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110
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Introduction
Current institution
Additional affiliations
February 2008 - March 2010
January 2022 - present
INSERM RSMS U1309
Position
- Research Associate
January 2022 - present
UMR CNRS 6051
Position
- Research Associate
Publications
Publications (110)
The COVID-19 pandemic overwhelmed health systems, resulting in a surge in excess deaths. This study clustered countries based on excess mortality to understand their response to the pandemic and the influence of various factors on excess mortality within each cluster.
This ecological study is part of the COVID-19 MORtality (C-MOR) Consortium. Morta...
Background
Territorial health inequalities are of growing concern in countries with universal health systems. From 2003, three successive national cancer plans were launched in France, aiming to improve prevention and treatment. Regions in France are responsible for strategic and financial management of healthcare within their boundaries, which, un...
Introduction: To examine the impact of the COVID-19 pandemic on mortality, we estimated excess all-cause mortality in 24 countries for 2020 and 2021, overall and stratified by sex and age.
Methods: Total, age-specific and sex-specific weekly all-cause mortality was collected for 2015–2021 and excess mortality for 2020 and 2021 was calculated by co...
Context
There is concern in France about geographical access to health care, particularly in remote areas with scarce medical services. The objective of our study was to compare the care pathway of stroke patients according to their residence context (rural/urban) and their affiliation to the “agricultural social security” scheme (“MSA”).
Methods...
Health services research (HSR) must now integrate the technological and methodological developments of ‘Big Data’ that are transforming health research as a whole. E-health devices, social networks, and electronic medical records (EHR) are all sources that can enrich HSR. For example, social networks have become tools for hospital evaluation (ranki...
The development of medico-administrative databases over the last few decades has led to an evolution and to a significant production of epidemiological studies on infectious diseases based on retrospective medical data and consumption of care. This new form of epidemiological research faces numerous methodological challenges, among which the assess...
Context
There is concern in France about geographical access to health care, particularly in remote areas with scarce medical services. The objective of our study was to compare the care pathway of stroke patients according to their residence context (rural/urban) and their affiliation to the “agricultural social security” scheme (“MSA”).
Method
T...
Background
To understand the impact of the COVID-19 pandemic on mortality, this study investigates overall, sex- and age-specific excess all-cause mortality in 20 countries, during 2020.
Methods
Total, sex- and age-specific weekly all-cause mortality for 2015–2020 was collected from national vital statistics databases. Excess mortality for 2020 wa...
Purpose:
To compare the safety of outpatient versus inpatient endovascular treatment of lower extremity arterial disease (LEAD) using real-life data.
Materials and methods:
This retrospective observational study used real-life data from the French national health data information system on adult patients who underwent stenting for LEAD between 2...
Objectives
Despite evidences of efficiency and safety ambulatory endovascular revasculatisation for lower extremity arterial disease (LEAD) concerned only 5% of the interventions in France in 2016. Such low rate suggested temporal and geographical space disparities. The aim of this study was to describe the space-time development of ambulatory endo...
Background:
Understanding the impact of the burden of COVID-19 is key to successfully navigating the COVID-19 pandemic. As part of a larger investigation on COVID-19 mortality impact, this study aims to estimate the Potential Years of Life Lost (PYLL) in 17 countries and territories across the world (Australia, Brazil, Cape Verde, Colombia, Cyprus...
Background
Understanding the impact of the burden of COVID-19 is key to successfully navigating the COVID-19 pandemic. As part of a larger investigation on COVID-19 mortality impact, this study aims to estimate the Potential Years of Live Lost (PYLL) in 17 countries and territories across the world (Australia, Brazil, Cape Verde, Colombia, Cyprus,...
Background: This study aimed to investigate overall and sex-specific excess all-cause mor
Background:
This study aimed to investigate overall and sex-specific excess all-cause mortality since the inception of the COVID-19 pandemic until August 2020 among 22 countries.
Methods:
Countries reported weekly or monthly all-cause mortality from January 2015 until the end of June or August 2020. Weekly or monthly COVID-19 deaths were reporte...
The French national health insurance information system created in 1999 is one of the largest global data warehouse of medico-administrative data, covering nearly 66 million inhabitants and containing more than 160 billion records, including all outpatient health expenditures. Recent legislation has enlarged the scope of information and access to t...
Objective
To assess whether disparities in rates of same-day discharge for lower extremities arterial disease (5%) and varicose vein interventions (90%) are associated with the burden of postprocedural rehabilitation process, measured through the duration of sick leave.
Design
Retrospective observational study using French National Health Insuranc...
Background
In France, 90% of varicose vein interventions are performed in ambulatory setting while it concerns 7% of angioplasty for lower extremities arterial disease (LEAD). In this study, we made the hypothesis that such disparities may partly be due to the burden of the post-procedural rehabilitation and its relation to patients’ care-pathway a...
Contexte
Peu d’indicateurs d’accessibilité décrivent à fine échelle la distribution de l’offre et de la demande des soins. C’est dans ce contexte que notre projet, visant à explorer l’existence d’inégalités territoriales en matière d’accès aux soins, a développé un nouvel indicateur nommé « Index of Spatial Accessibility » (ISA).
Méthodologie
Afin...
In public health research and more precisely in the reuse of electronic health data, selecting patients, identifying specific events and interpreting results typically requires biomedical knowledge. The queryMed R package aims to facilitate the integration of medical and pharmacological knowledge stored in formats compliant with the Linked Data par...
Background
Patients with chronic diseases, like patients with end-stage renal disease (ESRD), have long history of care driven by multiple determinants (medical, social, economic, etc.). Although in most epidemiological studies, analyses of health care determinants are computed on single health care events using classical multivariate statistical r...
Background
Spatial accessibility indices are increasingly applied when investigating inequalities in health. Although most studies are making mentions of potential errors caused by the edge effect, many acknowledge having neglected to consider this concern by establishing spatial analyses within a finite region, settling for hypothesizing that acce...
Background:
The public health burden resulting from infectious diseases requires efforts in surveillance and evaluation of health care. The use of administrative health databases (AHD) and in particular the French national health insurance database (SNIIRAM) is an opportunity to improve knowledge in this field. The SNIIRAM data network (REDSIAM) w...
Comparing care trajectories helps improve health services. Medico-administrative databases are useful for automatically reconstructing the patients' history of care. Care trajectories can be compared by determining their overlapping parts. This comparison relies on both semantically-rich representation formalism for care trajectories and an adequat...
La recomposition hospitalière observable depuis plus de 20 ans en France résulte de décisions prises dans le cadre des politiques de planification et des stratégies adoptées par les établissements. Au-delà de ses conséquences, comment dans un premier temps rendre compte du maillage territorial des établissements de santé ? Pour identifier les facte...
Background
In France, there are important regional disparities of access to the renal transplant waiting list and transplantation. Our objectives were to compare the characteristics of patients with end-stage renal disease (ESRD) of two French regions (Ile-de-France and Bretagne) and to identify determinants of access to the waiting list and subseq...
Introduction
La chirurgie ambulatoire est un mode de prise en charge permettant de raccourcir la durée d’hospitalisation à une seule journée. Elle connaît un réel développement en angioplastie. Néanmoins, comme toute chirurgie, elle n’est pas exempte de complications. Nous avons mené une étude pilote pour étudier la pertinence du PMSI pour la reche...
Introduction
En France, l’acces a la greffe renale est marque par d’importantes variations entre les regions. L’objectif de cette etude est de comparer :
– les determinants de l’acces a la greffe des patients atteints d’insuffisance renale chronique terminale (IRCT) en Bretagne et en Ile-de-France ;
– les periodes de mise en contre-indications te...
Background
The evaluation of geographical healthcare accessibility in residential areas provides crucial information to public policy. Traditional methods - such as Physician Population Ratios (PPR) or shortest travel time - offer only a one-dimensional view of accessibility. This paper developed an improved indicator: the Index of Spatial Accessib...
Introduction
La sclérose en plaques (SEP) est une maladie neurologique chronique affectant environ 100 000 personnes en France pour lesquelles la consommation précise de soins est peu connue.
Objectifs
Décrire les soins auxquels les personnes atteintes de SEP dans l’échantillon généraliste des bénéficiaires (EGB) ont recours et créer une typologie...
Introduction
La sclerose en plaques (SEP) est une maladie chronique du jeune adulte affectant 100 000 personnes en France et entrainant une consommation de soins importante. L’ouverture recente des bases medico-administratives de l’Assurance maladie aux chercheurs, telle que l’EGB (Echantillon generaliste des beneficiaires), permet l’acces a ces do...
Introduction
Le traitement statistique de données provenant des bases médico-administratives, comme le Programme médicalisé des systèmes d’information (PMSI) et l’Échantillon généraliste des bénéficiaires de l’Assurance maladie (EGB), est en plein essor. Cependant, le volume, l’hétérogénéité ou la complexité des données issues de ces systèmes d’inf...
Background:
Surgical site infection surveillance (SSI) is important for the improvement of care and patient safety. Most SSI surveillance systems focus on hospital settings, whereas numerous infectious events occur after discharge.
Aim:
To evaluate the patient care trajectory after discharge, we linked the hospital discharge database and the Nat...
Introduction
L’accès à la transplantation rénale est marqué par d’importantes variations de pratiques d’inscription sur la liste d’attente. L’objectif de l’étude est de comparer les déterminants de l’accès à la liste des patients en insuffisance rénale chronique terminale (IRCT) en Bretagne et en Île-de-France (IDF).
Patients et méthodes
L’étude p...
In order to study social inequalities, indices can be used to summarize the multiple dimensions of the socioeconomic status. As a part of the Equit'Area Project, a public health program focused on social and environmental health inequalities; a statistical procedure to create (neighborhood) socioeconomic indices was developed. This procedure uses s...
Suite aux difficultés de gestion et d'exploration de données issues des bases médico-administratives françaises, une méthode basée sur les technologies du Web Sémantique a été mise en place. L'objectif est d'être en mesure de gérer et d'explorer des données de parcours de soins de ville et d'hôpital, de manière pertinente et efficace, pour facilite...
Pregnant women are a vulnerable population. Although regular follow-ups are recommended during pregnancy, not all pregnant women seek care. This pilot study wanted to assess whether the integration of data from administrative health information systems and socio-economic features allows identifying disparities in prenatal care trajectories.
Prenata...
Cell proliferation is a hallmark of cancer and depends on complex signaling networks that are chiefly supported by protein kinase activities. Therapeutic strategies have been used to target specific kinases but new methods are required to identify combined targets and improve treatment. Here, we propose a small interfering RNA genetic screen and an...
Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent bran...
Introduction
In order to study social health inequalities, contextual (or ecologic) data may constitute an appropriate alternative to individual socioeconomic characteristics. Indices can be used to summarize the multiple dimensions of the neighborhood socioeconomic status. This work proposes a statistical procedure to create a neighborhood socioec...
We sought to evaluate, on a model of sepsis, the clinical relevance of new parameters obtained on a white blood cell (WBC) differential by flow cytometry, implemented in the routine workflow of our hematology laboratory.
A WBC with differential by flow cytometry was done on 459 patients at admission in intensive care unit. They were retrospectively...
Recent advances in miniaturization and automation of technologies have enabled cell-based assay high-throughput screening, bringing along new challenges in data analysis. Automation, standardization, reproducibility have become requirements for qualitative research. The Bioconductor community has worked in that direction proposing several R package...
R is a powerful language and widely used software tool for the analysis and visualization of data. Its core capabilities can be extended through many different add-on packages. Among the many packages are some which offer a broad range of facilities for analyzing statistical properties of graphs. This chapter provides a practical tutorial covering...
Diagram of the algorithm leading to the construction of a set of (l, d)SSM for a pair of genes. A) Representation of the atomic motifs for 2 genes (gray). Gene 1 and Gene 2 have 3 and 2 atomic motifs, respectively. The colored areas stress some subsequences of length l of the atomic motifs used as examples in the following panels, matching colors i...
Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration o...
List of the individual z-scores for methylene blue data obtained from MCF-7 cells.
(XLS)
The human kinase library used for the RNAi screen. Positions and sequences of siRNA.
(XLS)
Methylene blue pictures. Pictures of 3 plates (7-9) among 30 for the 3 independent experiments. The z-scores, obtained by using cellHTS2 package for methylene blue data, were also illustrated. Negative controls: wells A12, B12 and G12, H12.
(TIF)
List of the mean z-scores for methylene blue data obtained from MCF-7 cells.
(XLS)
R Script for the cellHTS2 analysis using the preprocessing work-flow for two-channel screens (EROD and methylene blue data).
(TIF)
Hypothetical Schema. The diagram shows a hypothetical schema to resume the AhR signaling pathway leading to nuclear translocation of AhR and consecutive CYP1A1 up-regulation and activity (EROD). Ligands of AhR such as TCDD are known to induce a transient elevation of intracellular concentration of IP3 and calcium. Calcium and calmodulin (cam) are r...
Methylene blue data analyses. A, Flow diagram of the strategy used to identify kinases interfering with cell density in MCF-7 cells. B, a screen-wide image plot to visualize the position in plates of hits. Here, the picture corresponds to individual z-scores calculated from 3 experiments for individual siRNA. One experiment corresponds to 30 plates...
The aryl hydrocarbon receptor (AhR) is a transcription factor activated by several environmental pollutants, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and involved in carcinogenesis and various physiological processes, including immune response and endocrine functions. Characterization of kinases-related AhR transduction pathway remains a...
Synthetic genetic interactions experiments are now being conduct to better understand cellular interactions. The generated data have already proven to be extremely valuable (Davierwala et al., 2005; A et al., 2004; Zhao et al., 2005). Synthetic lethality especially defines a genetic interaction were the combination of mutations in two or more genes...
Several malignancies are known to exhibit a "field effect," whereby regions beyond tumor boundaries harbor histologic or molecular changes that are associated with cancer. We sought to determine if histologically benign prostate epithelium collected from men with prostate cancer exhibits features indicative of premalignancy or field effect.
Prostat...
Le TGF-b est une cytokine qui possède de nombreuses fonctions biologiques ; croissance, différenciation cellulaire, régulation de la réponse inflammatoire, sécrétion de la matrice extracellulaire et apoptose. La fixation du TGF-b sur des récepteurs membranaires de type thréonine kinases, déclenche une cascade de phosphorylation des protéines SMAD d...
Recent advances in automation technologies have enabled the use of flow cytometry high content screening (FH-HCS), in both basic and clinical research, generating large complex data sets with any covariates. However, data management and data analysis methods have not yet progressed sufficiently far from the initial small-scale studies to support mo...
Modeling biological systems requires precise temporal concepts. Biological observations are often issued from discrete event measurements, which make discrete modeling especially interesting. However time is absent of these models or defined a priori. In this paper, we propose a new formalism to specify time in discrete logical model and illustrate...
A systems biology interpretation of genome-scale RNA interference (RNAi) experiments is complicated by scope, experimental variability and network signaling robustness. Over representation approaches (ORA), such as the Hypergeometric or z-score, are an established statistical framework used to associate RNA interference effectors to biologically an...
The transforming growth factor beta is known to have pleiotropic effects, including differentiation, proliferation and apoptosis. However the underlying mechanisms remain poorly understood. The regulation and effect of TGF-beta signaling is complex and highly depends on specific protein context. In liver, we have recently showed that the disintegri...
Risk stratification in advanced heart failure (HF) is crucial for the individualization of therapeutic strategy, in particular for heart transplantation and ventricular assist device implantation. We tested the hypothesis that cardiac gene expression profiling can distinguish between HF patients with different disease severity. We obtained tissue s...
Journée satellite "Modélisation dynamique et simulation des réseaux biologiques "
Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the...
Synthetic lethality defines a genetic interaction where the combination of mutations in two or more genes leads to cell death. The implications of synthetic lethal screens have been discussed in the context of drug development as synthetic lethal pairs could be used to selectively kill cancer cells, but leave normal cells relatively unharmed. A cha...
Detailed information about the data sources used in the main manuscript. We also present and discuss additional analysis performed for comparison with the results presented in the main paper.
Each file has 13 columns: P and P-values (adjusted), P-values and adjusted P-values of the hypergeometric test; Odds, odds ratios; Expected,: expected number of synthetic genetic interactions between complexes; Interact (observed), number of synthetic genetic interactions observed; Tested, number of interaction tested; Essential genes, number of es...
Unlabelled:
Automated analysis of flow cytometry (FCM) data is essential for it to become successful as a high throughput technology. We believe that the principles of Trellis graphics can be adapted to provide useful visualizations that can aid such automation. In this article, we describe the R/Bioconductor package flowViz that implements such v...
Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningfu...
Understanding regulatory mechanisms in complex biological systems is an important challenge, in particular to understand disease mechanisms, and to discover new therapies and drugs. In this paper, we consider the important question of cellular regulation of phenotype. Using single gene deletion data, we address the problem of linking a phenotype to...
The recent development of semiautomated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the developm...
Gene-expression changes in atrial fibrillation patients reflect both underlying heart-disease substrates and changes because of atrial fibrillation-induced atrial-tachycardia remodeling. These are difficult to separate in clinical investigations. This study assessed time-dependent mRNA expression-changes in canine models of atrial-tachycardia remod...
Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in...
To investigate regulatory processes and protective mechanisms leading to desiccation tolerance (DT) in seeds, 16086-element microarrays were used to monitor changes in the transcriptome of desiccation-sensitive 3-mm-long radicles of Medicago truncatula seeds at different time points during incubation in a polyethylene glycol (PEG) solution at -1.7...
Pseudorabies virus (PRV) is an alpha herpesvirus that causes Aujezsky disease in the pig. To characterize the impact of PRV infection on cellular expression, we used microarrays consisting of 9850 oligonucleotides corresponding to human genes and examined the expression levels of mRNA isolated 0.5, 3, 6, and 9 h post infection (hpi) from cultures o...
By triggering an adaptive response to hypoxia which is a common feature of tumor microenvironments, endothelial cells contribute to the onset of angiogenic responses involved in tumor growth. Therefore, identifying hypoxic markers represent a challenge for a better understanding of tumor angiogenesis and for the optimization of anti-angiogenic ther...
Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture the full scope of FCM experiments and there is a demand for software tools that can assist in the exploration and analysis of larg...
High liver iron content is a risk factor for developing hepatocellular carcinoma (HCC). However, HCC cells are always iron-poor. Therefore, an association between hepatocyte iron storage capacity and differentiation is suggested. To characterize biological processes involved in iron loading capacity, we used a cDNA microarray to study the different...
Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia in humans. The pathophysiology of AF involves electrical, structural and contractile remodeling, which is associated with changes in cardiac gene expression. Previous studies of gene-expression changes in clinical AF have mostly been limited to a small number of candidate gene...
Dendritic cell (DC) maturation is the process by which immature DC in the periphery differentiate into fully competent antigen-presenting cells that initiate the T cell response. However, DC respond to many distinct maturation stimuli, and different types of mature DC induce qualitatively different T cell responses. As DC maturation involves the co...
Valvular heart disease (VHD), which often leads to atrial fibrillation (AF), and AF both cause ion-channel remodeling. We evaluated the ion-channel gene expression profile of VHD patients, in permanent AF (AF-VHD) or in sinus rhythm (SR-VHD), in comparison with patients without AF or VHD, respectively.
We used microarrays containing probes for huma...
