A5103237769- Gene expression and cancer classification
- Cellular Mechanics and Interactions
- Plant Disease Resistance and Genetics
- Molecular Biology Techniques and Applications
- Microtubule and mitosis dynamics
- Bioinformatics and Genomic Networks
- Cell Adhesion Molecules Research
- Statistical Methods and Inference
- Advanced Clustering Algorithms Research
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Bayesian Methods and Mixture Models
- Cancer-related Molecular Pathways
- Cancer Treatment and Pharmacology
- Advanced Breast Cancer Therapies
- Genetic Associations and Epidemiology
- Plant Stress Responses and Tolerance
- RNA modifications and cancer
- RNA Interference and Gene Delivery
- Genomic variations and chromosomal abnormalities
- Tissue Engineering and Regenerative Medicine
- Photosynthetic Processes and Mechanisms
- Data Mining Algorithms and Applications
- RNA and protein synthesis mechanisms
- Plant Micronutrient Interactions and Effects
Institut Curie
2008-2023
Centre National de la Recherche Scientifique
2014-2023
Université Paris-Saclay
2017-2023
Institut des Sciences des Plantes de Paris Saclay
2014-2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2014-2023
Université Paris Cité
2016-2023
Université d'Évry Val-d'Essonne
2014-2023
École Nationale Supérieure d’Informatique pour l’Industrie et l’Entreprise
2017-2023
Laboratoire de Mathématiques
2016-2023
Laboratoire de Mathématiques et Modélisation d'Évry
2016-2023
Research Article17 June 2010Open Access Oxidative stress promotes myofibroblast differentiation and tumour spreading Aurore Toullec Laboratory of strem cancer, Inserm U830, Institut Curie, 75248 Paris, Cedex, France Search for more papers by this author Damien Gerald These authors contributed equally to study. Gilles Despouy Brigitte Bourachot Melissa Cardon Sylvain Lefort Marion Richardson Département de Transfert, Laboratoire signalisation, Guillem Rigaill Maria-Carla Parrini Inserm,...
Many common approaches to detecting changepoints, for example based on statistical criteria such as penalised likelihood or minimum description length, can be formulated in terms of minimising a cost over segmentations. We focus class dynamic programming algorithms that solve the resulting minimisation problem exactly, and thus find optimal segmentation under given criteria. The standard implementation these methods have computational scales at least quadratically length time-series....
Abstract Introduction Basal-like carcinomas (BLCs) and human epidermal growth factor receptor 2 overexpressing (HER2+) are the subgroups of breast cancers that have most aggressive clinical behaviour. In contrast to HER2+ carcinomas, no targeted therapy is currently available for treatment patients with BLCs. order discover potential therapeutic targets, we aimed deregulated signalling pathways in Methods this study, focused on oncogenic phosphatidylinositol 3-kinase (PI3K) pathway 13 BLCs,...
Breast cancers are composed of molecularly distinct subtypes with different clinical outcomes and responses to therapy. To discover potential therapeutic targets for the poor prognosis-associated triple-negative breast cancer (TNBC), gene expression profiling was carried out on a cohort 130 samples. Polo-like kinase 1 (PLK1) found be significantly overexpressed in TNBC compared other subtypes. High PLK1 confirmed by reverse phase protein tissue microarrays. In cell lines, RNAi-mediated...
Triple-negative breast cancer (TNBC) represents a subgroup of cancers (BC) associated with the most aggressive clinical behavior. No targeted therapy is currently available for treatment patients TNBC. In order to discover potential therapeutic targets, we searched protein kinases that are overexpressed in human TNBC biopsies and whose silencing cell lines causes death. A cohort including BC obtained at Institut Curie as well normal tissues has been analyzed gene-expression level. The data...
Many traditional methods for identifying changepoints can struggle in the presence of outliers, or when noise is heavy-tailed. Often they will infer additional to fit outliers. To overcome this problem, data often needs be preprocessed remove though difficult applications where analyzed online. We present an approach changepoint detection that robust The idea adapt existing penalized cost approaches detecting changes so use loss functions are less sensitive argue bounded, such as classical...
RNA editing is converting hundreds of cytosines into uridines during organelle gene expression land plants. The pentatricopeptide repeat (PPR) proteins are at the core this posttranscriptional modification. Even if a PPR protein defines site, DYW domain same or another believed to catalyze deamination. To give insight editosome, we performed tandem affinity purification plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) factor. Two proteins, dually targeted mitochondria and chloroplasts, were...
Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are very frequent type structural variant. However, their direct impact on gene content expression had not been determined. Here, we used tissue-specific mRNA-Seq dataset to measure consequences (HE) in Brassica napus, representative allotetraploid crop. We demonstrate that changes proportional change copy...
The canonical Wnt/β-catenin pathway is activated in triple-negative breast cancer (TNBC). activation of this leads to the expression specific target genes depending on cell/tissue context. Here, we analyzed transcriptome two different TNBC cell lines define a comprehensive list Wnt genes. treatment cells with Wnt3a for 6h up-regulated (fold change > 1.3) 59 MDA-MB-468 and 241 HCC38 cells. Thirty were common both lines. Beta-catenin may also be transcriptional repressor found that 18 166...
Abstract TNBC is a highly heterogeneous and aggressive breast cancer subtype associated with high relapse rates, for which no targeted therapy yet exists. Protein arginine methyltransferase 5 (PRMT5), an enzyme catalyzes the methylation of arginines on histone non‐histone proteins, has recently emerged as putative target therapy. Potent specific PRMT5 inhibitors have been developed, but therapeutic efficacy targeting in not demonstrated. Here, we examine expression human cohort obtained from...
Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most them based on similar frameworks after normalization, differing primarily in choice data distribution, mean and variance estimation strategy filtering. We propose an evaluation impact these choices when few biological replicates through use synthetic sets. This framework is real sets allows exploration various scenarios proportion non-differentially...
The Anthropocene epoch is associated with the spreading of metals in environment increasing oxidative and genotoxic stress on organisms. Interestingly, c. 520 plant species growing metalliferous soils acquired capacity to accumulate tolerate a tremendous amount nickel their shoots. wide phylogenetic distribution these suggests that hyperaccumulation evolved multiple times independently. However, exact nature mechanisms whether they have been recruited convergently distant not known. To...
In recent years, there have been a large number of proposed approaches to detecting changes in mean. A natural question for an analyst is which method most appropriate their applications. Answering this difficult because current empirical studies often give conflicting conclusions. This paper aims show the similarities and differences between different changepoint methods. We highlight that are two aspects estimating changepoints: locations, comparisons should separately evaluate these...
Whilst there are a plethora of algorithms for detecting changes in mean univariate time-series, almost all struggle real applications where is autocorrelated noise or the fluctuates locally between abrupt that one wishes to detect. In these cases, default implementations, which often based on assumptions constant and independent noise, can lead substantial over-estimation number changes. We propose principled approach detect such models local fluctuations as random walk process via an AR(1)...
Summary Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype‐by‐environment interactions shape phenotypes. Here, we analyzed impact water deficit onto levels tomato at genome‐wide scale. We sequenced transcriptome growing leaves and fruit pericarps cell expansion stage a cherry large fruited accession their F 1 hybrid grown under two watering regimes. Gene were steadily affected by genotype regime. Whereas phenotypes...
// Sylvie Maubant 1, * , Tania Tahtouh Amélie Brisson 1 Virginie Maire Fariba Némati 2 Bruno Tesson 3 Mengliang Ye Guillem Rigaill 4, 5 Maïté Noizet Aurélie Dumont David Gentien 6 Bérengère Marty-Prouvost Leanne de Koning 7 Sardar Faisal Mahmood Didier Decaudin Francisco Cruzalegui 8 Gordon C. Tucker Sergio Roman-Roman 9 and Thierry Dubois Institut Curie, PSL Research University, Translational Department, Breast Cancer Biology Group, Paris, France Preclinical Investigation Laboratory, INSERM...
Abstract Background Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix high-resolution, locus-level measurements. An intuitive way doing this is to perform modified Hierarchical Agglomerative Clustering (HAC), where only adjacent clusters (according ordering positions within chromosome) allowed be merged. But major practical drawback method its...
Traditional methods that aim to identify biomarkers distinguish between two groups, like Significance Analysis of Microarrays or the t-test, perform optimally when such show homogeneous behavior within each group and differential groups. However, in many applications, this is not case. Instead, a subgroup samples one shows with respect all other samples. To successfully detect markers showing imbalanced patterns signal, different approach required. We propose novel method, specifically...
Abstract Motivation: Affymetrix SNP arrays can be used to determine the DNA copy number measurement of 11 000–500 000 SNPs along genome. Their high density facilitates precise localization genomic alterations and makes them a powerful tool for studies cancers polymorphism. Like other microarray technologies it is influenced by non-relevant sources variation, requiring correction. Moreover, amplitude variation induced effects similar or greater than biologically relevant effect (i.e. true...
Higher plants have to cope with increasing concentrations of pollutants both natural and anthropogenic origin. Given their capacity concentrate metabolize various compounds including pollutants, can be used treat environmental problems - a process called phytoremediation. However, the molecular mechanisms underlying stabilization, extraction, accumulation partial or complete degradation by remain poorly understood.Here, we determined events involved in early plant response phenanthrene, as...
We describe a new algorithm and R package for peak detection in genomic data sets using constrained changepoint models. These detect changes from background to regions by imposing the constraint that mean should alternately increase then decrease. An existing this problem exists, gives state-of-the-art accuracy results, but it is computationally expensive when number of large. propose dynamic programming jointly estimates peaks their locations minimizing cost function which consists fitting...
Abstract Triple‐negative breast cancer (TNBC) is the subtype with worst prognosis. New treatments improving survival of TNBC patients are, therefore, urgently required. We performed a transcriptome microarray analysis to identify new treatment targets for TNBC. found that low‐density lipoprotein receptor‐related protein 8 (LRP8) was more strongly expressed in estrogen receptor‐negative tumors, including TNBCs and those overexpressing HER2, than luminal tumors normal tissues. LRP8 depletion...