Jean-Christophe Aude

Jean-Christophe Aude
Atomic Energy and Alternative Energies Commission | CEA · Institute of Biology and Technology Saclay (iBiTec-S)

PhD
Data Science for Biology and Health

About

60
Publications
5,223
Reads
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1,726
Citations
Additional affiliations
December 1999 - present
Atomic Energy and Alternative Energies Commission
Position
  • Researcher

Publications

Publications (60)
Preprint
Full-text available
Mammalian SWI/SNF complexes (mSWI/SNF) are ATP-dependent chromatin remodelling factors that possess tumour suppressor properties. Brg1 (Smarca4), the catalytic subunit of mSWI/SNF, is essential for chromatin opening at enhancers, but the detailed mechanism of this activity remains unclear. Using mouse embryonic stem (ES) cells, we show that Brg1 ge...
Article
Full-text available
Protein adsorption on nanoparticles is an important field of study, particularly with regard to nanomedicine and nanotoxicology. Many factors can influence the composition and structure of the layer(s) of adsorbed proteins, the so-called “protein corona”. However, the role of protein size has not been specifically investigated, although some eviden...
Article
Full-text available
Methods to control the blood glucose (BG) levels of patients in intensive care units (ICU) improve the outcomes. The development of continuous BG levels monitoring devices has also permitted to optimize these processes. Recently it was shown that a complexity loss of the BG signal is linked to poor clinical outcomes. Thus, it becomes essential to d...
Article
Full-text available
Biomolecules, and particularly proteins, bind on nanoparticle (NP) surfaces to form the so-called protein corona. It is accepted that the corona drives the biological distribution and toxicity of NPs. Here, the corona composition and structure were studied using silica nanoparticles (SiNPs) of different sizes interacting with soluble yeast protein...
Article
Full-text available
Proteins adsorption on surfaces is generally evaluated in terms of evolution of the proteins’ structures and functions. However, considering a nanoparticle, the protein corona formed at its surface possesses a particular supramolecular structure that gives a "biological identity" to the new object. Little is known about the actual shape of the prot...
Article
Full-text available
BRCA1 mutations have been identified that increase the risk of developing hereditary breast and ovarian cancers. Genetic screening is now offered to patients with a family history of cancer, to adapt their treatment and the management of their relatives. However, a large number of BRCA1 variants of uncertain significance (VUS) are detected. To bett...
Article
Full-text available
BRCA1 mutations have been identified that increase the risk of developing hereditary breast and ovarian cancers. Genetic screening is now offered to patients with a family history of cancer, in order to adapt their treatment and the management of their relatives. However, a large number of BRCA1 variants of uncertain significance (VUS) are detected...
Preprint
Full-text available
BRCA1 mutations have been identified that increase the risk of developing hereditary breast and ovarian cancers. Genetic screening is now offered to patients with a family history of cancer, in order to adapt their treatment and the management of their relatives. However, a large number of BRCA1 variants of uncertain significance (VUS) are detected...
Article
Full-text available
Upon contact with biological fluids, nanoparticles (NPs) are readily coated by cellular compounds, particularly proteins, which are determining factors for the localization and toxicity of NPs in the organism. Here, we improved a methodological approach to identify proteins that adsorb on silica NPs with high affinity. Using large-scale proteomics...
Article
Full-text available
ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4...
Article
Full-text available
We investigated the relationship between unfolded proteins, silica nanoparticles and chaperonin to determine whether unfolded proteins could stick to silica surfaces and how this process could impair heat shock protein activity. The HSP60 catalyzed green fluorescent protein (GFP) folding was used as a model system. The adsorption isotherms and adso...
Article
Full-text available
The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy co...
Article
Full-text available
We show that the Synechocystis AbrB2 repressor of hydrogen production, down regulates the defence against oxidative stress. The single widely conserved cysteine of AbrB2 is also shown to play a crucial role in AbrB2 oligomerisation, and in AbrB2-mediated repression of the hydrogenase encoding operon (hoxEFUYH) and a wealth of other genes. Very inte...
Article
Full-text available
We report the development of new tools and methods for facile integration and meaningful representation of high throughput data generated by the genome-wide analyses of the model cyanobacterium Synechocystis PCC6803, to genetic engineering increasing its level of hydrogen photoproduction. These robust tools comprise new oligonucleotide DNA microarr...
Article
High-throughput omic technologies are now commonly used in large-scale experimental biology. The main characteristic of these omic approaches is that they usually produce large amounts of data. Results obtained through these analyses are mostly interpreted or assessed in terms of given hypotheses. In most cases, huge amount of results need to be tr...
Article
Full-text available
RNA polymerase (Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of Pol III and its associated transcription factors on the genome of mouse embryonic stem cells using a highly specific tandem ChIP-...
Article
Cadmium (Cd(2+)) is a very toxic metal that causes DNA damage, oxidative stress and apoptosis. Despite many studies, the cellular and molecular mechanisms underlying its high toxicity are not clearly understood. We show here that very low doses of Cd(2+) cause ER stress in Saccharomyces cerevisiae as evidenced by the induction of the unfolded prote...
Article
Full-text available
Human PC4 and the yeast ortholog Sub1 have multiple functions in RNA polymerase II transcription. Genome-wide mapping revealed that Sub1 is present on Pol III-transcribed genes. Sub1 was found to interact with components of the Pol III transcription system and to stimulate the initiation and reinitiation steps in a system reconstituted with all rec...
Article
Full-text available
Protein-protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein interacti...
Article
Motivation: Protein–protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of prote...
Article
Full-text available
TFIIS is a transcription elongation factor that stimulates transcript cleavage activity of arrested RNA polymerase II (Pol II). Recent studies revealed that TFIIS has also a role in Pol II transcription initiation. To improve our understanding of TFIIS function in vivo, we performed genome-wide location analysis of this factor. Under normal growth...
Article
Full-text available
Protein-protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of its cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein-prote...
Data
Kinetic analysis of the transcriptional responses to cadmium. The data provided indicate for each gene (column 1), encoding the indicated protein (column 12), the log-ratio of response to the indicated duration of the cadmium treatment (columns 2 to 10) and the p-value obtained by the analysis (column 11).
Data
Relevant List of Stress-Responsive Genes. The data provided indicate for each gene (extreme left and right columns), sorted by the physiological function they operate in, the log-ratio of response to the indicated duration of stresses.
Data
Dye-Swap-correlations. The data provided indicate (for each time of the 5 kinetics) the correlation coefficient between the two ratio samples obtained with the two microarrays of each dye-swap.
Data
GSM numbers of all microarray experiments. This table provides the links for accessing our microarray data which have been deposited in the GEO website.
Data
Analysis of the unstressed versus unstressed control experiment. These file describe the distribution of allexpression ratio for the unstressed versus unstressed control experiment, showing the extreme, mean and quantile values.
Data
Kinetic analysis of the transcriptional responses to hydrogen peroxide. The data provided indicate for each gene (column 1), encoding the indicated protein (column 8), the log-ratio of response to the indicated duration of the hydrogen peroxide treatment (columns 2 to 6), and the p-value obtained by the analysis (column 7).
Article
Full-text available
Cadmium is a persistent pollutant that threatens most biological organisms, including cyanobacteria that support a large part of the biosphere. Using a multifaceted approach, we have investigated the global responses to Cd and other relevant stresses (H2O2 and Fe) in the model cyanobacterium Synechocystis PCC6803. We found that cells respond to the...
Chapter
This paper is a review of promising applications of pyramidal classification to biological data. We show that overlapping and ordering properties can give new insights that can not be achieved using more classical methods. We examplify our point using three applications: (i) a genome scale sequence analysis, (ii) a new progressive multiple sequence...
Article
Full-text available
To better understand the response of the model cyanobacterium Synechocystis to environ mental stresses, we aim at building regulatory networks by a co mbination of gene expression data and protein-protein interactions. The experimental generation of the interaction network remains difficult, but some large-scale interaction networks are available f...
Article
Idiopathic nephrotic syndrome is a proteinuric disease secondary to the release of a nonidentified circulating glomerular permeability factor by T cells. Because specificities of T-cell activation in idiopathic nephrotic syndrome remain unknown, we evaluated transcriptional activation of T cells in nephrotic patients during proteinuria. Transcripto...
Article
Full-text available
To identify genetic conservation relative to precise aspects of developmental diversity, an essential question in computational biology, we developed a new comparative method that allows conserved modules for the best balance between protein sequence similarity and gene co-expression to be constructed, in invertebrates. Our method, referred to as t...
Article
Full-text available
As an approach to understanding how mammals regulate H(2)O(2) toxicity, intracellular concentration to prevent its we analyzed the genome-wide mRNA profile changes of human cells after treatment with a non-toxic H(2)O(2) concentration. We identified a large and essentially late H(2)O(2) response of induced and repressed genes that unexpectedly comp...
Article
Full-text available
Motivation: Different automatic methods of sequence alignments are routinely used as a starting point for homology searches and function inference. Confidence in an alignment probability is one of the major fundamentals of massive automatic genome-scale pairwise comparisons, for clustering of putative orthologs and paralogs, sequenced genome annot...
Article
Full-text available
To gain a molecular understanding of kidney functions, we established a high-resolution map of gene expression patterns in the human kidney. The glomerulus and seven different nephron segments were isolated by microdissection from fresh tissue specimens, and their transcriptome was characterized by using the serial analysis of gene expression (SAGE...
Article
The Z-value (Comput. Chem. 23 (1999) 333) is an extension of the Z-score that is classically used to compare sets of biological sequences. The Z-value has been successfully used to handle complete genome studies as well as analyze large sets of proteins. The Z-value computation is based on a Monte Carlo approach to estimate the statistical signific...
Article
Genome-wide studies have recently revealed the unexpected complexity of the genetic response to apparently simple physiological changes. Here, we show that when yeast cells are exposed to Cd(2+), most of the sulfur assimilated by the cells is converted into glutathione, a thiol-metabolite essential for detoxification. Cells adapt to this vital meta...
Article
Characterization of tissue-specific gene expression profiles, or transcriptomes, may serve two purposes: a) establishing relationships between cell transcriptomes and functions (i.e. molecular and physiological phenotypes) under physiological and pathophysiological conditions serves to elucidate gene functions, and b) determination of the totality...
Article
Progress accomplished by complete genomes and cDNA-sequencing projects calls for methods that fully use these resources to study gene expression patterns in characterized cell populations. However, since the number of functional genes cannot be readily inferred from the genomic sequence, it is highly desirable to make use of methods enabling to stu...
Article
Full-text available
An all-by-all comparison of all the publicly available protein sequences from plants has been performed, followed by a clusterization process. Within each of the 1064 resulting clusters-containing sequences that are orthologous as well as paralogous-the sequences have been submitted to a pyramidal classification and their domains delineated by an a...
Article
The Z-value is an attempt to estimate the statistical significance of a Smith-Waterman dynamic alignment score (SW-score) through the use of a Monte-Carlo process. It partly reduces the bias induced by the composition and length of the sequences. This paper is not a theoretical study on the distribution of SW-scores and Z-values. Rather, it present...
Article
In conventional hierarchical clustering methods, any object can belong to only one class or cluster. We present here an application of the pyramidal classification method to biological objects, which illustrates the intuitively appealing idea that some objects may belong simultaneously to two classes. In a first step, we performed an all-by-all com...
Article
Full-text available
All of the aminoacyl-tRNA synthetase (aaRS) sequences currently available in the data banks have been subjected to a systematic analysis aimed at finding gene duplications, genetic recombinations, and horizontal transfers. Evidence is provided for the occurrence (or probable occurrence) of such phenomena within this class of enzymes. In particular,...
Article
Full-text available
La deuxième moitié du siècle dernier a vu l'émergence et le succès de l'approche réductionniste en physiologie rénale, approche qui a permis de caractériser les mécanismes cellulaires de transport tubulaire et de leur régulation, et d'en déter-miner le support moléculaire. Il s'est agi d'une approche essentiellement déductive de type gène cible : a...

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