Papers by jonathan vincent
Bioinformatics
WIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accu... more WIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp-long phage contigs. Over the best current tool, WisH shows much improved accuracy on phage sequences of a few kbp length and runs hundreds of times faster, making it suited for metagenomics studies.
ABSTRACT In cereals seed, the accumulation of storage compounds is tightly regulated at the trans... more ABSTRACT In cereals seed, the accumulation of storage compounds is tightly regulated at the transcriptional level providing interesting models for the analysis of regulatory networks. This accumulation is programmed but also influenced both by nitrogen and sulfur availability. Study of the global transcriptional time and/or tissue specific programming as well as regulation arising from various nitrogen and sulfur supply levels provides valuable information toward nutritional value improvement. In this work, three distinct microarray experiments were carried out on wheat (Triticum aestivum L.) to measure the expression of 40 642 genes, including 2 891 transcription factors (TFs) in 98 conditions of time, tissue and nutrition. An extensive comparative transcriptomic analysis was thereby carried out to observe spatial and time-specific gene expression. Focus was made on TFs and an innovative network inference method was applied to highlight those implied in this regulation. It was observed that more than 60% of the expressed genes are expressed in at least 2 different tissues and are therefore not tissue-specific. Out of all the expressed genes, 25% were found to be expressed in all the tissues and at all the stages of development while 19% of the expressed TFs showed such aspecific expression. In all five tissues and at all stages, the proportion of TFs among expressed genes was never significantly different, varying from 6.9 to 9%. Classification of the wheat tissues performed via a dimensional reduction technique showed differences in the transcriptome between tissues rather than between stages, and suggest that plant tissue identity is directly linked to their respective transcriptome. 70 TFs expressed specifically in the seed identified in our study, may be key regulators of seed development. They represent 3% of TFs expressed in seed. Similarly to what is observed in barley, the most represented families in seed development are the NAC, MYB, bZIP, AP2-EREBP and Zinc finger. In addition, the TF specifically expressed during the grain filling have been identified and belong to families: Zinc finger, MYB, bZIP and NAM, suggesting a conservation of regulatory mechanisms between the two species. These results are consistent with studies showing that wheat and barley transcriptome share great similarities. A restricted number of TFs tend to be involved in the response to nitrogen and sulfur nutrition. Networks inferred to highlight putative interactions between these transcription factors provides a first insight into gene regulatory networks involved in the response to nitrogen and sulfur availability. At this point, this study constitutes a major step towards the identification of gene regulatory networks involved in major biological processes in wheat, and selection of candidates involved in the accumulation of storage compounds. An additional investigation is underway to integrate proteomics and metabolomics data acquired and build global networks regulating storage compounds accumulation in response to nitrogen and sulfur in wheat seed.
In cereals seed, the accumulation of storage compounds is tightly regulated at the transcriptiona... more In cereals seed, the accumulation of storage compounds is tightly regulated at the transcriptional level providing interesting models for the analysis of regulatory networks. This accumulation is programmed but also influenced both by nitrogen and sulfur availability. Study of the global transcriptional time and/or tissue specific programming as well as regulation arising from various nitrogen and sulfur supply levels provides valuable information toward nutritional value improvement. In this work, three distinct microarray experiments were carried out on wheat (Triticum aestivum L.) to measure the expression of 40 642 genes, including 2 891 transcription factors (TFs) in 98 conditions of time, tissue and nutrition. An extensive comparative transcriptomic analysis was thereby carried out to observe spatial and time-specific gene expression. Focus was made on TFs and an innovative network inference method was applied to highlight those implied in this regulation. It was observed that...
2020 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)
In dynamic environments, performance of visual SLAM techniques can be impaired by visual features... more In dynamic environments, performance of visual SLAM techniques can be impaired by visual features taken from moving objects. One solution is to identify those objects so that their visual features can be removed for localization and mapping. This paper presents a simple and fast pipeline that uses deep neural networks, extended Kalman filters and visual SLAM to improve both localization and mapping in dynamic environments (around 14 fps on a GTX 1080). Results on the dynamic sequences from the TUM dataset using RTAB-Map as visual SLAM suggest that the approach achieves similar localization performance compared to other state-of-the-art methods, while also providing the position of the tracked dynamic objects, a 3D map free of those dynamic objects, better loop closure detection with the whole pipeline able to run on a robot moving at moderate speed.
Http Www Theses Fr, Sep 10, 2014
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The development of–omics methods has been followed by an explosion of the amount of data produced... more The development of–omics methods has been followed by an explosion of the amount of data produced in functional genomics research projects. Retrieving biologically relevant information and knowledge on molecular regulations from such massive amount ...
Frontiers in Plant Science, 2014
The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in whe... more The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression. Citation: Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Michard R and Martre P (2014) Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits. Front. Plant Sci. 5:621.
PLOS ONE, 2015
With the increasing amount of -omics data available, a particular effort has to be made to provid... more With the increasing amount of -omics data available, a particular effort has to be made to provide suitable analysis tools. A major challenge is that of unraveling the molecular regulatory networks from massive and heterogeneous datasets. Here we describe RulNet, a weboriented platform dedicated to the inference and analysis of regulatory networks from qualitative and quantitative -omics data by means of rule discovery. Queries for rule discovery can be written in an extended form of the RQL query language, which has a syntax similar to SQL. RulNet also offers users interactive features that progressively adjust and refine the inferred networks. In this paper, we present a functional characterization of RulNet and compare inferred networks with correlation-based approaches. The performance of RulNet has been evaluated using the three benchmark datasets used for the transcriptional network inference challenge DREAM5. Overall, RulNet performed as well as the best methods that participated in this challenge and it was shown to behave more consistently when compared across the three datasets. Finally, we assessed the suitability of RulNet to analyze experimental -omics data and to infer regulatory networks involved in the response to nitrogen and sulfur supply in wheat (Triticum aestivum L.) grains. The results highlight putative actors governing the response to nitrogen and sulfur supply in wheat grains. We evaluate the main characteristics and features of RulNet as an all-in-one solution for RN inference, visualization and editing. Using simple yet powerful RulNet queries allowed RNs involved in the adaptation of wheat grain to N and S supply to be discovered. We demonstrate the effectiveness and suitability of RulNet as a platform for the analysis of RNs involving different types of -omics data. The results are promising since they are consistent with what was previously established by the scientific community.
The Plant Journal, 2015
Wheat (Triticum aestivum L.) grain storage proteins (GSPs) are major determinants of flour end-us... more Wheat (Triticum aestivum L.) grain storage proteins (GSPs) are major determinants of flour end-use value. Biological and molecular mechanisms underlying the developmental and nutritional determination of GSP accumulation in cereals are as yet poorly understood. Here we timed the accumulation of GSPs during wheat grain maturation relative to changes in metabolite and transcript pools in different conditions of nitrogen (N) and sulfur (S) availability. We found that the N/S supply ratio modulated the duration of accumulation of S-rich GSPs and the rate of accumulation of S-poor GSPs. These changes are likely to be the result of distinct relationships between N and S allocation, depending on the S content of the GSP. Most developmental and nutritional modifications in GSP synthesis correlated with the abundance of structural gene transcripts. Changes in the expression of transport and metabolism genes altered the concentrations of several free amino acids under variable conditions of N and S supply, and these amino acids seem to be essential in determining GSP expression. The comprehensive data set generated and analyzed here provides insights that will be useful in adapting fertilizer use to variable N and S supply, or for breeding new cultivars with balanced and robust GSP composition.
Database, 2013
Citation details: Vincent,J., Dai,Z.W., Ravel,C. et al. dbWFA: a web-based database for functiona... more Citation details: Vincent,J., Dai,Z.W., Ravel,C. et al. dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts.
In cereals seed, the accumulation of storage compounds is tightly regulated at the transcriptiona... more In cereals seed, the accumulation of storage compounds is tightly regulated at the transcriptional level providing interesting models for the analysis of regulatory networks. This accumulation is programmed but also influenced both by nitrogen and sulfur availability. Study of the global transcriptional time and/or tissue specific programming as well as regulation arising from various nitrogen and sulfur supply levels provides valuable information toward nutritional value improvement. In this work, three distinct microarray experiments were carried out on wheat (Triticum aestivum L.) to measure the expression of 40 642 genes, including 2 891 transcription factors (TFs) in 98 conditions of time, tissue and nutrition. An extensive comparative transcriptomic analysis was thereby carried out to observe spatial and time-specific gene expression. Focus was made on TFs and an innovative network inference method was applied to highlight those implied in this regulation. It was observed that...
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Papers by jonathan vincent