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Some news about the lab members

 I have been slacking on the news section lately, so let me introduce who is currently in the lab and give some news of everyone.

Antoine Szatkownik is doing a joint PhD in the bioinfo and the machine learning TAU teams of LISN.  He's working on designing novel methods for artificial genome generation and their evaluation. This project was started by Burak Yelmen during his PhD in Estonia. He later came to our lab for two years and has now secured a position in the institute of Genomics back in Tartu, Estonia (congrats!). So we are all working on this project with Burak, Antoine, Guillaume Charpiat, Cyril Furtlehner and Aurélien Decelle.

Arnaud Quelin is doing a joint PhD in the bionfo team at LISN and Musée de l'Homme on testing and designing machine learning and deep learning tools for inferring multi-population demographic history. He had started as an intern in the lab to collaborate on our project on Cultural transmission of reproductive success - together with Frédéric Austerlitz, Jérémy Guez, Ferdinand Petit, Fanny Pouyet (who is an assistant Professor in the lab), Evelyne Heyer and Bruno Toupance.

Léo Planche is doing a postdoc on  the HFSP project that focuses on the evolutionary history of Mexico, a joint project  with Emilia Huerta-Sanchez (U Brown, USA) and Maria Avila-Arcos (UNAM, Mexico). He's currently developping tools for local ancestry inference and digging out Neandertal and Denisovan genetic material in modern and ancient human genomes. A project that started in SE University (Russia) with Vladimir Shchur.

Théo Boury was in the lab for a master internship on the use of large language models for paleogenetics and he is now doing a PhD with Yann Ponty at LIX.

Finally, they are not in my lab but I am happily collaborating with Bogdan Iorga (DR CNRS), Elsa Denepko (PhD student at ICSN) and Nicolas Dias (Master student), all at ICSN (CNRS, U Paris-Saclay) on the development of tools for predicting antibiotic resistance in bacteria.

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Where are they now?

Burak Yelmen  has  a position in the institute of Genomics back in Tartu, Estonia.

Jean Cury is now a CNRS researcher at Institute Pasteur.

Jérémy Guez is a postoc in Karczewski Lab at ATGU and the Broad Institute of MIT and Harvard.

Théophile Sanchez is a postdoc in WSL and ETH Zurich.

Federica Pierini is a postdoc at Max Planck Institute for Evolutionary 

Anthropology

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If you want to know more about them you can find their homepage: People

LEGO day December 9th in Paris

We are organizing the 4th LEGO day on December 9th in Paris. Free registration: https://lego-fall-2024.sciencesconf.org/

Follow LEGO, the machine learning for genomics working group, at https://gt-lego.cnrs.fr/animation/ and subscribe to our newsletter.

 

First research day of LEGO (working group of GdR BIM)

Dear colleagues,

We are happy to invite you to the first day of the LEGO (machine LEarning for GenOmics) working group of the GDR BIM on May 31, 2023 in Paris.

 

LEGO is a working group affiliated with the GDR BIM of the CNRS and dedicated to machine learning for genomics. Like many scientific fields, genomics has benefited from the rise of machine learning over the past decade. The French research community in machine learning for genomics is active but dispersed throughout the territory within teams traditionally competent in other methodological areas of genomics, such as statistics, algorithms or bioinformatics. The objective of the LEGO working group is to facilitate exchanges within this community, to foster collaborations and to allow monitoring of the progress made by the participating teams.

 

We welcome abstracts of up to 300 words on recently published or ongoing research related to machine learning for genomics (for talks or posters).

 

Abstracts must be submitted via https://lego2023.sciencesconf.org/

Deadline: May 5, 2023.

 

Location: SCAI Building Esclangon - Sorbonne University, Paris, France

See you soon

 

Laurent Jacob, Flora Jay, Elodie Laine and Raphael Mourad

for the Program Committee.

 

Email: lego@services.cnrs.fr

Website: https://gt-lego.cnrs.fr/

 

To stay informed of LEGO working group activities, you can subscribe to the mailing list by sending an email to:

sympa@services.cnrs.fr

with the subject line:

subscribe lego yourFirstName yourLastName

ECML-PKDD 2022 workshop on machine learning for microbial genomics

We invite submissions to MLMG 2022, the ECML-PKDD 2022 workshop on machine learning for microbial genomics to be held virtually, on September 23rd.

The improvement and increasing accessibility of Next Generation Sequencing data calls for innovative data analysis strategies to extract meaningful and actionable information. Machine learning approaches are more and more popular in this context, offering alternative and complementary tools beyond bioinformatics to analyze genomic data. However, despite the recent advances, their application remains challenging and new approaches that are robust, scalable to large-scale high-dimensional data and interpretable are needed.

This workshop aims to bring together interdisciplinary researchers working at the interface of machine learning and computational biology for the study of microbial genomic data to discuss recent advances in this field. We will also have the privilege of hosting two distinguished speakers from this community to discuss and present their current research.

Typical topics of interest include:

- Improving microbial genome wide association studies (GWAS).
- Phenotype prediction from microbial genomes.
- Inferring population parameters from a set of microbial genomes.
- Visualization of microbial genomes in a way that highlights relevant
  elements with respect to a phenotype of interest.
- Study of the constitution of a microbial flora.

Key dates:

- Submission deadline: June 20th 2022 (instructions here)
- Decisions: July 13th 2022
- Online workshop: September 23rd

Meriem El Azami
Laurent Jacob
Flora Jay
Pierre Mahé

https://mlmg2022.github.io/

Lea Boulos joined the lab in February as a master 2 student. She works with Burak Yelmen, Guillaume Charpiat and I on generative models for large-scale genomic data - based on our previous work creating realistic genomes based on generative neural networks (GANs and RBMs). Lea's stipend is supported by ANR.

Lindsay Goulet also joined (in May) as a master 1 student working with Fanny Pouyet, Louis Ollivier and myself on demographic inference for yeast populations. Lindsay's stipend is upported by Fanny's grant.

DigiCosme Thematic School 2021 Graph as models in life sciences: Machine learning and integrative approaches - online - October 25th - 29th

We are organizing an online thematic school in bioinformatics and machine learning. You can register and spread the news.

Website: https://digicosme.cnrs.fr/ecole-thematique-2021-graph-as-models-in-life-sciences-machine-learning-and-integrative-approaches/

Registration form: https://framaforms.org/digicosme-thematic-school-2021-registration-1626095320
(free but mandatory, limited number of places for the tutorials)

 Flora Jay, CR CNRS, LISN
 Yann Ponty, DR CNRS, LIX
 Ariane Migault, Chargée de communication du Labex DigiCosme

 Burak Yelmen is joining the lab as a postdoctoral fellow to extend our previous work on creating realistic genomes based on generative neural networks (GANs and RBMs). Burak's salary is supported by ANR.

Pierre Jobic is doing a master internship in the lab and exploring deep architectures for population size inference. It will lead to a potentially substantial extension of our work with Théophile Sanchez, Jean Cury and Guillaume Charpiat :

T Sanchez, J Cury, G Charpiat, F Jay (2020). Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation. Molecular Ecology Ressources DOI:10.1111/1755-0998.13224 Link

Pierre is also helping  beta testing and improving our DNADNA software developed by the lab and in particular by Erik Madison Bray based on initial code by Théophile and Jean.

Mathieu Michel recently joined the lab for a master internship. He will help us benchmarking machine learning and deep learning methods for population genetics inference.

Federica Pierini is joining the lab as a postdoc to work on our newly awarded Human Frontier Science Program (HFSP) project "Evolutionary changes in human hosts and their pathogens during first contact in the New World".

This is a joint project with Emilia Huerta-Sanchez (brown University, USA) and Maria Avila Arcos (UNAM, Mexico)

Jérémy Guez is starting a PhD with Musée de l'Homme (National Museum of natural history, Paris) and our lab (LRI) on TransIA a project for Infering Cultural Transmission of Reproductive Success using Genomic Data.

Joint work with Evelyne Heyer, Fréderic Austerlitz, Romain Laurent, Bruno Toupance from the Eco-anthropology department (MNHN). Funded by CNRS 80PRIME.

Nicolas Zimmermann joined the lab part time and is currently working on demographic inference for human populations using Approximate Bayesian Computation and Random Forest methodologies. He is doing his M1 internship under the supervision of Frédéric Austerlitz (MNHN) and myself.

Join us for the PASADENA workshop (GT Digicosme) on Friday, February 15th
Speakers: 
    Chloé-Agathe Azencott,CBIO, Mines ParisTech/Institut Curie/INSERM
    Romain Brault, Thalès
    Julien Chiquet, AgroParisTech/INRA MIA Paris
    Chloé Clavel, LTCI, Telecom-ParisTech
    Stanley Durrleman, Aramis Lab, ICM
    Joseph Salmon, Université de Montpellier 

Program and information

Burak Yelmen is visiting from the Institute of Genomics (Estonian Biocentre, University of Tartu, Estonia). He will stay for 2 months and a half and collaborate on deep learning methods for population genetics.

Benjamin Demaille is joining the lab to work on dimension reduction, imputation, visualization of paleogenomic data. This will be a follow-up and extension of Séverine Liegeois master work.

I'm helping organizing the

Institut Pascal Research Program "Ecosystem dynamics : state, data and models" 

17 June – 12 July 2019

coordinators: Stéphane Dupas, Camille Coron, Arnaud Becheler and Adelaïde Olivier

It consists in 3 weeks of Research (seminars and working groups) and 1 of Summer School. Contact us if you are interested and want to know more.

Congratulations to Séverine Liegeois who just got the prize for best poster at the Paris-Saclay Junior Conference on Data Science and Engineering 2018 for her work on Dimension Reduction Adapted to Paleogenomics !
This work is done in collaboration Olivier François, TIMC-IMAG

I'm happy to say that Théophile Sanchez presented his work on End-to-End Deep Learning Approach for Demographic History Inference in
- a talk at MCEB conference,  Mathematical and Computational Evolutionary Biology, Montpellier, France, June 2018
- a talk at Paris-Saclay Junior Conference on Data Science and Engineering, Orsay, France, Sept. 2017 HAL reference 
- a poster at Human Evolution: Fossils, Ancient and Modern Genomes conference, Cambridge, UK, Nov. 2017
This work is done in collaboration with Guillaume Charpiat, LRI

Agnès Barnabé joined the lab for a Master 1 internship, mentored by Jean Cury and myself. She is developing a pipeline for the Demographic inference of bacterial populations using the software BEAST and testing it on Jean's simulated genomic datasets.