Alphy

Welcome 2023

duret — 2023-04-19T14:38:50Z

Alphy/AIEM 2023

Le but central du GDR "Approche Interdisciplinaire de l'Evolution Moléculaire" (AIEM) est d'adresser un éventail de questions fondamentales en biologie de l'évolution allant par exemple de l'avantage des méthodes de statistiques quantitatives ou des mathématiques appliquées à des discussions sur les perspectives philosophiques et historiques dans ce domaine.

ALPHY est un groupe de travail du GdR "Bioinformatique Moléculaire" (BiM) et se traduit par une rencontre annuelle dédiée aux champs de la bioinformatique et de la génomique évolutive (ALPHY = ALignements and PHYlogénie). Le but principal de ces rencontres est la promotion d'échanges informels dans ces champs extrêmement interdisciplinaire, et l'encouragement auprès des jeunes scientifiques à présenter leurs travaux de recherche.

La prochaine rencontre conjointe Alphy & AIEM aura lieu sur 4 demi-journées en janvier 2023, du lundi 23 après-midi au mercredi 25 matin, sur le site de l'Université Grenoble Alpes (UGA), dans l'amphithéâtre du bâtiment André Boucherle des facultés de Médecine et de Pharmacie sur le campus de La Tronche (Isère, 38).
La conférence a vocation à être gratuite, mais l'inscription y est obligatoire (onglet "Mes dépôts"). Nous sommes désolés de ne pas pouvoir accueillir plus de 100 personnes cette fois-ci. Seules les premières inscriptions seront donc retenues ("First Come, First Served" process).

Au final, 31 étudiants et post-doctorants ont bénéficié de la prise en charge de l'hôtel (que nous avons réservé pour eux).

30 communications orales courtes ont été retenues, et
16 posters seront présentés.

Le programme détaillé d'Alphy/AIEM 2023 est ici: https://alphy-aiem-2023.sciencesconf.org/

Welcome

duret — 2023-04-19T14:31:14Z

ALPHY/AIEM 2022
March 14-16 2022 – Rennes.

WARNING: due to the covid situation, the ALPHY/AIEM meeting (initially planned on January 24-26, 2022) has been postponed to March 14-16. If you already have registered, please use the following form to confirm your participation:
https://framaforms.org/meeting-aiem-alphy-1641810599

The central goal of the GDR "Approche Interdisciplinaire de l'Evolution Moléculaire" (AIEM) is to address fundamental questions in evolutionary biology by taking advantage of methods from quantitative statistics and applied mathematics as well as by discussing historical and philosophical perspectives of the field.

ALPHY is an annual meeting dedicated to the field of Bioinformatics and Evolutionary Genomics (ALPHY = ALignments and PHYlogeny). The main goal of this meeting is to promote informal exchanges in this highly multidisciplinary field, and to encourage young scientists to present their work.

This year, Alphy and AIEM decided to organize a joint meeting, in Rennes, organized by members of ECOBIO (Sylvain Glémin, Morgane Ollivier and Armelle Salmon) and IGEPP labs (Julie Jaquiery and Jean-Christophe Simon).

The program will include three invited speakers (Claire Lemaitre, Jens Bast, Amaury Lambert) and 20 contributed talks.

Registration to the meeting is free, but mandatory. Please use the link (top left of this page) to register.

If you wish to present your work, submit your abstract in the registration form.

To encourage the participation of young colleagues, we will directly book and pay hotel rooms for students and postdocs. If our budget permits, we will also book rooms for other participants. Please indicate if you are interested in the registration form.

Important dates:
• Deadline for abstract submission: December 3 2021
• Notification: December 13 2021
• Deadline for registration : December 20 2021.

WARNING: due to the current Covid pandemy, all participants will have to present a valid 'pass sanitaire' to attend the meeting.

A bientôt – see you at Alphy/AIEM 2022!

Contact: Sylvain Glémin (sylvain.glemin@univ-rennes1.fr)

Alphy/AIEM is supported by the GDR BiM and by the GDR AIEM.

Organizing committee 2021

duret — 2021-10-01T14:08:57Z

Organizing committee:

Sophie Abby (Laboratoire TIMC-IMAG, CNRS, Université Grenoble Alpes ): sophie.abby@univ-grenoble-alpes.fr

Thomas Hindré (Laboratoire TIMC-IMAG, CNRS, Université Grenoble Alpes )

Ivan Junier (Laboratoire TIMC-IMAG, CNRS, Université Grenoble Alpes )

Hugo Mathé-Hubert (Laboratoire TIMC-IMAG, CNRS, Université Grenoble Alpes )

Fabien Pierrel (Laboratoire TIMC-IMAG, CNRS, Université Grenoble Alpes )

Nelle Varoquaux (Laboratoire TIMC-IMAG, CNRS, Université Grenoble Alpes )

Laurent Duret (Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon1): laurent.duret@univ-lyon1.fr

Céline Scornavaca (Institut des Sciences de l'évolution de Montpellier, CNRS, Université Montpellier 2): celine.scornavacca@umontpellier.fr

List of participants 2021

duret — 2021-10-01T14:07:34Z

1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 14

Registration Alphy 2021
First name	Last name	Institution
Laurent	Duret	LBBE
Celine	Scornavacca	ISEM, CNRS
Sophie	Abby	CNRS, TIMC-IMAG, Université Grenoble Alpes
Nelle	Varoquaux	TIMC (Équipe Tree)
Ivan	Junier	TIMC-IMAG
hugo	mathé-hubert
Chrystelle	Delord	IRD La Réunion
Igor	Rouzine	Sorbonne Université, Pierre et Marie Curie
Remi	Denise	University of Florida
Ilkay Basak	UYSAL	IRD/MIVEGEC-Montpellier
Ingrid	Lafontaine	Sorbonne Université
Benedicte	Condamine	IAME
Alice	Balard	Humboldt university, Berlin, Germany
Josquin	Daron	CNRS
Ksenia	Juravel	LMU
zeyuan	chen	SNSB - Zoologische Staatssammlung München
Jean-Nicolas	VOLFF	IGFL/ENS Lyon
Anaïs	Bardet	CNRS
Corentin	Dechaud	IGFL
Dina Mae	Rañises	Université libre de Bruxelles

Abstracts 2021

duret — 2021-10-01T14:06:09Z

Abstracts Alphy 2021


Abstracts Alphy 2021

Program 2021

duret — 2021-09-29T15:47:50Z

The conference will be accessible via this link:
https://univ-grenoble-alpes-fr.zoom.us/j/94570672285

In case of problem with your connection, please contact Sophie Abby (sophie.abby@univ-grenoble-alpes.fr).

Tuesday February 2
8:45-9:15		Speakers technical check
9:15-9:30		Introduction
Session 1:		L. Duret (chair), S. Abby (co-chair)
9:30-10:15	Eduardo Rocha	Interplay between mobile elements, gene flow and functional innovation
10:15-10:30	Igor Rouzine	An evolution-based high-fidelity method of epistasis measurement: theory and application to influenza
10:35-10:50	Marie Morel	A simulation-based approach to reveal evolutionary convergence at the amino acid level
10:55-11:25	Coffee Break
Session 2:		C. Scornavacca (chair), S. Abby (co-chair)
11:25-11:40	Paul De Boissier	SLiMs-TITAN : a pipeline to study the conservation of protein motifs in a structural context
11:45-12:00	Benjamin Linard	PEWO: a community effort to benchmark phylogenetic placements
12:05-12:20	Yann Spöri	HaplowebMaker: An online web tool for species delimitation using haplowebs
12:25-12:40	Nika Abdollahi	ClonalTree: exploring minimum spanning tree and the observed abundance of genotypes in the reconstruction of B-cell receptor lineage trees
12:45-14:00	Lunch Break
Session 3:		T. Hindré (chair), N. Varoquaux (co-chair)
13:30-14:00		Speakers technical check
14:00-14:45	Philippe Remigi	Experimental evolution of a plant pathogen into a legume symbiont: a population perspective
14:45-15:00	Célia Domingues	Human connections drive the evolution of metagenomes with virulence and antibiotic-resistance genes
15:05-15:20	Diego Santos Garcia	Did Coxiella-like endosymbionts evolve from a parasitic ancestor?
15:25-15:40	Julie Boisard	Challenges and solutions for studying divergent eukaryotic genomes of non-model and non-cultivable species
15:45-16:00	Nicolas Leurs	Evolution of collagen type VI protein coding genes in Vertebrates

Wednesday February 3
9:00-9:30		Speakers technical check
Session 4:		I. Junier (chair), N. Varoquaux (co-chair)
9:30-10:15	Camille Berthelot	Synteny-guided correction of gene trees
10:15-10:30	Florian Bénitière	Paramecium sonneborni : a promiscuous species ?
10:35-10:50	Alexandre Laverré	Comparative analyses of chromatin conformation capture data shed light on the evolution of gene expression cis-regulatory landscapes
10:55-11:25	Coffee Break
Session 5:		L. Duret (chair), S. Abby (co-chair)
11:25-11:40	Josquin Daron	Worldwide population genetic structure of Plasmodium vivax support an Southeast Asia origin
11:45-12:00	Carine Rey	Characterization of the purged DNA in a new nematode undergoing programmed-genome elimination in the soma
12:05-12:20	Jérémy Ganofsky	Inverted hourglass pattern of gene sequence and expression evolution in rodent molar development
12:25-12:40	Djivan Prentout	Plant genera Cannabis and Humulus share the same pair of well- differentiated sex chromosomes
12:45-14:00	Lunch Break
13:30-14:00		Speakers technical check
Session 6:		S. Abby (chair), I. Junier (co-chair)
14:00-14:45	Guillaume Borrel	Diversity and evolution of methane metabolism
14:45-15:00	Benjamin Guinet	Domestication of viruses by parasitic wasps: a bioinformatic approach
15:05-15:20	Najwa Taib	Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
15:25-15:40	Theo Tricou	Ghost lineages deceive introgression tests and call for a new null hypothesis
15:45-	Final words

Welcome 2021

duret — 2021-09-29T15:43:54Z

ALPHY 2021: Bioinformatics and Evolutionary Genomics
February 2 and 3, 2021 – Virtual Meeting.

This year, Alphy is organized by Sophie Abby and her colleagues (TIMC-IMAG
Equipe Génomique et Evolution des Microorganismes, CNRS, Université Grenoble Alpes). Given the covid situation, we decided that Alphy 2021 will be entirely virtual (too bad for the view on snowy mountains!).

The conference will be accessible via this link:
https://univ-grenoble-alpes-fr.zoom.us/j/94570672285

The program will include four invited speakers (Camille Berthelot, Guillaume Borrel,, Philippe Remigi and Eduardo Rocha) and 20 contributed talks.

Registration to the meeting is free, but mandatory. Please use the link (top left of this page) to register.

If you wish to present your work, submit your abstract in the registration form.

Important dates:
• Deadline for abstract submission: December 18 2020
• Deadline for registration : February 3 2021.

A bientôt – see you (virtually) at Alphy 2021!

Contact: Sophie Abby (sophie.abby@univ-grenoble-alpes.fr)

Alphy is supported by the GDR BiM .

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Announcement: the 24th Evolutionary Biology Meeting at Marseille will be held on September 21-24 2021. For more information, click here: EBM.

Registration 2020

duret — 2020-11-13T16:42:40Z

Registration is free but mandatory. Please fill in the form below to register.

If you wish to present your work, please copy/paste the title and abstract of your presentation in the form below.

We propose grants to help covering the travel and lodging expenses of some students and postdocs (priority will be given to those who submitted an abstract). If you wish to apply for a travel grant, do not forget to indicate it in the form below.

Important dates:

Deadline for abstract submission: December 19 2019
Deadline for travel grant application: December 19 2019
Deadline for registration : January 10 2020

Organizing committee 2020

duret — 2020-11-13T16:31:14Z

Organizing committee:
Guillaume Beslon (INRIA - LIRIS - équipe Beagle): guillaume.beslon@inria.fr
Laurent Duret (Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon1): laurent.duret@univ-lyon1.fr
Céline Scornavaca (Institut des Sciences de l'évolution de Montpellier, CNRS, Université Montpellier 2): celine.scornavacca@umontpellier.fr

- 2020 (Lyon)

List of participants 2020

duret — 2020-11-13T16:30:22Z

1 | 2 | 3 | 4 | 5

Registration Alphy 2020
First name	Last name	Institution
Laurent	Duret	CNRS, UCBL
Laurent	Modolo	LBMC
Daniel	Kahn	Ecologie Microbienne, INRA
Bergot	Marine	CIRI
Adel Amar	Amouri	Département de Biologie. BP 1524. Faculté SNV. Université d'Oran 1. Algérie
Thomas	Brazier
GANOFSKY	jérémy	LBMC
Carine	Rey	LBMC
Céline	Brochier	Université Claude Bernard
Duvermy	Arnaud
Evguenia	Kopylova
Nicolas	Galtier	ISEM - CNRS - Université Montpellier
Xavier	VEKEMANS	University of Lille
Clotilde	Garrido	IBPC UMR7141
Corentin	Dechaud	ENS de Lyon - IGFL
Léopold	Carron	LCQB
Arthur	Weyna	Institut des Sciences de l'Evoluton de Montpellier
Laure	Segurel	CNRS
Céline	CATTELIN	IBPC UMR7141 - Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues
Maxime	Policarpo	EGCE - CNRS