Mathieu Dubois

ORCID: 0000-0003-1490-7271
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Research Areas
  • Communism, Protests, Social Movements
  • French Historical and Cultural Studies
  • Political and Social Issues
  • European history and politics
  • Historical Studies and Socio-cultural Analysis
  • Social Policies and Family
  • European Socioeconomic and Political Studies
  • Sparse and Compressive Sensing Techniques
  • Embedded Systems Design Techniques
  • Medical Image Segmentation Techniques
  • Genomics and Phylogenetic Studies
  • Advanced Image and Video Retrieval Techniques
  • Historical Geopolitical and Social Dynamics
  • French Urban and Social Studies
  • Simulation Techniques and Applications
  • Robotics and Sensor-Based Localization
  • Image Retrieval and Classification Techniques
  • Photoacoustic and Ultrasonic Imaging
  • Parallel Computing and Optimization Techniques
  • Microbial Metabolic Engineering and Bioproduction
  • Radiomics and Machine Learning in Medical Imaging
  • Social Sciences and Governance
  • Bioinformatics and Genomic Networks
  • Advanced MRI Techniques and Applications
  • European Political History Analysis

Sciences Po Rennes
2014-2025

Institut d'Etudes Politiques de Paris
2014-2025

Arènes: politique, santé publique, environnement, médias
2025

Fondation de Rothschild
2024

Sorbonne - Identités, Relations Internationales et Civilisations de l’Europe
2013-2023

Nantes Université
2023

Université catholique de l'ouest
2022

Centre National de la Recherche Scientifique
2009-2019

CEA Paris-Saclay
2016-2019

Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2007-2019

Abstract Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount new information that completely transforms our understanding thousands microbial species. However, despite development powerful bioinformatics approaches, full interpretation content these genomes remains difficult task. Launched in 2005, MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous provides analysis for prokaryotic...

10.1093/nar/gkz926 article EN cc-by Nucleic Acids Research 2019-10-08

The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms occurrence a given species. These usually lack multivariate statistical models infer the partitions optimal number classes don't account genome organization. We introduce graph structure model pangenomes which nodes represent edges genomic neighborhood. Our method, named PPanGGOLiN, using an Expectation-Maximization algorithm based on Bernoulli Mixture...

10.1371/journal.pcbi.1007732 article EN cc-by PLoS Computational Biology 2020-03-19

Plasmid prediction may be of great interest when studying bacteria medical importance such as Enterobacteriaceae well Staphylococcus aureus or Enterococcus . Indeed, many resistance and virulence genes are located on replicons with major impact in terms pathogenicity spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported particular for some extended-spectrum beta-lactamase- carbapenemase-producing Several tools now available to explore the ‘plasmidome’ from...

10.1099/mgen.0.000211 article EN cc-by Microbial Genomics 2018-09-01

Objective: In CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy), white matter hyperintensities (WMH) are considered to result from hypoperfusion. We hypothesized that in fact the burden of WMH results combination several regional populations different mechanisms clinical consequences. Methods: To identify populations, we used a 4-step approach. First, an unsupervised principal component algorithm determine, without priori knowledge, main...

10.3389/fneur.2018.00526 article EN cc-by Frontiers in Neurology 2018-07-10

In order to increase the sensitivity of liquid chromatography/mass spectrometry (LC/MS) assays recombinant proteins for pharmacokinetics studies, we have developed an immuno-mass assay EPI-hNE4, a 6237 Da protein currently respiratory distress syndromes. After immunocapture analyte in human plasma with magnetic beads coated anti-EPI-hNE4 antibodies, intact was eluted and separated reversed-phase LC then analysed by tandem mass (MS/MS) selected reaction monitoring (SRM) mode. The problem...

10.1002/rcm.2844 article EN Rapid Communications in Mass Spectrometry 2007-01-03

Principal component analysis (PCA) is an exploratory tool widely used in data to uncover the dominant patterns of variability within a population. Despite its ability represent set low-dimensional space, PCA's interpretability remains limited. Indeed, components produced by PCA are often noisy or exhibit no visually meaningful patterns. Furthermore, fact that usually non-sparse may also impede interpretation, unless arbitrary thresholding applied. However, neuroimaging, it essential...

10.1109/tmi.2017.2749140 article EN IEEE Transactions on Medical Imaging 2017-09-04

The use of machine-learning in neuroimaging offers new perspectives early diagnosis and prognosis brain diseases. Although such multivariate methods can capture complex relationships the data, traditional approaches provide irregular (ℓ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> penalty) or scattered (£1 predictive pattern with a very limited relevance. A penalty like Total Variation (TV) that exploits natural 3D structure images...

10.1109/prni.2014.6858517 article EN International Workshop on Pattern Recognition in NeuroImaging 2014-06-01

article Free Access Share on A logic of action for supporting goal-oriented elaborations requirements Author: M. S. Dubois Philips Research Laboratory, 2, Avenue van Becelaere, B-1170 Brussels (Belgium) (Belgium)View Profile Authors Info & Claims ACM SIGSOFT Software Engineering NotesVolume 14Issue 3May 1989 pp 160–168https://doi.org/10.1145/75200.75225Published:01 April 1989Publication History 17citation290DownloadsMetricsTotal Citations17Total Downloads290Last 12 Months9Last 6 weeks0 Get...

10.1145/75199.75225 article EN 1989-01-01

In a previous paper (Rudolph & Destexhe, 2006), we proposed various models, the gIF neuron of analytical integrate-and-fire (IF) neurons with conductance-based (COBA) dynamics for use in event-driven simulations. These models are based on an approximation differential equation describing IF exponential synaptic conductances and were successfully tested respect to their response random oscillating inputs. Because they mathematically simple, best suited fast simulation strategies. However,...

10.1162/neco_a_00278 article EN Neural Computation 2012-02-24

Predictive models can be used on high-dimensional brain images to decode cognitive states or diagnosis/prognosis of a clinical condition/evolution. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk overfitting model while providing interpretable neuroimaging signatures by forcing solution adhere domain-specific constraints. Total variation (TV) is promising candidate for penalization: it enforces spatial smoothness segmenting...

10.1109/tmi.2018.2829802 article EN IEEE Transactions on Medical Imaging 2018-04-24

Abstract The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms occurrence a given species. These usually lack multivariate statistical models infer the partitions optimal number classes don’t account genome organization. We introduce graph structure model pangenomes which nodes represent edges genomic neighborhood. Our method, named PPanGGOLiN, using an Expectation-Maximization algorithm based on...

10.1101/836239 preprint EN cc-by bioRxiv (Cold Spring Harbor Laboratory) 2019-11-09

10.1016/s1877-1203(12)70238-0 article FR Revue des Maladies Respiratoires Actualités 2012-09-01

Ultrasound images appearance is characterized by speckle, shadows, signal dropout and low contrast which make them really difficult to process leads a very poor noise ratio. Therefore, for main imaging applications, denoising step necessary apply successfully medical algorithms on such images. However, due speckle statistics, enhancing edges these without inducing additional blurring real challenging problem usual filters often fail. To deal with problems, large number of papers are working...

10.1117/12.844388 article EN Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE 2010-03-04

This paper presents an original approach for visual place recognition and categorization. The simple idea behind our model is that, a mobile robot, use of the previous frames, not only one, can ease recognition. We present algorithm integrating answers from different images. In this perspective, scenes are encoded thanks to global signature (the context scene) then classified in unsupervised way with Self-Organizing Map. prototypes form dictionary which roughly describe environment. A be...

10.5220/0003353202860295 preprint EN cc-by-nc-nd 2011-01-01

In this paper we will present a detailed study of implementing double-precision matrix-matrix multiplication (DGEMM) utilizing the Intel Xeon Phi Coprocessor. We discuss DGEMM algorithm implementation running natively on coprocessor, minimizing communication with host CPU. run across range matrix sizes as well using Math Kernel Library. Our optimizations were designed to support maximal reuse on-die cache, which significantly reduces transfer from GDDR.  Finally analyze improvement classic...

10.4304/jcp.9.7.1566-1571 article EN Journal of Computers 2014-06-23

Platypnea–orthodeoxia syndrome ( POS ) is a rare clinical disorder characterized by dyspnea caused the upright position and relieved at recumbent position. Few cases of stroke were reported in literature, association between with evidence patent foramen ovale PFO rare. Stroke may occur patients cardiac shunt who undergo contrast echocardiography. We present patient experienced transitory ischemic attack TIA most likely injection agitated saline microbubbles during screen for . No case report...

10.1111/echo.12970 article EN Echocardiography 2015-06-24

Social support, coping and psychological health after a flood Two years serious flooding, study was conducted involving 177 disaster victims. This article presents the results of analyses aiming to identify principal factors associated with post-disaster problems by examining mediating or moderating influences social support adjustment strategies in stressor-health link. The show, within variables studied, that there are very few significant differences between men women; however, women did...

10.3406/sosan.2005.1648 article EN Sciences sociales et santé 2005-01-01
Oscar Estéban Christopher J. Markiewicz Hans J. Johnson Erik Ziegler Alexandre Manhães-Savio and 95 more Dorota Jarecka Christopher Burns David Gage Ellis Carlo Hamalainen Michael Notter Benjamin Yvernault Taylor Salo Michael Waskom Mathias Goncalves Kesshi Jordan Jason H. Wong Blake E Dewey Cindee Madison Erin Benderoff Daniel J. Clark Fred Loney Dav Clark Anisha Keshavan Michael Joseph Dylan M. Nielson Michael Dayan Marc Modat Alexandre Gramfort Salma Bougacha Basile Pinsard Shoshana Berleant Horea Christian Ariel Rokem Matteo Visconti di Oleggio Castello Yaroslav O. Halchenko Jakub Kaczmarzyk Gaël Varoquaux Rastko Ćirić Brendan Moloney Elizabeth DuPré Serge Koudoro Michael G. Clark Ben Cipollini Demián Wassermann Jérémy Guillon Ross D. Markello Michael Hanke Colin R. Buchanan Rosalia Tungaraza Ashley Gillman Wolfgang M. Pauli Gilles de Hollander Sharad Sikka Jessica Forbes David Mordom Shariq Iqbal Matteo Flavio Mancini Ian B. Malone Mathieu Dubois Yannick Schwartz Caroline Frohlich Alejandro Tabas David Welch Adam Richie-Halford Steven Tilley Aimi Watanabe B. Nolan Nichols Julia M. Huntenburg Arman Eshaghi Daniel Ginsburg Alexander Schaefer Katherine L. Bottenhorn Chad Cumba Benjamin Acland Anibal Sólon Heinsfeld Erik Kastman James D. Kent Jens Kleesiek Ali Ghayoor Drew Erickson Steven Giavasis Alejandro de la Vega Franz Liem René Küttner Martin Felipe Perez-Guevara John A. Lee Jarrod Millman Jeff Lai Dale Zhou Christian Haselgrove Daniel Glen Anna Doll Mandy Renfro Carlos Gabriel Piffaretti Correa Siqi Liu Leonie Lampe Xiangzhen Kong Michael Hallquist Sin Kim Ari E. Kahn

10.5281/zenodo.3668316 article PL 2020-02-14
Oscar Estéban Christopher J. Markiewicz Christopher Burns Mathias Goncalves Dorota Jarecka and 95 more Erik Ziegler Shoshana Berleant David Gage Ellis Basile Pinsard Cindee Madison Michael Waskom Michael Notter Daniel J. Clark Alexandre Manhães-Savio Dav Clark Kesshi Jordan Michael Dayan Yaroslav O. Halchenko Fred Loney Taylor Salo Blake E Dewey Hans J. Johnson Salma Bougacha Anisha Keshavan Benjamin Yvernault Carlo Hamalainen Horea Christian Rastko Ćirić Mathieu Dubois Michael Joseph Ben Cipollini Steven Tilley Matteo Visconti di Oleggio Castello Jason H. Wong Alejandro de la Vega Jakub Kaczmarzyk Julia M. Huntenburg Michael G. Clark Erin Benderoff Drew Erickson James D. Kent Michael Hanke Steven Giavasis Brendan Moloney B. Nolan Nichols Rosalia Tungaraza Caroline Frohlich Demián Wassermann Gilles de Hollander Arman Eshaghi Jarrod Millman Matteo Flavio Mancini Dylan M. Nielson Gaël Varoquaux Aimi Watanabe David Mordom Jérémy Guillon Serge Koudoro Andrey Chetverikov Ariel Rokem Benjamin Acland Jessica Forbes Ross D. Markello Ashley Gillman Xiangzhen Kong Daniel Geisler Salvatore John Alexandre Gramfort Anna Doll Colin R. Buchanan Elizabeth DuPré Siqi Liu Alexander Schaefer Jens Kleesiek Sharad Sikka Yannick Schwartz John A. Lee Aaron Mattfeld Adam Richie-Halford Franz Liem Martin Felipe Perez-Guevara Anibal Sólon Heinsfeld Christian Haselgrove Joke Durnez Leonie Lampe Russell A. Poldrack Tristan Glatard Alejandro Tabas Chad Cumba Fernando Pérez‐García Ross Blair Shariq Iqbal David Welch William Triplett Ali Ghayoor R. Cameron Craddock Carlos Gabriel Piffaretti Correa Dimitri Papadopoulos Orfanos Jörg Stadler Joshua Warner

10.5281/zenodo.4035081 article PL 2020-09-17

Interconnecting modules in a SoC platform requires compatibility. Several solutions are available, but they either lack the necessary throughput or flexibility. This paper proposes an interconnection architecture for flexible on-chip high-performance communication medium that can provide variable bandwidth. It is based on AHB AMBA bus. The proposed has been implemented Seamless environment and laid out using 0.18 /spl mu/m CMOS with Cadence tools to validate concept.

10.1109/icm.2003.238564 article EN 2003-01-01

Heterogeneous systems design requires simulating models using different simulators. In this paper, we propose new approaches for interconnecting simulators based on interoperability and managed code. Managed code has many introspection safety mechanisms. We demonstrate that SystemC can be encapsulated in a order to interoperate with environments such as Esys.Net. have also explored mechanisms where Esys.Net, Matlab/Simulink co-simulate. Interoperability between is implemented COM, TCP/IP,...

10.1109/icecs.2005.4633510 article EN 2005-12-01

Platform-based design requires flexibility and compatibility between components in order to derivative applications without changing hardware or software. Several solutions are available, but they lack either the necessary throughput flexibility. The paper proposes a generic multi-frequency interconnection infrastructure module that facilitates development of flexible on-chip high-performance buses. It is based on AMBA high-speed bus (AHB). proposed architecture has been implemented with HDL...

10.1109/secon.2005.1423208 article EN 2005-04-25
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