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
Searched keyword : Motifs and patterns detection
Related people (3)
2015 – . – Institut Pasteur, Paris, France – Unit : Bioinformatics and Biostatistics HUB 2012 – 2015 – Institut Pasteur, Paris, France – Unit : Molecular Genetics of Yeasts Supervisor : Prof. B. Dujon 2012 – Institut Pasteur, Paris, France – Unit : Integrated Mycobacterial Pathogenomics Supervisor: Dr. R. Brosch Education 2012– MSc. Bioinformatics – Université Paris Diderot (Paris VII)
Genome assemblySequence analysisGenome analysisOrthology and paralogy analysisRead mappingSequence homology analysisDNA structure analysisGenome rearrangementsMotifs and patterns detection
- Duplications in bacteriophage genomes.(Luisa DE SORDI - Molecular Biology of Gene in Extremophiles) - New
- De novo sequencing and analysis of three unassigned species of non tuberculous mycobacteria.(RIM GHARBI - Integrated Mycobacterial Pathogenomics) - Awaiting Publication
- Differentiation of Shigella species from Escherichia coli by MALDI-TOF mass spectrometry(Sophie LEFÈVRE - Enteric Bacterial Pathogens) - In Progress
After a PhD in Biology in 2011 on population genetics and phylogeography on amazing little amphipods (Crangonyx, Crymostygius) at the University of Reykjavik (Iceland), I pursued my interest in Bioinformatics and Evolutionary Biology in various post-docs in Spain (MNCN Madrid, UB Barcelona). During this time, I investigated transcriptomic landscapes for various non-model species (groups Conus, Junco and Caecilians) using de novo assemblies and participated in the development of TRUFA, a web platform for de novo RNA-seq analysis. In July 2016, I integrated the Revive Consortium and the Epigenetic Regulation unit at Pasteur Institute, where my main focus were transcriptomic and epigenetic analyses on various thematics using short and long reads technologies, with a special interest in alternative splicing events detection. I joined the Bioinformatics and Biostatistics Hub in January 2018. My latest interests are long reads technologies, alternative splicing and achieving reproducibility in Bioinformatics using workflow managers, container technologies and literate programming.
Data managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
- Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing(allemand ERIC - Epigenetic Regulation) - Pending
- Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets(Catherine BOURGOUIN - Functional Genetics of Infectious Diseases) - In Progress
- Mapping of Enhancers from transcriptome data(Christian MUCHARDT - Epigenetic Regulation) - In Progress
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.
ClusteringData managementSequence analysisTranscriptomicsWeb developmentDatabaseGenome analysisProgram developmentScientific computingExploratory data analysisData and text miningIllumina HiSeqRead mappingLIMSIllumina MiSeqHigh Throughput ScreeningMultidimensional data analysisWorkflow and pipeline developmentRibosome profilingMotifs and patterns detection
- Identification of eukaryotic 5'UTRs(Arnaud ECHARD - Membrane Traffic and Cell Division) - Closed
- Super-resolution imaging and reconstructions of human cell chromosome architecture(Xian HAO - Imaging and Modeling) - In Progress
- Utilize mouse models to study infection by HIV-1(Valentina LIBRI - Center for Translational Science) - Awaiting Publication
Related projects (2)
Cellular senescence is a complex stress response that durable (yet not irreversibly) arrests cell proliferation and is accompanied by widespread changes in chromatin structure, metabolism and gene exp