Data Science for Life Sciences

Life and health sciences are changing rapidly: new technologies provide large-scale individual data (“omics” data) that can be related to health-related outcomes and medical imaging data. Identifying predisposition factors for disease and making predictions about health is a tremendous challenge for data scientists that we will address by conceiving original data science methods, algorithms, and software to relate omics data to health-related traits. This action is the WP2 of Grenoble Alpes Data Institute.

Activities
  • Focus on... Laura Fancello and proteogenomics
    on the February 15, 2021
    Laura Fancello is a bioinformatician working at the “Exploring the Dynamics of Proteomes” (Edyp) team (Univ. Grenobles Alpes, CEA, Inserm, IRIG-BGE). In 2019, she obtained a Junior Chair from the Data Institute and she is investigating the use of transcriptome information to enhance protein identification in proteomics.
  • One World ABC Seminar: Matti Vihola
    on the December 10, 2020
    For this fifteenth session of the One World ABC Seminar, Matti Vihola from University of Jyväskylä will talk about "On the use of ABC-MCMC with inflated tolerance and post-correction".
  • One World ABC Seminar: David Nott
    on the November 12, 2020
    For this fourteenth session of the One World ABC Seminar, David Nott from National University of Singapore will talk about "Marginally-calibrated deep distributional regression".
  • One World ABC Seminar: Agnieszka Borowska
    on the October 29, 2020
    For this thirteenth session of the One World ABC Seminar, Agnieszka Borowska from University of Glasgow and CLDS will talk about "Gaussian process enhanced semi-automatic ABC for inference in a stochastic differential equation system for chemotaxis".
  • One World ABC Seminar: David Frazier
    on the October 15, 2020
    For this twelfth session of the One World ABC Seminar, David Frazier from Monash University will talk about "Robust and Efficient Approximate Bayesian Computation: A Minimum Distance Approach".
  • One World ABC Seminar: Marko Järvenpää
    on the October 1, 2020
    For this eleventh session of the One World ABC Seminar, Marko Järvenpää from the university of Oslo will talk about "Batch simulations and uncertainty quantification in Gaussian process surrogate ABC".
  • One World ABC Seminar: Flora Jay
    on the September 17, 2020
    For this tenth session of the One World ABC Seminar, Flora Jay from Paris-Sud University/Paris-Saclay/CNRS/INRIA will talk about "Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation".
  • One World ABC Seminar: Pierre-Alexandre Mattei and Samuel Wiqvist
    on the September 3, 2020
    For this ninth session of the One World ABC Seminar, Pierre-Alexandre Mattei from Inria and Samuel Wiqvist from Lund university will talk about "Partially Exchangeable Networks and Architectures for Learning Summary Statistics in Approximate Bayesian Computation".
  • One World ABC Seminar: Ruth Baker
    on the July 16, 2020
    For this eighth session of the One World ABC Seminar, Chris Drovandi from University of Oxford will talk about "Multi-fidelity Approximate Bayesian computation"
  • Internships on data and societal issues
    on the July 15, 2020
    The Grenoble Alpes Data Institute launched an interdisciplinary call on ethical, environmental and societal practices and issues of data processing. The first internships present their projects.
  • One World ABC Seminar: Chris Drovandi
    on the July 2, 2020
    For this seventh session of the One World ABC Seminar, Chris Drovandi from the Queensland University of Technology (QUT) will talk about "Improving Bayesian Synthetic Likelihood via Transformations".
  • One World ABC Seminar: Hien Duy Nguyen
    on the June 18, 2020
    For this sixth session of the One World ABC Seminar, Hien Duy Nguyen from La Trobe University will talk about "Approximate Bayesian computation via the energy statistic".
  • One World ABC Seminar: Irene Tubikanec
    on the June 4, 2020
    For this fifth session of the One World ABC Seminar, Irene Tubikanec from the Institute for Stochastics at the Johannes Kepler University Linz will talk about "Focused Bayesian Prediction".
  • One World ABC Seminar: Gael Martin
    on the May 21, 2020
    For this fourth session of the One World ABC Seminar, Gael Martin from Monash University will talk about "Focused Bayesian Prediction"
  • ABC World Seminar: Umberto Picchini
    on the May 7, 2020
    For this third session of the ABC World Seminar, Umberto Picchini from Chalmers University of Technology and University of Gothenburg will talk about "Stratified sampling and bootstrapping for approximate Bayesian computation"
  • ABC World Seminar: Ivis Kerama and Richard Everitt
    on the April 23, 2020
    For this second session of the ABC World Seminar, Ivis Kerama from the University of Reading and Richard Everitt from the University of Warwick will talk about "Rare event ABC-SMC^2"
  • Results of the call for proposals 2020
    on the April 15, 2020
    The Grenoble Alpes Data Institute launched an interdisciplinary call on ethical, environmental and societal practices and issues of data processing. The committee selected 10 projects.
  • One World ABC Seminar
    from April 9, 2020 to July 16, 2020
    Inspired by the "One World Probability Seminar", we decided to run The One World ABC Seminar, a weekly/fortnightly series of seminars that will take place on Blackboard Collaborate on Thursdays at 11.30am [UK time]. The idea is to gather members and disseminate results and innovation during these weeks and months under lockdown.
  • ABC World Seminar: Dennis Prangle
    on the April 9, 2020
    For this first session of the ABC World Seminar, Dennis Prangle the University of Newcastle will talk about "Distilling importance sampling"
  • Workshop Approximate Bayesian Computation (ABC) in Grenoble
    from March 19, 2020 to March 20, 2020
    It is with regret that we have to cancel the ABC in Grenoble workshop due to COVID19 outbreak.The actual plan is to reschedule for a future date.
  • Focus on... Johanna Lepeule and the causal analysis in epigenetic epidemiology
    on the March 13, 2020
    Johanna Lepeule is an epidemiologist at IAB. She is working on the Developmental Origins of Health and Disease (DOHaD). She obtained a funding from the Grenoble Alpes Data Institute for her project “causal analysis in epigenetic epidemiology”.
  • Focus on... Magali Richard (TIMC - BCM)
    on the February 6, 2020
    Magali Richard was a Junior Chair in the Grenoble Alpes Data Institute. She is involved in the WP2 Data Science for Life Sciences.
  • Call for proposals 2020
    from January 27, 2020 to February 20, 2020
    The Grenoble Alpes Data Institute launches an interdisciplinary call on ethical, environmental and societal practices and issues of data processing.
  • Data stewardship committee
    on the December 18, 2019
    In a national and international context of open science, research data management is of paramount importance. In order to meet the needs of the scientific communities on these issues, GRICAD and its partners are setting up a data stewardship committee, whose objectives are to provideconcrete and operational support to scientists on all these issues.
  • Health Data Challenge (2nd edition): Matrix factorization and deconvolution methods to quantify tumor heterogeneity in cancer research
    from November 25, 2019 to November 29, 2019
    This interdisciplinary challenge will be dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on transcriptomic and methylation data.
  • Focus on... Guillaume Bottaz-Bosson, Théo Falquès and the treatment compliance in sleep apnea
    on the October 15, 2019
    The HP2 laboratory from UGA and Inserm studies the sleep apnea. Thanks to the Grenoble Alpes Data Institute’s funding, the team get two students in statistics and data science to work on the clustering of patient compliance trajectories and individual prediction of treatment compliance in sleep apnea from large national databases.
  • Focus on... Nagham Badreddine and the procedural memory
    on the September 12, 2019
    Nagham Badreddine is a PhD student at the Grenoble Institute of Neuroscience (GIN) and the GIPSA-Lab. She is studying how procedural memory is formed in the brain. She is using a combination of experimental and computational approaches to probe the neural substrates and develop models of neuronal activity associated to memory.
  • Online Health Data Challenge
    from July 23, 2019 to August 23, 2019
    We organize an online health data challenge about quantification of intra-tumor heterogeneity
  • Focus on... Sophie Abby and the evolution of enzymes' regio-selectivity
    on the July 15, 2019
    Sophie Abby, a young researcher at TIMC-IMAG, CNRS and Université Grenoble Alpes, is involved in the project “Deciphering the origins of enzymes substrate specificity using large-scale sequence analyses”. This interdisciplinary project received funding from the Grenoble Alpes Data Institute.
  • Publication: "Yam genomics supports West Africa as a major cradle of crop domestication"
    on the May 21, 2019
    Olivier François (TIMC-IMAG) has contributed to "Yam genomics supports West Africa as a major cradle of crop domestication" published in Science Advances, in the framework of the Data Institute’s work package 2 “Data Science for Life Sciences”.
  • CompSysBio 2019
    from March 31, 2019 to April 6, 2019
    The Advanced Lecture Course on Computational Systems Biology will be held in Aussois between March 31st and April 6th, 2019.
  • Data Institute Seminar: Antoine Frenoy
    on the March 22, 2019
    Antoine Frenoy (Institut Pasteur) will give a talk on "Inferring ecological lifestyles of bacterial species from metagenomic datasets: application to horizontal transfer and virulence". The event will take place on March 22th from 2 pm in Pavillon Taillefer, room R32.
  • 2019 Thales AIChallenge4Health
    on the March 21, 2019
    The 2019 Thales AIChallenge4Health will take place at Ensimag the March 21st from 2:00 pm.
  • Publication: "LFMM 2: Fast and accurate inference of gene-environment associations in genome-wide studies"
    on the February 5, 2019
    Kevin Caye, Basile Jumentier, Johanna Lepeule and Olivier François publish "LFMM 2: Fast and accurate inference of gene-environment associations in genome-wide studies" in Molecular Biology and Evolution in the framework of the Data Institute’s work package 2 “Data Science for Life Sciences”.
  • Data Institute Seminar: Computational methods for system biology
    on the January 25, 2019
    Maxime Folschette (LS2N , Nantes) will give a talk on "Computational methods for system biology". The event will take place on January 25th from 2 pm in Pavillon Taillefer, room R32.
  • Data Institute Seminar: Deep learning applications in drug discovery and protein structure analysis
    on the January 11, 2019
    Mehmet Serkan Apaydin (INRIA Sophia Antipolis) will give a talk on "Deep learning applications in drug discovery and protein structure analysis". The event will take place on January 11th from 2 pm in Pavillon Taillefer, room R32.
  • Focus on… Laurent Guyon and gene selection
    on the December 17, 2018
    Laurent Guyon is a researcher in bioinformatics at The Biology of Cancer and Infection laboratory (UMR of Grenoble Alpes University, CEA and Inserm). In the framework of Data Institute, he is developing methods to identify genes correlated with cancer patient lifetime.
  • Publication: "Bioinformatics Methods to Select Prognostic Biomarker Genes from Large Scale Datasets: A Review"
    on the December 17, 2018
    Rémy Jardillier, Florent Chatelain and Laurent Guyon publish "Bioinformatics Methods to Select Prognostic Biomarker Genes from Large Scale Datasets: A Review" in Biotechnology Journal in the framework of the Data Institute’s work package 2 “Data Science for Life Sciences”.
  • Seminar: Credal sum-product networks
    on the December 12, 2018
    Cassio P. de Campos from University of Utrecht (Netherlands) will talk about "Credal sum-product networks". The event will take place on December 12 at 3 pm at INRIA Montbonnot Saint-Martin, room F107.
  • Health Data Challenge: Matrix factorization and deconvolution methods to quantify tumor heterogeneity in cancer research
    from December 10, 2018 to December 14, 2018
    The challenge will be dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on cancer omics data. It will take place from December 10th to 14th, at Aussois.
  • Seminar: Optimization-based Sampling Approaches for Hierarchical Bayesian Inference
    on the December 3, 2018
    Tiangang Cui from Monash University (Melbourne, Australia) will talk about "Optimization-based Sampling Approaches for Hierarchical Bayesian Inference". The event will take place on December 3 at 2 pm at INRIA Montbonnot Saint-Martin, room F107.
  • Call for proposals: Exchange program
    on the October 15, 2018
    The Grenoble Alpes Data Institute launches a call for international collaborations with Data Institutes.
  • Seminar: Minibatch and incremental learning of exponential family mixtures, and the soft k-means clustering problem
    on the September 17, 2018
    Hien Nguyen from La Trobe University (Melbourne, Australia) will talk about "Minibatch and incremental learning of exponential family mixtures, and the soft k-means clustering problem". The event will take place on September 17 at 2 pm at INRIA Montbonnot Saint-Martin, room F107.
  • Summer school GRAPHSIP
    from September 10, 2018 to September 14, 2018
    This school is about graph signal processing, in particular, development of signal processing tools for data structured as graphs. The graph consists in nodes corresponding to the studied variables and edges that link the nodes.
  • Bayesian workshop: 2nd Italian-French Statistics Seminar
    from September 6, 2018 to September 7, 2018
    We are organizing a two-day Bayesian workshop in Grenoble in September 6-7, 2018. It will be the second edition of the Italian-French statistics seminar, titled this year: Bayesian learning theory for complex data modeling.
  • Feedback and videos of the workshop "Data Science in the Alps"
    on the April 10, 2018
    The Grenoble Alpes Data Institute organized the workshop "Data Science in the Alps" on March 20, 2018. More than 90 persons attended the workshop that took place at the Stade des Alpes, Grenoble. We are looking forward for the 2019 session!
  • Workshop: Data Science in the Alps
    on the March 20, 2018
    Grenoble Alpes Data Institute is pleased to organize the first “data science in the Alps” workshop. It will take place on March, 20th at the Stade des Alpes, salon sud-ouest.
  • Data Institute Seminar: Integration of heterogeneous data for the implementation of learning techniques by Johan Montagnat
    on the November 30, 2017
    Johan Montagnat from CNRS I3S Laboratory will give a talk on "Integration of heterogeneous data for the implementation of learning techniques". The event will take place on Thursday November, 30th at 11:30 am at GIN.
  • Data Institute Seminar: Introduction to graph signal processing by Pierre Borgnat from ENS Lyon
    on the October 5, 2017
    Pierre Borgnat from ENS Lyon will give a talk on “An invitation to Graph Signal Processing with Applications to Clustering”. The event will take place on Thursday 5 October at GIPSA-lab.
  • Data Institute Seminar: co-clustering through optimal transport by Charlotte Laclau (LIG)
    on the September 21, 2017
    A novel method for co-clustering will be presented : an unsupervised learning approach that aims at discovering homogeneous groups of data instances and features by grouping them simultaneously.
  • Call for projects - September 2017
    from September 18, 2017 to October 15, 2017
    The Grenoble Alpes Data Institute launches a call for 2-years research projects with applications of data sciences in Life Science or in Earth, Space, and Environmental Sciences.
  • Data challenge on software and statistical methods for population genetics (SSMPG 2017)
    from September 11, 2017 to September 15, 2017
    The aim of the summer school is to provide a comprehensive overview on software and statistical methods for detecting genes involved in local adaptation. Lectures and software demos will be given during the summer school.
  • French speaking international conference on teaching statistics
    from September 6, 2017 to September 8, 2017
    The fifth edition of the conference « Colloque Francophone International sur l’Enseignement de la Statistique » will take place in Grenoble from 6 to 8 September 2017.
  • Meet-up event between Data scientists and domain scientists
    on the July 3, 2017
    On Monday July 3 from 09:00 to 14:00, come and meet scientists with complementary research topics
  • Data Challenge "Epigenetic & High-Dimension Mediation"
    from June 7, 2017 to June 9, 2017
    Progresses in high-throughput sequencing make it possible to study how epigenetic changes mediate the effect of environmental risk factors on diseases. Epigenetic changes are said to be mediators when they intervene in the causal pathway between environmental exposures and diseases.
  • Feedback on the Data Challenge "Epigenetic & High-Dimension Mediation"
    from June 7, 2017 to June 9, 2017
    From June 7 to 9, 30 researchers and students from all over Europe and from the USA contributed to the data challenge « Epigenetic & High-Dimension Mediation » in Aussois.
  • Open seminars about reproducible research
    from March 23, 2017 to March 30, 2017
    Arnaud Legrand (LIG) will start the open seminar series by giving a talk about reproducible research. Although reproducibility is one of the main principles of the scientific method, it has been shown that a substantial proportion of published research is not reproducible leading to the scientific 'crisis' of reproducibility.

Recruited
Information to come