tag:blogger.com,1999:blog-3301257638802566112024-03-20T08:11:26.309-07:00Flora Jay - PhD - population genetics statistic and machine learning methods applied to population genetics inferenceUnknownnoreply@blogger.comBlogger27125tag:blogger.com,1999:blog-330125763880256611.post-50828849710754740282023-06-11T04:21:00.000-07:002023-06-11T10:37:22.364-07:00<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTGNQ1j5uDpgtUzuhiW1zfFGzGVPhO7GflolYBgkhtsyvD6ACbcNxzI5UgTfNACM4ErdrwxPzu4x68hE1nOVizvOzSoH-7CmIswfglXC6PqtYA6WD1y_YhxWlBCyFS1oN4p_VsbKhVavu_/s1600/evolution_ore.JPG" style="margin-left: auto; margin-right: auto;"><img border="0" height="268" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTGNQ1j5uDpgtUzuhiW1zfFGzGVPhO7GflolYBgkhtsyvD6ACbcNxzI5UgTfNACM4ErdrwxPzu4x68hE1nOVizvOzSoH-7CmIswfglXC6PqtYA6WD1y_YhxWlBCyFS1oN4p_VsbKhVavu_/s320/evolution_ore.JPG" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span class="st"><span style="font-size: xx-small;">©</span></span> Oré</td></tr>
</tbody></table>
<br />Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-34011434919427515262023-04-11T09:31:00.011-07:002023-06-11T09:38:30.628-07:00First research day of LEGO (working group of GdR BIM)<p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">Dear colleagues,</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">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.</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"> </p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;"><b>LEGO
is a working group affiliated with the GDR BIM of the CNRS and
dedicated to machine learning for genomics. </b>Like many scientific fields,
genomics has benefited from the rise of machine learning over the past
decade. The French research community in mac</span><span style="color: black; font-family: Arial; font-size: 10pt;">hine
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 faci</span><span style="color: black; font-family: Arial; font-size: 10pt;">litate
exchanges within this community, to foster collaborations and to allow
monitoring of the progress made by the participating teams.</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"> </p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">We
welcome abstracts of up to 300 words on recently published or ongoing
research related to machine learning for genomics (for talks or
posters).</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"> </p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">Abstracts must be submitted via </span><a href="https://lego2023.sciencesconf.org/">https://lego2023.sciencesconf.org/</a></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">Deadline: May 5, 2023.</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"> </p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">Location: SCAI Building Esclangon - Sorbonne University, Paris, France</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><span style="color: black; font-family: Arial; font-size: 10pt;">See you soon</span></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b> </b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">Laurent Jacob, Flora Jay, Elodie Laine and Raphael Mourad</span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">for the Program Committee.</span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b> </b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">Email: <a href="mailto:lego@services.cnrs.fr">lego@services.cnrs.fr</a></span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">Website: <a href="https://gt-lego.cnrs.fr/">https://gt-lego.cnrs.fr/</a></span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b> <br /></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">To stay informed of LEGO working group activities, you can subscribe to the mailing list by sending an email to:</span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;"><a href="mailto:sympa@services.cnrs.fr">sympa@services.cnrs.fr</a></span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">with the subject line:</span></b></p><p style="border: medium none; margin-bottom: 0pt; margin-top: 0pt;"><b><span style="color: black; font-family: Arial; font-size: 10pt;">subscribe lego yourFirstName yourLastName</span></b></p><p></p>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-83758847904738519072022-05-27T04:20:00.004-07:002023-06-11T09:35:04.288-07:00ECML-PKDD 2022 workshop on machine learning for microbial genomics <div style="text-align: justify;"><p></p></div><p style="text-align: justify;">We invite submissions to <a href="https://mlmg2022.github.io/">MLMG 2022</a>, the ECML-PKDD 2022 workshop on machine learning for microbial genomics to be held virtually, on September 23rd.<br /><br />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.<br /><br />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.<br /><br />Typical topics of interest include:<br /><br />- Improving microbial genome wide association studies (GWAS).<br />- Phenotype prediction from microbial genomes.<br />- Inferring population parameters from a set of microbial genomes.<br />- Visualization of microbial genomes in a way that highlights relevant<br /> elements with respect to a phenotype of interest.<br />- Study of the constitution of a microbial flora.<br /><br />Key dates:<br /><br />- Submission deadline: June 20th 2022 (instructions <a href="https://mlmg2022.github.io/call/">here</a>)<br />- Decisions: July 13th 2022<br />- Online workshop: September 23rd<br /><br />Meriem El Azami<br />Laurent Jacob<br />Flora Jay<br />Pierre Mahé</p><p style="text-align: justify;"><a href="https://mlmg2022.github.io/">https://mlmg2022.github.io/</a></p>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-27722110464816070512022-02-01T03:06:00.003-08:002022-05-09T03:14:05.690-07:00<p>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 <a href="(https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009303" target="_blank">creating realistic genomes based on generative neural networks (GANs and RBMs)</a>. Lea's stipend is supported by ANR.</p><p><br /></p><p>Lindsay Goulet also joined (in May) as a master 1 student working with <a href="https://www.lri.fr/membre_en.php?mb=2850">Fanny Pouyet</a>, Louis Ollivier and myself on demographic inference for yeast populations. Lindsay's stipend is upported by Fanny's grant.</p>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-16799885976212176152021-09-02T08:41:00.000-07:002021-09-03T08:41:46.787-07:00DigiCosme Thematic School 2021 Graph as models in life sciences: Machine learning and integrative approaches - online - October 25th - 29th<p>We are organizing an online thematic school
in bioinformatics and machine learning. You can register and spread the news.<br />
</p><p>Website:
<a class="moz-txt-link-freetext" href="https://digicosme.cnrs.fr/ecole-thematique-2021-graph-as-models-in-life-sciences-machine-learning-and-integrative-approaches/">https://digicosme.cnrs.fr/ecole-thematique-2021-graph-as-models-in-life-sciences-machine-learning-and-integrative-approaches/</a></p>
<p>Registration form:
<a class="moz-txt-link-freetext" href="https://framaforms.org/digicosme-thematic-school-2021-registration-1626095320">https://framaforms.org/digicosme-thematic-school-2021-registration-1626095320</a><br />
(free but mandatory, limited number of places for the tutorials)</p> Flora Jay, CR CNRS, LISN<br />
Yann Ponty, DR CNRS, LIX<br />
Ariane Migault, Chargée de communication du Labex DigiCosme<br />
Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-87251304444014542782021-09-01T08:29:00.007-07:002021-09-03T08:34:57.783-07:00<p><a href="https://www.researchgate.net/profile/Burak-Yelmen"> Burak Yelmen</a> is joining the lab as a postdoctoral fellow to extend our previous work on <a href="(https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009303" target="_blank">creating realistic genomes based on generative neural networks (GANs and RBMs)</a>. Burak's salary is supported by ANR.<br /></p>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-11130844097680639242020-05-15T08:36:00.002-07:002021-09-03T08:39:04.781-07:00<b>Pierre Jobic</b> 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 :<br />
<br />
<span style="font-size: xx-small;"><span style="font-size: xx-small;">T
Sanchez, J Cury, G Charpiat, F Jay (2020). </span>Deep learning for population size
history inference: design, comparison and combination with approximate
Bayesian computation.</span><span style="font-size: xx-small;"><span class="order-article"> Molecular Ecology Ressources <span style="font-size: xx-small;">DOI:10.1111/1755-0998.13224</span> </span></span><span style="font-size: xx-small;"><a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13224"><span style="font-size: xx-small;"><span data-seleniumid="undefinedarticle-doi">Link</span></span></a></span> <br />
<br />
Pierre is also helping beta testing and improving our <a href="https://gitlab.com/mlgenetics/dnadna">DNADNA software</a> developed by the lab and in particular by <a href="https://www.lri.fr/membre.php?mb=2165"><b>Erik Madison Bray</b></a> based on initial code by Théophile and Jean<b>.</b>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-34555460231796760912020-02-04T03:43:00.000-08:002020-03-23T06:59:34.583-07:00<b>Mathieu Michel</b> recently joined the lab for a master internship. He will help us benchmarking machine learning and deep learning methods for population genetics inference.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-73450337197017930042020-01-08T03:47:00.000-08:002020-02-04T03:49:55.677-08:00<b>Federica Pierini</b> is joining the lab as a postdoc to work on our newly awarded Human Frontier Science Program (HFSP) project <b>"Evolutionary changes in human hosts and their pathogens during first contact in the New World"</b>.<br />
<br />
This is a joint project with Emilia Huerta-Sanchez (brown University, USA) and Maria Avila Arcos (UNAM, Mexico)Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-60998597606898079772019-10-01T03:55:00.000-07:002020-02-04T03:58:53.214-08:00<b>Jérémy Guez</b> is starting a PhD with Musée de l'Homme (National Museum of natural history, Paris) and our lab (LRI) <span class="il">on <b>TransIA</b> a project for Infering </span>Cultural Transmission of Reproductive Success using Genomic Data.<br />
<br />
<i>Joint work with Evelyne Heyer, Fréderic Austerlitz, Romain Laurent, Bruno Toupance from the <a href="https://www.ecoanthropologie.fr/en">Eco-anthropology department (MNHN).</a><i> Funded by CNRS 80PRIME.</i> </i>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-47558286407695644432019-04-01T07:58:00.000-07:002019-05-22T07:59:19.644-07:00Nicolas 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.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-83223270854847162322019-02-06T08:48:00.000-08:002019-02-06T08:51:28.319-08:00Join us for the<b> PASADENA workshop </b>(GT Digicosme) on Friday, February 15th<br />
Speakers: <br />
Chloé-Agathe Azencott,CBIO, Mines ParisTech/Institut Curie/INSERM<br /> Romain Brault, Thalès<br /> Julien Chiquet, AgroParisTech/INRA MIA Paris<br /> Chloé Clavel, LTCI, Telecom-ParisTech<br /> Stanley Durrleman, Aramis Lab, ICM<br /> Joseph Salmon, Université de Montpellier <br />
<br />
<a href="http://www.lpsm.paris/pageperso/sangnier/pasadena_program.html">Program and information</a>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-21196571670989774972019-02-04T08:39:00.000-08:002019-02-06T08:50:11.100-08:00<b>Burak Yelmen</b> 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.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-41868882084712720752018-11-23T03:10:00.001-08:002019-02-06T08:37:10.482-08:00Benjamin Demaille is joining the lab to work<b> on dimension reduction, imputation, visualization of paleogenomic data</b>. This will be a follow-up and extension of Séverine Liegeois master work. Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-58451688351392140082018-11-19T03:31:00.000-08:002018-11-23T03:34:47.222-08:00I'm helping organizing the<br />
<div style="text-align: center;">
<b><i>Institut Pascal</i> Research Program<a href="https://www.universite-paris-saclay.fr/fr/programme-ecosystem-dynamics-stakes-data-and-models"> "Ecosystem dynamics : state, data and models"</a> </b></div>
<div style="text-align: center;">
<b>17 June – 12 July 2019</b></div>
<div style="text-align: center;">
<i>coordinators: Stéphane Dupas, Camille Coron, Arnaud Becheler and Adelaïde Olivier</i></div>
<div style="text-align: center;">
<br /></div>
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.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-33473179371774971762018-09-16T14:32:00.003-07:002018-11-23T03:36:06.875-08:00<span style="font-family: inherit;">Congratulations to <b>Séverine Liegeois</b> who just got the prize for best poster at the <span style="white-space: pre-wrap;">Paris-Saclay Junior Conference on Data Science and Engineering 2018 for her work on </span><span style="font-family: "arial";"><span style="white-space: pre-wrap;"><b>Dimension Reduction Adapted to Paleogenomics</b> !</span></span></span><br />
<span style="font-family: "arial";"><span style="font-family: inherit; white-space: pre-wrap;"><i>This work is done in collaboration Olivier François, TIMC-IMAG</i></span></span>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-21069010200503267852018-07-10T14:28:00.000-07:002018-11-23T03:36:34.654-08:00I'm happy to say that <b>Théophile Sanchez</b> presented his work on <b>End-to-End Deep Learning Approach for Demographic History Inference</b> in<br />
- a talk at MCEB conference, Mathematical and Computational Evolutionary Biology, Montpellier, France, June 2018<br />
- a talk at Paris-Saclay Junior Conference on Data Science and Engineering, Orsay, France, Sept. 2017<i> <a href="https://hal.archives-ouvertes.fr/hal-01679385">HAL reference</a> </i><br />
- a poster at Human Evolution: Fossils, Ancient and Modern Genomes conference, Cambridge, UK, Nov. 2017<br />
<i>This work is done in collaboration </i><i>with Guillaume Charpiat, LRI</i>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-27283432517158568042018-07-01T14:40:00.000-07:002018-09-16T14:49:52.342-07:00<b>Agnès Barnabé </b>joined the lab for a Master 1 internship, mentored by Jean Cury and myself. She is developing a pipeline for<b> </b>the <b>Demographic inference of bacterial populations using the software BEAST</b> and testing it on Jean's simulated genomic datasets.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-83359646106200162662018-05-02T03:16:00.004-07:002018-05-02T03:16:42.149-07:00<a href="https://www.lri.fr/membre.php?mb=2463">Séverine Liegeois</a> is currently doing a M2 internship on the visualization of modern and ancient DNA data through PCA or related techniques.Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-47432641488016830022018-03-01T03:13:00.000-08:002018-09-16T14:47:53.200-07:00<a href="https://www.lri.fr/membre.php?mb=2447">Jean Cury</a> started a postdoc in January. He will work on the inference of demography and selection for bacterial populations using machine learning and deep learning techniques. This project is a collaboration with Philippe Glaser (Insitut Pasteur), Guillaume Achaz (MNHN) and Eduardo Rocha (Institut Pasteur) and is funded by DIM-1Health. Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-13247281017595302902017-10-18T08:50:00.002-07:002017-10-18T08:50:48.530-07:00We are happy to announce that Théophile Sanchez obtained a bursary from ED STIC and is starting a PhD with us (Guilluame Charpiat, Marc Schoenauer and myself) to follow up his master internship <i><a href="https://github.com/jayflora/internships/blob/master/CDS_Reconstructingthepastdeeplearningforpopulationgenetics.pdf">Reconstructing the past: deep learning for population genetics!</a></i>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-14474290883574207942017-05-29T06:30:00.001-07:002017-10-18T09:26:37.756-07:00The <b>2nd Junior Conference on Data Science and Engineering</b>, Paris-Saclay will be hosted by the LAL on<b> September 14th and 15th</b>, 2017 (co-chairing with Sarah Cohen-Boulakia).<br />
All the information on <a href="http://junior-data-science.org/">http://junior-data-science.org/</a><br />
<a href="https://twitter.com/JDSEParisSaclay">Follow us on Twitter!</a><br />
<br />
<a href="https://www.universite-paris-saclay.fr/fr/actualite/jdse-2017-les-jeunes-chercheurs-a-loeuvre">Article sur la JDSE17</a>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-9078392849024136882017-03-28T02:49:00.001-07:002017-03-28T02:49:05.017-07:00 <a href="https://www.lri.fr/%7Egcharpia/">Guillaume Charpiat (TAU - INRIA/LRI)</a> and I are pleased to welcome Théophile Sanchez, who is doing a master 2 internship thanks to a grant we obtained from the <a href="https://project.inria.fr/saclaycds/">Center for Data Science</a>.<br />
Théophile is working on <i><a href="https://github.com/jayflora/internships/blob/master/CDS_Reconstructingthepastdeeplearningforpopulationgenetics.pdf">Reconstructing the past: deep learning for population genetics.</a></i>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-20627667049626731552013-01-25T14:02:00.002-08:002017-03-28T02:49:39.815-07:00NewsYou are a student interested in doing an internship about
population genetics, statistics and machine learning? Feel free to
contact me and tell me a bit about your experience and motivation!<br />
<br />
<i>Outdated:</i> Together with <a href="https://www.lri.fr/~gcharpia/">Guillaume Charpiat (TAO - INRIA/LRI)</a> we propose M2 internships on deep learning for population genetics. The proposals are focused either on more applied or more theoretical part of the work. Contact us to discuss what you think would suit you the best! We would be happy to have both biologists interested in stats/info/machine learning, or the other way around.<br />
<a href="https://github.com/jayflora/internships/blob/master/DL_popgen_bio.pdf">Fr: Reconstruire notre passé : apprentissage statistique (deep learning) pour la génétique des populations</a>.<br />
<a href="https://github.com/jayflora/internships/blob/master/DL_popgen_info.pdf">Fr: Architectures souples pour le deep learning avec application en génétique des populations.</a><br />
<a href="https://github.com/jayflora/internships/blob/master/CDS_Reconstructingthepastdeeplearningforpopulationgenetics.pdf"> En: Reconstructing the past: deep learning for population genetics.</a>Unknownnoreply@blogger.comtag:blogger.com,1999:blog-330125763880256611.post-28530511630461483072013-01-25T13:35:00.002-08:002016-09-14T07:29:35.920-07:00Research<h3 class="post-title entry-title" itemprop="name">
<br /></h3>
<div class="post-header">
I would define myself as a population geneticist with a math/info background, eager to learn from different fields.</div>
<br />
<h3>
Areas of research:</h3>
<br />
- <u>Models and methods</u>: developing statistical/mathematical approaches for analyzing biological data (mostly genetics but not only)<br />
- <u>Application</u> in population genetics and ecology<br />
<br />
I am particularly interested in genetic anthropology, spatial processes
that shape genetic diversity, relationships between genes and
environment, and reconstructing demographic history of populations (any
species).<br />
<br />
Methodological keywords: statistical inference, Bayesian statistics, applied probability, machine learning (starting)Unknownnoreply@blogger.com