Expertise

Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise

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Searched keyword : Illumina HiSeq

Related people (6)

Thomas COKELAER

Group : DETACHED - Detached : Biomics

I joined the Bioinformatics and Biostatistics Hub at Institut Pasteur in 2016 where I am currently developing pipelines related to NGS for the Biomics Pôle. I have an interdisciplinary research experience: after a PhD in Astronomy (gravitational wave data analysis), I joined several research institute to work in the fields of plant modelling (INRIA, Montpellier, 2008-2011), System Biology — in particular logical modelling (EMBL-EBI Cambridge, U.K., 2011-2015), and drug discovery (Sanger Institute, Cambridge, U.K.), 2015). On a daily basis, I use data analysis and machine learning techniques within high-quality software to tackle scientific problems.

Keywords
Algorithmics Data management Data Visualization Genome assembly Genomics Machine learning Modeling Scientific computing Databases and ontologies Sofware development and engineering Data and text mining Illumina HiSeq Graph theory and analysis Illumina MiSeq
Organisms

Projects (2)

Marie-Agnès DILLIES

Group : HEAD - Hub Core

I obtained an engineering degree in Biomedical engineering from Université de Technologie de Compiègne (UTC) in 1989, a master degree in Control of Complex Systems from UTC in 1990, a PhD in Control of Complex Systems from UTC in 1993, a University Degree in Human Genetics from The University of Rennes 1 in 2001 and a master degree in Functional Genomics from University Paris Diderot (Paris 7) in 2002. I worked as a statistician at the Transcriptome and Epigenome Platform from 2002 to 2017, where I was responsible for the statistical analyses of the data and had an important training activity (on the campus and outside). Since 2015 I have been co-head of the Bioinformatics and Biostatistics Hub within the Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI). I am co-director of the Pasteur course Introduction to Data Analysis and co-organiser of the sincellTE summer school (a school dedicated to single cell transcriptome and epigenome data analysis). I am also co-managing the StatOmique group which gathers more than 60 statisticians from France.

Keywords
RNA-seq Statistical inference Transcriptomics Biostatistics Application of mathematics in sciences Exploratory data analysis Illumina HiSeq Statistical experiment design Sequencing
Organisms

Projects (3)

Amine GHOZLANE

Group : SINGLE - Hub Core

After a PhD in informatics on graph analysis (metabolic networks and sRNA-mRNA interaction graphs) at the LaBRI (Université de Bordeaux), I joined the DSIMB team (INTS) for a post-doc on structural modeling. Then, I performed a second post-doc at Metagenopolis – INRA Jouy-en-Josas, where I was initiated to the analysis of metagenomic data. I was recruited at the HUB in 2015, and since I pursue the development of methods dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, the statistics, the protein structural modeling and the graph analysis.

Keywords
Algorithmics Clustering Genome assembly Genomics Metabolomics Modeling Non coding RNA Sequence analysis Structural bioinformatics Targeted metagenomics Database Genome analysis Biostatistics Program development Scientific computing Databases and ontologies Exploratory data analysis Data and text mining Illumina HiSeq Comparative metagenomics Read mapping Illumina MiSeq Sequence homology analysis Gene prediction Multidimensional data analysis Sequencing Shotgun metagenomics
Organisms

Projects (26)

Bernd JAGLA

Group : PLATEFORM - Detached : Biomarker Discovery

Bernd Jagla received his PhD in bioinformatics (department of Biology, Chemistry, and Parmacy) from the Free University in Berlin, Germany in 1999. Before joining the Institut Pasteur, he worked for almost ten years in New York City, including as an associate research scientist in the Joint Centers for System Biology (Columbia University) and at the Columbia University Screening Center led by Dr J.E. Rothman. He joined the Institut Pasteur in 2009 to take charge of the bioinformatic needs at the Transcriptome et Epigenome platform, focusing on Next Generation Sequencing. As of 2016 he is member of the C3BI – HUB Team detached to the Human immunology center (CIH) and provides support for cytometry, next generation sequencing, and microarray data analysis. His areas of interest include the quality assurance and data analysis and visualization at the facility. He also has strong expertise in developing algorithms for function prediction from sequence data, image analysis, analysis of mass spectrometry data, workflow management systems. While at Pasteur he developed: KNIME extensions for Next Generation Sequencing (Link) Post Alignment Visualization and Characterization of High-Throughput Sequencing Experiments (Link) Post Alignment statistics of Illumina reads (Link)

Keywords
Algorithmics ChIP-seq Data management Data Visualization Image analysis Machine learning Sequence analysis Database Genome analysis Biostatistics Program development Scientific computing Data and text mining Illumina HiSeq Graphics and Image Processing Illumina MiSeq High Throughput Screening Flow cytometry/cell sorting Pac Bio
Organisms

Projects (1)

A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community(Milena HASAN - Department of Immunology) - In Progress

Rachel LEGENDRE

Group : GORE - Hub Core

Rachel Legendre is a bioinformatics engineer. She completed her master degree in apprenticeship for two years at INRA in Jouy-en-Josas in the Genetic Animal department. She was involved in a project aiming at the detection and the expression analysis of micro-RNA involved in an equine disease. In 2012, she joined the Genomic, Structure and Translation Team at Paris-Sud (Paris XI) university. She worked principally on Ribosome Profiling data analysis, a new technique that allows to identify the position of the ribosome on the mRNA at the nucleotide level. Since november 2015, she worked at Institut Pasteur. During 4 years, she was detached to the Biomics Platform, where she was in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She was also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics. Since november 2019, she has joined the Hub of Bioinformatics and Biostatistics, et more precisely the Genome Organization Regulation and Expression group.

Keywords
Algorithmics ChIP-seq Epigenomics Non coding RNA Transcriptomics Genome analysis Program development Scientific computing Sofware development and engineering Illumina HiSeq Read mapping Sequencing Workflow and pipeline development Chromatin accessibility assays Pac Bio Ribosome profiling
Organisms
Bacteria Fungi Parasite Human Insect or arthropod Other animal
Projects (19)

Christophe MALABAT

Group : HEAD - Hub Core

After a PhD in biochemistry of the rapeseed proteins, during which I developed my first automated scripts for handling data processing and analysis, I join Danone research facility center for developing multivariate models for the prediction of milk protein composition using infrared spectrometry.
As I was already developing my own informatics tools, I decided to join the course of informatic for biology of the Institut Pasteur in 2007. At the end of the course I was recruited by the Institute and integrate the unit of “génétique des interactions macromoléculaires” of Alain Jacquier. Within this group, I learn to handle sequencing data and I developed processing and analysis tools using python and R. I also create a genome browser and database system for storing, retrieving and visualizing microarray data. After 8 years within the Alain Jacquier’s lab, I join the Hub of bioinformatics and biostatistics as co-head of the team.

Keywords
Clustering Data management Sequence analysis Transcriptomics Web development Database Genome analysis Program development Scientific computing Exploratory data analysis Data and text mining Illumina HiSeq Read mapping LIMS Illumina MiSeq High Throughput Screening Multidimensional data analysis Workflow and pipeline development Ribosome profiling Motifs and patterns detection
Organisms

Projects (11)

Related project (1)

Identification of the genetic basis of bacteriophage-resistant isolates

Bacteria exposed to bacteriophages deploy several defence systems that we wished to identify by genomes sequencing of bacteriophage-resistant isolates

Project keywords

Genotyping
Genetics
Evolution

Project organisms
Bacteria Pseudomonas aeruginosa