text available
The vision of ubiquitous computing is a network of small, inexpensive, robust processing devices, distributed throughout everyday life. Wireless Sensor Networks (WSNs) are an essential part to realize this dream. Sensor Networks can be seen as sources of input, delivering data from the real world into the digital world.
Conference Paper
Full-text available
Modern communication networks are reaching a high level of complexity. As their global dimensioning and performance evaluation are very hard tasks, a multi-layer approach is generally applied to divide them in smaller problems easier to tackle. Within this approach, tools only address one or two network layers. To perform an enhanced analysis encom...

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