Yves Vandenbrouck

Yves Vandenbrouck
Atomic Energy and Alternative Energies Commission | CEA · l’Institut Thématique Multi Organismes Technologie pour la Santé (ITMO TS)

PhD
Genomic Medicine - Numeric Health

About

86
Publications
8,733
Reads
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2,003
Citations
Additional affiliations
January 2013 - April 2017
French Proteomics Infrastructure (ProFI)
Position
  • Training coordinator
January 2011 - present
Atomic Energy and Alternative Energies Commission
Position
  • Principal Investigator
Description
  • Bioinformatics - Proteomics
January 2005 - December 2010
Atomic Energy and Alternative Energies Commission
Position
  • Managing Director
Education
January 1997 - April 1997
Institut Pasteur International Network
Field of study
  • Computer science for biology
November 1991 - May 1995
Sorbonne Université
Field of study
  • Cellular and Molecular Physiology

Publications

Publications (86)
Article
Full-text available
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely acc...
Article
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophys...
Article
Full-text available
Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the Lat (linker for activation of T cells) and the Mx2 (...
Article
Full-text available
Acute liver injury (ALI) is a severe disorder resulting from excessive hepatocyte cell death, and frequently caused by acetaminophen intoxication. Clinical management of ALI progression is hampered by the dearth of blood biomarkers available. In this study, a bioinformatics workflow was developed to screen omics databases and identify potential bio...
Chapter
With the increased simplicity of producing proteomics data, the bottleneck has now shifted to the functional analysis of large lists of proteins to translate this primary level of information into meaningful biological knowledge. Tools implementing such approach are a powerful way to gain biological insights related to their samples, provided that...
Article
Full-text available
Can we understand how plant cell metabolism really works? An integrated large-scale modelling of plant metabolism predictive model would make possible to analyse the impact of disturbances in environmental conditions on cellular functioning and diversity of plant-made molecules of interest. ChloroKB, a Web application initially developed for explor...
Article
Full-text available
Proteo3Dnet is a web server dedicated to the analysis of mass spectrometry interactomics experiments. Given a flat list of proteins, its aim is to organize it in terms of structural interactions to provide a clearer overview of the data. This is achieved using three means: (i) the search for interologs with resolved structure available in the prote...
Article
Full-text available
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics,...
Article
Full-text available
In the context of the Human Proteome Project, we built an inventory of 412 functionally unannotated human proteins for which experimental evidence at the protein level exists (uPE1) and which are highly expressed in tissues involved in human male reproduction. We implemented a strategy combining literature mining, bioinformatics tools to collate an...
Article
Protein–protein interactions play a major role in the molecular machinery of life and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hierarchical view of the interaction...
Article
The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, w...
Article
Full-text available
Secretome proteomics for the discovery of cancer biomarkers holds great potential to improve early cancer diagnosis. In this context, a knowledge‐based approach relying on mechanistic criteria related to the type of cancer should help to identify candidates from available “omics” information. Numerous bioinformatics tools, databases and “omics” dat...
Preprint
Full-text available
The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, w...
Article
Full-text available
Background Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bio...
Chapter
Knowledge-based approaches using large-scale biological (“omics”) data are a powerful way to identify mechanistic biomarkers, provided that scientists have access to computational solutions even when they have little programming experience or bioinformatics support. To achieve this goal, we designed a set of tools under the Galaxy framework to allo...
Article
Full-text available
To improve biomedical knowledge and to support biomarker discovery studies, it is essential to establish comprehensive proteome maps for human tissues and biofluids, and to make them publicly accessible. In this study, we performed an in-depth proteomics characterization of exhaled breath condensate (EBC), a sample obtained non-invasively by conden...
Article
The present study is a contribution to the “neXt50 challenge”, a coordinated effort across C-HPP teams to identify the 50 most tractable missing proteins (MPs) on each chromosome. We report the targeted search of 38 theoretically detectable MPs from chromosomes 2 and 14 in Triton X-100 soluble and insoluble sperm fractions from a total of 15 health...
Poster
Proteomics data is obtained using a combination of liquid chromatography and tandem mass spectrometry (MS/MS) where peptides are most commonly identified by matching MS/MS spectra against theoretical spectra of all candidate peptides represented in a generalist protein sequence reference database. The limitation of this approach is that variant pep...
Article
Full-text available
Context: Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (stoichiometry matrices) and pathway databases are extremely useful, they cannot describe the...
Article
Full-text available
Every data-rich community research effort requires a clear plan for ensuring the quality of the data interpretation and comparability of analyses. To address this need within the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), we have developed through broad consultation a set of mass spectrometry data interpretation guideli...
Article
Full-text available
Within the C-HPP, the French and Swiss teams are responsible for the annotation of proteins from chromosomes 14 and 2, respectively. neXtProt currently reports 1231 entries on chromosome 2 and 624 entries on chromosome 14; of these, 134 and 93 entries are still not experimentally validated and are thus considered as “missing proteins” (PE2-4), resp...
Article
Full-text available
The Chromosome-Centric Human Proteome Project aims to identify proteins classed as « missing » in the neXtProt knowledgebase. In this article, we present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using a range of protein extraction procedures and LC-MS/MS analysis, we detected a total...
Article
Full-text available
In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last four years, the French proteomics infrastructure has collected high quality datasets from 40 human samples, including a series of rarely stud...
Article
Full-text available
Metalloproteins represent a ubiquitous group of molecules which are crucial to the survival of all living organisms. While several metal-binding motifs have been defined, it remains challenging to confidently identify metalloproteins from primary protein sequences using computational approaches alone. Here, we describe a comprehensive strategy base...
Article
Full-text available
Uranium is a natural element which is mainly redistributed in the environment due to human activity, including accidents and spillages. Plants may be useful in cleaning up after incidents, although little is yet known about the relationship between metal speciation and plant response. Here, J-Chess modeling was used to predict U speciation and expo...
Article
Full-text available
Despite active research and the development of target-specific therapies, resistance to standard cytotoxic drugs still represents a challenge in cancer treatment. Many conventional anticancer drugs such as alkylating agents, antimetabolites and topoisomerase inhibitors induce DNA lesions as part of their cytotoxic effect. An important factor that a...
Article
Full-text available
Pseudomonas aeruginosa is a gram-negative bacterium that can inhabit a wide variety of environments and infect different hosts. Human infections by this microbe are nowadays perceived as a major health problem due notably to its multi-resistance. The present dataset provides the first description of P. aeruginosa inner membrane proteome. To achieve...
Article
Full-text available
The development of resistances to conventional anticancer drugs compromises the efficacy of cancer treatments. In the case of DNA-targeting chemotherapeutic agents, cancer cells may display tolerance to the drug-induced DNA lesions and/or enhanced DNA repair. However, the role of DNA damage response (DDR) and DNA repair in this chemoresistance has...
Data
For each cell line, treatments by lesion type were clustered according to their repair response and IC20 (standardized data). Unsupervised hierarchical clustering was performed, using Euclidean dissimilarity measure and average linkage agglomeration method. The cluster dendrogram is displayed together with the agglomeration criteria of average link...
Data
Mechanism of action of the drugs used. (DOC)
Data
IC20 expressed in molar concentration determined by MTS test. (DOC)
Data
Supplementary information on the following: Chemosensitivity assay, modified plasmid microarray, preparation of cell nuclear extracts, DNA excision/synthesis reaction, data normalization, statistical tests to evaluate degree of similarity, data analysis - clustering methods - results display. (DOC)
Data
Analysis of the DNA repair response clustering independently for cells treated with 5-FU (A) and BCNU (B) using the Euclidian dissimilarity. This analysis provided additional data for Fig. 3. A. RPMI8226 remained apart, whereas the two other cell line clusters previously identified clustered as a single significant group. The 5-FU treatment, in par...
Data
Clustering of the DNA repair pathways, represented by the lesions. The 2 sets of experiments (Set_1 (A) and Set_2 (B), noted _1 and _2) were clustered, using the Euclidian dissimilarity. Similar results were obtained when the correlation dissimilarity was considered. Four treated cell lines presenting unquantifiable repair (very low signals) in Set...
Article
Full-text available
Chemically synthesized small interfering RNA (siRNA) is a widespread molecular tool used to knock down genes in mammalian cells. However, designing potent siRNA remains challenging. Among tools predicting siRNA efficacy, very few have been validated on endogenous targets in realistic experimental conditions. We previously described a tool to assist...
Data
Total set of 128 siRNA sequences. Position in full-length transcript are given in bp relative to the 5′ extremity. SS sequence means sense strand siRNA sequence, in 5′ to 3′ orientation. AS sequence means antisense strand siRNA sequence (guide strand), in 5′ to 3′ orientation. DSIR corresponds to the efficacy score computed by the 21-nt linear mode...
Data
Features computed from the total set of siRNA sequences. siRNA_id: siRNA identifier; Target Length: full length in nucleotides; #Exon: number of exons in the target (as documented by the RefSeq division of the NCBI database, release 48); Target Position (in full-length): starting position of the region targeted by the siRNA (antisense strand); DSIR...
Data
Full-text available
Molecular analysis of gene silencing for seven targets. HeLa cells were transfected with siRNA against the target genes indicated, and with two control siRNA, (GFP as a negative control and CSNK2B as a positive control). All siRNA were used at a final concentration of 20 nM, and were transfected using Oligofectamine reagent. Cells were also mock tr...
Data
Full-text available
Target accessibility prediction profile for the eight mRNA targets and 88 corresponding siRNA sequences. Each full-length sequence target was submitted to the SFold server (siRNA section - http://sfold.wadsworth.org/cgi-bin/sirna.pl). The target accessibility probability profile for each site targeted by the siRNA is displayed. Blue circle highligh...
Data
qPCR primer sequences used in this study. (XLS)
Article
Full-text available
Epithelial-to-mesenchymal transition (EMT) is closely linked to conversion of early-stage tumours into invasive malignancies. Many signalling pathways are involved in EMT, but the key regulatory kinases in this important process have not been clearly identified. Protein kinase CK2 is a multi-subunit protein kinase, which, when overexpressed, has be...
Article
The cellular slime mold Dictyostelium discoideum is a soil-living eukaryote, which feeds on microorganisms engulfed by phagocytosis. Axenic laboratory strains have been produced that are able to use liquid growth medium internalized by macropinocytosis as the source of food. To better define the macropinocytosis process, we established the inventor...
Chapter
Full-text available
With the evolution of high-throughput techniques, performing organism-wide analyses of gene expression, protein content and metabolite profile is becoming easier. This new era of biology opens the way for incredibly promising advances but also extremely challenging difficulties in the aim of integrating these datasets into biologically relevant mod...
Conference Paper
Full-text available
The rapid accumulation of microarray data is promising for discovering regulatory relationship from high-throughput gene expression data. One of the most com-mon ways is to compute co-expression clusters to find groups of co-expressed genes that are likely to be con-trolled by the same set of transcription factors. However such approach may lead to...
Data
Sequence similarities for for the FPI encoded proteins. Details of sequence similarities detected for the FPI encoded proteins against the NCBI non-redundant databank and the Conserved Domain Database.
Data
Full-text available
Mean linkage hierarchical clustering of the 13 trees obtained with the most conserved COG groups. Result of the mean linkage hierarchical clustering applied to the split distances computed with TOPD/FMTS [23] on the 13 trees obtained with the most conserved COG groups. Red colours indicate value higher than the mean. Blue colours reveal value lower...
Data
List of bacterial species containing multiple T6SS gene clusters. Table containing the numbers of T6SS gene clusters predicted in species encoding more than one T6SS.
Data
Full-text available
Relationship between the inferred phylogeny for the T6SS loci and their VgrG content. Each row represents a T6SS locus. Boxes represent VgrG proteins. Inside the boxes, each rectangle indicates a COG hit. Colours indicate the nature of the COG hit: COG3501 (purple), COG4253 (blue) or other COGs (green). VgrG that contain C-terminal repeats are stri...
Data
Full-text available
Relationship between phylogeny and T6SS gene content. Rows represent T6SS loci and columns represent protein functional classes (based on COG assignment and TribeMCL protein clusters). The tree on the left is the consensus phylogenetic tree (super-tree, see Materials and Methods §5, manually rooted) whereas the two upper dendrograms represent a hie...
Data
Full-text available
Repeats identified in VgrG C-terminal regions. Proteic sequences of the VgrG proteins and the repeats identified in their C-terminal regions.