Vincent MIELE

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Publications

Multilayer Network Analysis Reveals Connectivity Synergies Between Protected Area Levels Across Various Taxonomic Groups

Marie‐caroline Prima , Lucia Oliveira-Cruz , Vincent Miele , Sara Si-Moussi , Paul Rouveyrol et al.

Conservation Letters, 2025, 18 (5), ⟨10.1111/conl.13148⟩

Article dans une revue hal-05308071v1
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Zero‐shot animal behaviour classification with vision‐language foundation models

Gaspard Dussert , Vincent Miele , Colin van Reeth , Anne Delestrade , Stéphane Dray et al.

Methods in Ecology and Evolution, 2025, 16 (7), pp.1460-1472. ⟨10.1111/2041-210x.70059⟩

Article dans une revue hal-05093147v1
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ORCHAMP: an observation network formonitoring biodiversity and ecosystem functioning across space and time inmountainous regions

Wilfried Thuiller , Amélie Saillard , Sylvain Abdulhak , Vincent Augé , Carole Birck et al.

Comptes Rendus. Biologies, 2024, 347, pp.223-247. ⟨10.5802/crbiol.165⟩

Article dans une revue hal-04793697v1
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Being confident in confidence scores: calibration in deep learning models for camera trap image sequences

Gaspard Dussert , Simon Chamaillé-Jammes , Stéphane Dray , Vincent Miele

Remote Sensing in Ecology and Conservation, 2024, 11 (1), pp.88-99. ⟨10.1002/rse2.412⟩

Article dans une revue hal-04749328v1
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The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images

Noa Rigoudy , Gaspard Dussert , Abdelbaki Benyoub , Aurélien Besnard , Carole Birck et al.

European Journal of Wildlife Research, 2023, 69 (6), pp.113. ⟨10.1007/s10344-023-01742-7⟩

Article dans une revue hal-04278674v2
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Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Marc Ohlmann , Catherine Matias , Giovanni Poggiato , Stéphane Dray , Wilfried Thuiller et al.

Ecological Modelling, 2023, 483, pp.110424. ⟨10.1016/j.ecolmodel.2023.110424⟩

Article dans une revue hal-03172480v4
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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, 2022, 13 (1), pp.203-216. ⟨10.1111/2041-210X.13738⟩

Article dans une revue hal-03191630v2
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Revisiting animal photo-identification using deep metric learning and network analysis

Vincent Miele , Gaspard Dussert , Bruno Spataro , Simon Chamaillé-Jammes , Dominique Allainé et al.

Methods in Ecology and Evolution, 2021, 12 (5), pp.863-873. ⟨10.1111/2041-210X.13577⟩

Article dans une revue hal-03425925v1
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Images, écologie et deep learning

Vincent Miele , Stéphane Dray , Olivier Gimenez

Regards sur la biodiversité, 2021

Article dans une revue hal-03142486v1
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Core–periphery dynamics in a plant–pollinator network

Vincent Miele , Rodrigo Ramos-Jiliberto , Diego Vázquez

Journal of Animal Ecology, 2020, 89 (7), pp.1670-1677. ⟨10.1111/1365-2656.13217⟩

Article dans une revue hal-03418817v1
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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, 2019, 15 (8), pp.e1007269. ⟨10.1371/journal.pcbi.1007269⟩

Article dans une revue hal-02331446v1
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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 et al.

PLoS Genetics, 2019, 15 (2), pp.e1007965. ⟨10.1371/journal.pgen.1007965⟩

Article dans une revue hal-02140494v1
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The diversity of interaction types drives the functioning of ecological communities

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

PLoS Computational Biology, 2019, 15 (8), pp.e1007269. ⟨10.1101/411249⟩

Article dans une revue hal-03009740v1
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Diversity indices for ecological networks: a unifying framework using Hill numbers

Marc Ohlmann , Vincent Miele , Stéphane Dray , Loic Chalmandrier , Louise O’connor et al.

Ecology Letters, 2019, 22 (4), pp.737-747. ⟨10.1111/ele.13221⟩

Article dans une revue hal-02078993v1
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Nine Quick Tips for Analyzing Network Data

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

PLoS Computational Biology, 2019, 15 (12), pp.e1007434. ⟨10.1371/journal.pcbi.1007434⟩

Article dans une revue hal-02089501v2
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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 et al.

Algorithms for Molecular Biology, 2017, 12 (1), pp.2. ⟨10.1186/s13015-017-0091-2⟩

Article dans une revue hal-01474524v1
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Ecological networks to unravel the routes to horizontal transposon transfers

Samuel Venner , Vincent Miele , Christophe Terzian , Christian Biemont , Vincent Daubin et al.

PLoS Biology, 2017, 15 (2), ⟨10.1371/journal.pbio.2001536⟩

Article dans une revue hal-01608245v1
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Statistical clustering of temporal networks through a dynamic stochastic block model

Catherine Matias , Vincent Miele

Journal of the Royal Statistical Society: Series B, 2017, 79 (4), pp.1119-1141. ⟨10.1111/rssb.12200⟩

Article dans une revue hal-01167837v2
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Revealing the hidden structure of dynamic ecological networks

Vincent Miele , Catherine Matias

Royal Society Open Science, 2017, 4, pp.170251. ⟨10.1098/rsos.170251⟩

Article dans une revue hal-01426652v1

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 et al.

The American Naturalist, 2016, 188 (1), pp.66-75. ⟨10.1086/686684⟩

Article dans une revue hal-02049895v1
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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, 2016, 14 (8), pp.e1002527. ⟨10.1371/journal.pbio.1002527⟩

Article dans une revue hal-01938697v1
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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 et al.

GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩

Article dans une revue hal-01280238v1
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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 et al.

PLoS ONE, 2015, 10, pp.e0129427. ⟨10.1371/journal.pone.0129427⟩

Article dans une revue pasteur-01416841v1

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

Guillem Rigaill , Vincent Miele , Franck Picard

Lecture Notes in Computer Science, 2014, 8452, pp.248-258

Article dans une revue hal-02045097v1
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Spatially constrained clustering of ecological networks

Vincent Miele , Franck Picard , S. Dray

Methods in Ecology and Evolution, 2014, 5 (8), pp.771-779. ⟨10.1111/2041-210X.12208⟩

Article dans une revue hal-02045124v1

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele , Simon Penel , Vincent Daubin , Franck Picard , Daniel Kahn et al.

Bioinformatics, 2012, 28 (8), pp.1078-85. ⟨10.1093/bioinformatics/bts098⟩

Article dans une revue hal-00965711v1
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Toward community standards in the quest for orthologs

Christophe Dessimoz , Toni Gabaldon , David Roos , Erik L L Sonnhammer , Javier Herrero et al.

Bioinformatics, 2012, 28 (6), pp.900-904. ⟨10.1093/bioinformatics/bts050⟩

Article dans une revue hal-01636872v1

Ultra-fast sequence clustering from similarity networks with SiLiX

V. Miele , Simon Penel , L. Duret

BMC Bioinformatics, 2011, 12(116), pp.1-9. ⟨10.1186/1471-2105-12-116⟩

Article dans une revue hal-00698365v1

Strategies for online inference of model-based clustering in large and growing networks

H. Zanghi , Franck Picard , V. Miele , C. Ambroise

Annals of Applied Statistics, 2010, 4 (2), pp.687-714. ⟨10.1214/10-AOAS359⟩

Article dans une revue hal-00539318v1
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Deciphering the connectivity structure of biological networks using MixNet

Franck Picard , Vincent Miele , Jean-Jacques J.-J. Daudin , Ludovic Cottret , Stephane S. Robin

BMC Bioinformatics, 2009, 10, pp.1-11. ⟨10.1186/1471-2105-10-S6-S17⟩

Article dans une revue hal-02658961v1

Deciphering the connectivity structure of biological networks using MixNet

Franck Picard , V. Miele , L. Cottret , J.J. Daudin , S. Robin

BMC Bioinformatics, 2009, in press, pp.1-1

Article dans une revue hal-00391483v1

Deciphering the connectivity structure of biological networks using MixNet

Franck Picard , V. Miele , J.J. Daudin , L. Cottret , S. Robin

BMC Bioinformatics, 2009, 10, pp.1-11

Article dans une revue hal-00428390v1
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DNA physical properties determine nucleosome occupancy from yeast to fly.

Vincent Miele , Cédric Vaillant , Yves d'Aubenton-Carafa , Claude Thermes , Thierry Grange

Nucleic Acids Research, 2008, 36 (11), pp.3746-56. ⟨10.1093/nar/gkn262⟩

Article dans une revue hal-00319296v1

Fast online graph clustering via Erdos–Rényimixture

H. Zanghi , C. Ambroise , V. Miele

Pattern Recognition, 2008, 41, pp.3592-3599

Article dans une revue hal-00428182v1

DNA physical properties determine nucleosome occupancy from yeast to fly

V. Miele , C. Vaillant , Y. d'Aubenton-Carafa , C. Thermes , T. Grange

Nucleic Acids Research, 2008, 36, pp.3746-3756

Article dans une revue hal-00428131v1

Taking into account missing genotypes and errors in Family Based Association Testing using an Expectation-Maximization framework

V. Miele , Y. Slaoui , A. Rebai

incollection, 2008, --, pp.508-514

Article dans une revue hal-00428088v1

DNA sequence drives nucleosome occupancy of yeast promoters

V. Miele , C. Vaillant , Y. d'Aubenton , David Robelin , B. Prum et al.

incollection, 2006, --, pp.2783-2784

Article dans une revue hal-00427880v1

A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery

P. Nicolas , A.-S. Tocquet , V. Miele , F. Muri

Journal of Computational Biology, 2006, 13, pp.651-667

Article dans une revue hal-00428049v1

A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery

Pierre P. Nicolas , Anne-Sophie Tocquet , Vincent Miele , Florence Muri

Journal of Computational Biology, 2006, 13 (3), pp.651-667

Article dans une revue hal-02654141v1

Uncovering structure in biological networks

J.J. Daudin , Vincent Lacroix , M. Mariadassou , V. Miele , Franck Picard et al.

incollection, 2006, --, pp.471-483

Article dans une revue hal-00427936v1

seq++: a package for biological sequences analysis with a range of Markov-related models

V. Miele , P.Y. Bourguignon , David Robelin , Gregory Nuel , H. Richard

Bioinformatics, 2005, 21, pp.2783-2784

Article dans une revue hal-00427832v1

DeepFaune: A journey towards an efficient classifier for the european fauna

Vincent Miele

LifeCLEF, Alexis Joly; Henning Müller; Hervé Goëau, Sep 2024, Grenoble, France

Communication dans un congrès hal-04849520v1

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, Jun 2016, Badia di Moscheta, Italy

Communication dans un congrès hal-02793574v1

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, Jun 2017, Grimsö, Sweden

Communication dans un congrès hal-02793581v1

Fast and parallel algorithm for population-based segmentation of copy-number profiles

Guillem Rigaill , Vincent Miele , Franck Picard

10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), Jun 2013, Nice, France. 275 p., ⟨10.1007/978-3-319-09042-9_18⟩

Communication dans un congrès hal-02742012v1

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

Gustavo Sacomoto , Blerina Sinaimeri , Camille Marchet , Vincent Miele , Marie-France Sagot et al.

WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics, Sep 2014, Wroclaw, Poland. pp.82-96, ⟨10.1007/978-3-662-44753-6_7⟩

Communication dans un congrès hal-01079947v1

New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data

Alice Julien-Laferriere , Gustavo Sacomoto , Rayan Chikhi , Erwan Scaon , David P. Parsons et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France

Communication dans un congrès hal-02069363v1

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., Wiley, pp.117-134, 2022, ⟨10.1002/9781119902799.ch6⟩

Chapitre d'ouvrage hal-03811607v1
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Réseaux et connectivité

Etienne Edouard Cossart , Colin Fontaine , Grégor Marchand , Marie Balasse , Stéphanie Bréhard et al.

Stéphanie Thiébault et al. (coord.). Prospectives de l’Institut Écologie et environnement du CNRS, CNRS, pp.187-193, 2017, Les Cahiers Prospectives

Chapitre d'ouvrage hal-02473919v1

Calcul parallèle avec R

Vincent Miele , Violaine Louvet

EDP sciences, 2016, 978-2-7598-2060-3

Ouvrages hal-02090003v1