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 : Machine learning
Related people (10)

Christophe BÉCAVIN
CV Senior Bioinformatician August 2015 – Present : Institut Pasteur, Paris PostDoc fellow 2011 – 2015 : Pascale Cossart’s laboratory, Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris Phd fellow 2007 – 2010 : Institut des Hautes Etudes Scientifiques, ann Ecole Normale Supérieure, Paris Magister of Science, Theoretical Physics 2003 – 2007 : Dynamical systems and statistics of complex matter, Université Paris 7 and Université Paris 6
KeywordsBiophysicsMachine learningModelingProteomicsBiostatisticsDatabases and ontologiesHost-pathogen interactions
Organisms
ListeriaLeishmania
Projects (12)
- Analysis of DNA methylation in the presence and absence of antibiotics in wt and mutant V. cholerae(Baharoglu ZEYNEP - Bacterial Genome Plasticity) - Closed
- Finding and Predicting CRISPR-Cas9 Efficiency(Jerome WONG NG - Synthetic Biology) - Closed
- Characterization of a Salmonella mutant carrying a single amino-acid substitution in the stress sigma factor RpoS(Françoise NOREL - Biochemistry of Macromolecular Interactions) - Closed

Anne BITON
I received a Ph.D. in Biostatistics and Bioinformatics applied to Cancer Research in 2011 from the University Paris Sud XI, I was working at the Curie institute under the supervision of Emmanuel Barillot and François Radvanyi. My Ph.D. was about the unsupervised analysis of cancer transcriptome. During my postdoctoral time, I worked on the computational and statistical analysis of NGS data. My areas of interest and expertise include - functional genomics - human genetics - statistical analysis of high-dimensional data - normalization, batch-correction, meta-analysis of high-throughput data - unsupervised learning, independent component analysis - NGS data analysis (RNA-Seq, DNA-Seq, …) - analysis of the non-coding genome, transposable elements
KeywordsMachine learningModelingGenetics
Organisms
Projects (17)
- Left-right patterning of heart precursors(Tobias BØNNELYKKE - Heart Morphogenesis) - In Progress
- Collaboration between CETEA, C2RA and Hub for optimization of experimental designs (3R)(Myriam MATTEI - Center for Animal Resources and Research) - In Progress
- Mechanisms of HIV-1-infected cells susceptibility to Fc effector functions(Timothée BRUEL - Virus and Immunity) - In Progress

Freddy CLIQUET
One of my projects consists in developing GRAVITY, a java tool based on Cytoscape to integrate genetic variants within protein-protein interaction networks to allow the visual and statistical interpretation of next-generation sequencing data, ultimately helping geneticists and clinicians to identify causal variants and better diagnose their patients. I’m also involved in several other projects in the lab, taking part in the design of pipelines for the processing and the analysis of genomics data, including SNP arrays, whole-exome and whole-genome sequencing data. This means being confronted to the big data problematic, the unit having to manage hundreds of terabytes of genomics data. Finally, I am now analysing these data in order to identify possible causes for autism, to help clinicians with their diagnosis but also to better understand the biological mechanisms at play in this complex disease. This is done through the project aiming at understanding the genetic architecture of autism in the Faroe Islands, and also with the newly starting IMI2 European project AIMS2-Trials.
KeywordsAlgorithmicsData managementData VisualizationGenomicsMachine learningProteomicsGenome analysisBiostatisticsProgram developmentScientific computingApplication of mathematics in sciencesExploratory data analysisSofware development and engineeringData and text miningGenetics
Organisms
Projects (0)

Thomas COKELAER
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.
KeywordsAlgorithmicsData managementData VisualizationGenome assemblyGenomicsMachine learningModelingScientific computingDatabases and ontologiesSofware development and engineeringData and text miningIllumina HiSeqGraph theory and analysisIllumina MiSeq
Organisms
Projects (2)

Vincent GUILLEMOT
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KeywordsData VisualizationMachine learningStatistical inferenceBiostatisticsApplication of mathematics in sciencesDimensional reductionMultidimensional data analysis
Organisms
Projects (25)
- High content screening of mitochondrial morphology defects in mitochondrial genetic diseases: discovery of new therapeutic compounds(Claire PUJOL - Mitochondrial Biology) - New
- Red Cross health workers and the continuity of care in the COVID-19 pandemic: A mixed methods operational approach(Leonard HEYERDAHL - Group: Medical anthropology and environment) - New
- A genome-wide RNAi screening for mitochondrial fission factors(Erwan RIVIÈRE - Mitochondrial Biology) - Closed

Bernd JAGLA
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)
KeywordsAlgorithmicsChIP-seqData managementData VisualizationImage analysisMachine learningSequence analysisDatabaseGenome analysisBiostatisticsProgram developmentScientific computingData and text miningIllumina HiSeqGraphics and Image ProcessingIllumina MiSeqHigh Throughput ScreeningFlow cytometry/cell sortingPac Bio
Organisms
Projects (2)
- Identifying new population(s) of NK cells involved in memory to bacterial infection(Melanie HAMON - Chromatin and Infection) - In Progress
- 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

François LAURENT
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KeywordsData managementMachine learningStatistical inferenceScientific computingExploratory data analysisSofware development and engineeringParallel computingNeuroimaging and computational neuroscienceGrid and cloud computing
Organisms
Projects (1)

Natalia PIETROSEMOLI
Dr. Natalia Pietrosemoli is an Engineer with a M. Sc. in Modeling and Simulation of Complex Realities from the International Center for Theoretical Physics, ICTP and the International School of Advanced Studies, SISSA (Triest, Italy). During her M. Sc. internships she mostly worked in modeling, optimization, combinatorics and information theory applied to medical imaging. In 2012 she got a Ph. D in Computational Biology from the School of Bioengineering of Rice University (Houston, TX, US), where she specialized in computational structural biology and functional genomics. Her doctoral thesis “Protein functional features extracted with from primary sequences : a focus on disordered regions”, contributed to a better understanding of the functional and evolutionary role of intrinsic disorder in protein plasticity, complexity and adaptation to stress conditions. As part of her Ph. D., Natalia was a visiting scholar in two labs in Madrid: the Structural Computational Biology Group at the Spanish National Cancer Research Centre (CNIO), where she mainly worked in sequence analysis and the functional-structural relationships of proteins, and the Computational Systems Biology Group at the Spanish National Centre for Biotechnology (CNB-CSIC ), where she studied the functional implications of intrinsically disordered proteins at the genomic level for several organisms, collaborating with different experimental and theoretical groups. In 2013, she joined the Swiss Institute of Bioinformatics as a postdoctoral fellow in the Bioinformactics Core Facility. Her main project consisted in the molecular classification of a rare type of lymphoma, which involved the integration of transcriptomic, clinical and mutational data for the identification of molecular markers for classification, diagnosis and prognosis. This work was performed in collaboration with the Pathology Institute at the University Hospital of Lausanne (CHUV). In November of 2015 Natalia joined the Hub Team @ Pasteur C3BI as a Senior Bioinformatician. Natalia is especially interested in the integrative analysis of different omics data, both at large-scale and for small datasets, and loves collaborating in interdisciplinary environments and having feedback from her fellow experimental colleagues. Currently, she’s coordinating several projects performing functional and pathway analysis at the genomic level. By grouping genes, proteins and other biological molecules into the pathways they are involved in, the complexity of the analyses is significantly reduced, while the explanatory power increases with respect to having a list of differentially expressed genes or proteins.
KeywordsAlgorithmicsData managementGenomicsImage analysisMachine learningModelingProteomicsSequence analysisStructural bioinformaticsTranscriptomicsDatabaseGenome analysisBiostatisticsScientific computingDatabases and ontologiesApplication of mathematics in sciencesData and text miningGeneticsGraphics and Image ProcessingBiosensors and biomarkersClinical researchCell biology and developmental biologyInteractomicsBioimage analysis
Organisms
Projects (32)
- Exploring pathogenic mechanisms of chronic inflammatory disease: unresolved issues in IL-23/IL-17 biology(YAHIA HANANE - Immunoregulation) - In Progress
- Study of the role of cyclic dimeric guanosine mono-phosphate (c-di-GMP) in the regulation of virulence and biofilm formation in Leptospira interrogans(Gregoire DAVIGNON - Other) - In Progress
- Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms(Yves JACOB - Molecular Genetics of RNA Viruses) - In Progress

Stevenn VOLANT
After a diploma of statistician engineer from the Ensai (Ecole Nationale de la Statistique et de l’Analyse de l’Information) and a Ph.D in applied mathematics in the Statistics & Genome lab (AgroParisTech), I worked as a developer for the XLSTAT software. I have implemented some statistical methods such as mixture models, log-linear regression, mood test, bayesian hierarchical modeling CBC/HB, … Then I worked as a head teacher in statistics for one year. I was recruited in the Bioinformatic and biostatistic hub of the C3BI (Center of Bioinformatics, Biostatistics and Integrative Biology) in 2014, I am in charge of the statistical analysis and the development of R/R shiny pipelines.
KeywordsMachine learningStatistical inferenceTargeted metagenomicsBiostatisticsApplication of mathematics in sciencesStatistical experiment design
Organisms
Projects (34)
- Etude de la réponse immunitaire néonatale dans la coqueluche maligne : approche transcriptomique(Soraya MATCZAK - Biodiversity and Epidemiology of Bacterial Pathogens) - Pending
- FLAVIMMUNITY(Giovanna BARBA SPAETH - Structural Virology) - Pending
- Etude de l’évolution des Troubles Olfactifs chez les patients ayant une perte de l’odorat persistante des suites de la COVID-19(Erwan POIVET - Department of Neuroscience) - Pending