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Miele Vincent

Ingénieur de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 72 44 85 44

Email

I am working in CNRS @ Biometry and Evolutionary Biology Lab. With a background in mathematics and computer science, I am involved in projects in ecology, on two main axes :

- ecological networks : analysing original datasets, proposing new methodological developments and helping non specialists (see this "quick tips" paper) ;

- image, ecology & deep learning : as a leader of the imaginecology initiative (see imaginecology website), developping computer vision pipelines (co-leader of the DeepFaune project) and sharing knowledge with ecologists.

I am almost 100% degooglized, but you can still have a look at my scholar profile.

 

- Project member :

  • ANR FuturePred 2019-2022
  • ANR Horizon 2018-2022
  • ANR Colib’read 2012-2016
  • ANR Ancestrome 2011-2016
  • ANR NeMo 2007-2011

- Board member

 

- Reviewer :

- Jury member :

  • INRA IRE01, 2022 (président)
  • HCERES MISTEA, 2020
  • INRA IRE01, 2018 (président)
  • UGA IGE, 2017
  • CNRS IR43, 2017
  • INRA CEI, 2017
  • CNRS IE 13INSMI03, 2013
  • INRA IRE12, 2012
  • INRA IRE05, 2011
  • INRA IRE01, 2009
  • CNRS IE 155, 2008

- Organizing commitee :

  • CEMRACS, Méthodes numériques et algorithmes pour architectures hautes performances, Summer 2012 (le reportage de France3 ici)
  • Journées du groupe Calcul , November 2010.
  • Le coté Calcul de Jobim , June 2009.
  • Mathematics for Biological Networks , December 2007
  • European Conference on Computational Biology, September 2003

 

Here  (c)  means "co-supervision"

  • Gaspard Dussert (c), Doc, DeepFaune project, 2022-25
  • Elias Chetouane, M2 Informatique et Données,  Deep learning for camera traps, 2022
  • Marine Desprez (c) , Post Doc, Machine learning in ecology, 2022
  • Bastien Payre, M2 Maths en action, Deep learning et séquences d'images, 2021
  • Nathan Levray, M2 Maths en action, Higher order networks, 2021
  • Noa Rigoudy (c), ENS Lyon, Deep learning for camera traps, 2021
  • Julien Bonnier (c), M2 BEE, reconnaissance des pollens, 2021
  • Giusseppe Capizzi, M2 Data Science, Machine learning for botanics, 2020-21
  • Christophe Botella (c), Post Doc, Graph embeddings, 2020-21
  • Thibault Genissel (c), ENS Lyon, Réseaux de contact entre ongulés, 2020
  • Gaspard Dussert, ENSTA, imaginecology, 2019
  • Claire Gayral, M2 Maths en action, Algorithme EM classifiant dans dynSBM, 2018
  • Gonché Danesh (c), M2 Bioinformatique, Simulation de HTT, 2017
  • Florent Tessier, M2 Bioinformatique, Génomique comparative du manchot, 2015
  • Mamadou Dione, M2 Mathématiques, Etude de la température corporelle des marmottes en lien avec les conditions climatiques, 2014
  • Camille Marchet (c), Software Engineer INRIA Bamboo, 2013-2014
  • Thomas Bigot (c), Software Engineer ANR Ancestrome, 2013-2015
  • Mathilde Boutigny, M1 Ingénieur, Développement du package kissplice2reftranscriptome, 2014
  • Alice Julien (c), Software Engineer INRIA Bamboo, 2012-2013
  • Patrick Tran Van, L3 UCBL, Intégration de programmes de calcul dédiés aux NGS dans le système GALAXY, 2012
  • Vincent Lanore, M1 ENS Info, Hybrid parallel computing applied to DNA processing, 2011
  • Aurélie Siberchicot (c), CDD ANR, 2010-11 (C++ development manager)
  • Marie Jorandon, M1 INAPG, Etude statistique de données NGS sur l’espacement des nucléosomes, 2009
  • Laurent Modolo, L3 UCBL Bio, Packaging d’une application de recherche de motifs, 2008

 

  • deepfaune  Automatic identification of the French fauna in camera-trap images
    Collaboration with Simon Chamaillé-Jammes et Bruno Spataro
  • econetwork A collection of advanced tools, methods and models for the analysis of ecological networks,
    Collaboration with EcoNet group
  • dynsbm Dynamic stochastic block models,
    Collaboration with C.Matias
  • HiFiX + SiLiX Ultra-fast + High Fidelity Clustering of sequences,
    efficent parallel algorithms + network science.
    Collaboration with L.Duret, D.Kahn, V.Daubin & S.Penel

  • 2023- : Ingenieur de Recherche CNRS hors classe, Laboratory Biometry and Evolutionary Biology (U.Lyon)
  • 2017-2022 : Ingenieur de Recherche CNRS 1ère classe, Laboratory Biometry and Evolutionary Biology (U.Lyon)
  • 2008-2016 : Ingenieur de Recherche CNRS 2nd classe, Laboratory Biometry and Evolutionary Biology (U.Lyon)
  • 2001-2007 : Ingenieur de Recherche CNRS 2nd classe, Laboratory Statistics and Genome (U.Evry)
  • 2000 : Ingénieur "Grandes écoles" Mathematics and Modelling - (Polytech Clermond-Ferrand)
  • 2000 : Master Applied Mathematics (U.Clermont Auvergne)

Publications

Display of 1 to 30 publications on 48 in total

Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Marc Ohlmann, Catherine Matias, Giovanni Poggiato, Stéphane Dray, Wilfried Thuiller, Vincent Miele

Preprint

see the publication

The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images

Noa Rigoudy, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Yoann Bollet, Yoann Bunz...

DOI: 10.1101/2022.03.15.484324

Preprint

see the publication

Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks

Julie J. Aubert, Pierre M Barbillon, Sophie Donnet, Vincent Miele

Statistical Approaches for Hidden Variables in Ecology. . : 117-134

DOI: 10.1002/9781119902799.ch6

Book chapter

see the publication

An appraisal of graph embeddings for comparing trophic network architectures

Christophe Botella, Stéphane Dray, Catherine Matias, Vincent Miele, Wilfried Thuiller

Methods in Ecology and Evolution . 13 ( 1 ) : 203-216

DOI: 10.1111/2041-210X.13738

Journal article

see the publication

Core-periphery structure in mutualistic networks: an epitaph for nestedness?

Ana Martín González, Diego Vázquez, Rodrigo Ramos-Jiliberto, Sang Hoon Lee, Vincent Miele

DOI: 10.1101/2020.04.02.021691

Preprint

see the publication

Revisiting animal photo-identification using deep metric learning and network analysis

Vincent Miele, Gaspard Dussert, Bruno Spataro, Simon Chamaillé-Jammes, Dominique Allainé, Christophe Bonenfant

Methods in Ecology and Evolution . 12 ( 5 ) : 863-873

DOI: 10.1111/2041-210X.13577

Journal article

see the publication

Images, écologie et deep learning

Vincent Miele, Stéphane Dray, Olivier O. Gimenez

Regards sur la biodiversité .

Journal article

see the publication

Revisiting giraffe photo-identification using deep learning and network analysis

Vincent Miele, Gaspard Dussert, Bruno Spataro, Simon Chamaillé-Jammes, Dominique Allainé, Christophe Bonenfant

DOI: 10.1101/2020.03.25.007377

Preprint

see the publication

The diversity of interaction types drives the functioning of ecological communities

Vincent Miele, Christian Guill, Rodrigo Ramos-Jiliberto, Sonia Kéfi

DOI: 10.1101/411249

Preprint

see the publication

Core–periphery dynamics in a plant–pollinator network

Vincent Miele, Rodrigo Ramos‐jiliberto, Diego Vázquez

Journal of Animal Ecology . 89 ( 7 ) : 1670-1677

DOI: 10.1111/1365-2656.13217

Journal article

see the publication

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, Clément Gilbert...

PLoS Genetics . 15 ( 2 ) : e1007965

DOI: 10.1371/journal.pgen.1007965

Journal article

see the publication

Nine Quick Tips for Analyzing Network Data

Vincent Miele, Stephane S. Robin, Catherine Matias, Stéphane Dray

PLoS Computational Biology . 15 ( 12 ) : e1007434

DOI: 10.1371/journal.pcbi.1007434

Journal article

see the publication

Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model

Vincent Miele, Christian Guill, Rodrigo Ramos-Jiliberto, Sonia Kéfi

PLoS Computational Biology . 15 ( 8 ) : e1007269

DOI: 10.1371/journal.pcbi.1007269

Journal article

see the publication

Diversity indices for ecological networks: a unifying framework using Hill numbers

Marc Ohlmann, Vincent Miele, Stéphane Dray, Loic Chalmandrier, Louise O’connor, Wilfried Thuiller

Ecology Letters . 22 ( 4 ) : 737-747

DOI: 10.1111/ele.13221

Journal article

see the publication

Inferring the timing of territoriality and rut in male roe deer from movements? Some preliminary results - and new perspectives

Nicolas Morellet, Vincent Miele, Christophe Bonenfant

6. EURODEER meeting .

Conference paper

see the publication

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele...

Algorithms for Molecular Biology . 12 ( 1 ) : 2

DOI: 10.1186/s13015-017-0091-2

Journal article

see the publication

Statistical clustering of temporal networks through a dynamic stochastic block model

Catherine Matias, Vincent Miele

Journal of the Royal Statistical Society: Series B . 79 ( 4 ) : 1119–1141

DOI: 10.1111/rssb.12200

Journal article

see the publication

Ecological networks to unravel the routes to horizontal transposon transfers

Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biemont, Vincent Daubin, Cedric Feschotte...

PLoS Biology . 15 ( 2 ) : np

DOI: 10.1371/journal.pbio.2001536

Journal article

see the publication

Revealing the hidden structure of dynamic ecological networks

Vincent Miele, Catherine Matias

Royal Society Open Science . 4 : 170251

DOI: 10.1098/rsos.170251

Journal article

see the publication

Réseaux et connectivité

Etienne Edouard Cossart, Colin Fontaine, Grégor Marchand, Marie Balasse, Stéphanie Bréhard, Claire Manen...

Prospectives de l’Institut Écologie et environnement du CNRS . : 187-193

Book chapter

see the publication

Inferring the timing of territoriality and rut in male roe deer from movements?

Nicolas Morellet, Christophe Bonenfant, Vincent Miele, Marco Heurich, Stefano Focardi

8. EURODEER meeting .

Conference paper

see the publication

Fruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies

Samuel Venner, A. Siberchicot, P.F. Pélisson, E. Schermer, Marie-Claude Bel-Venner, M. Nicolas...

American Naturalist . 188 ( 1 ) : 66-75

DOI: 10.1086/686684

Journal article

see the publication

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, Claire Lemaitre...

GigaScience . 5 ( 1 )

DOI: 10.1186/s13742-015-0105-2

Journal article

see the publication

How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience

Sonia Kéfi, Vincent Miele, Evie Wieters, Sergio Navarrete, Eric Berlow

PLoS Biology . 14 ( 8 ) : e1002527

DOI: 10.1371/journal.pbio.1002527

Journal article

see the publication

Calcul parallèle avec R

Vincent Miele, Violaine Louvet

978-2-7598-2060-3

Book

see the publication

DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity

Monica Naughtin, Zofia Haftek-Terreau, Johan Xavier, Sam Meyer, Maud Silvain, Yan Jaszczyszyn...

PLoS ONE . 10 : e0129427

DOI: 10.1371/journal.pone.0129427

Journal article

see the publication

Spatially constrained clustering of ecological networks

Vincent Miele, Franck Picard, S. Dray

Methods in Ecology and Evolution . 5 ( 8 ) : 771-779

DOI: 10.1111/2041-210X.12208

Journal article

see the publication

Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles

Guillem Rigaill, Vincent Miele, Franck Picard

Lecture Notes in Computer Science . 8452 : 248-258

Journal article

see the publication

Navigating in a Sea of Repeats in RNA-seq without Drowning

Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix

WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96

DOI: 10.1007/978-3-662-44753-6_7

Conference paper

see the publication