Vincent MIELE

58
Documents

Publications

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-05308071 v1
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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-05093147 v1
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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-04793697 v1
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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, In press, ⟨10.1002/rse2.412⟩
Article dans une revue hal-04749328 v1
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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-04278674 v2
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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-03172480 v4
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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-03191630 v2
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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-03425925 v1
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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-03142486 v1
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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-03418817 v1
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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-02331446 v1
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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-02140494 v1
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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-03009740 v1
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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-02078993 v1
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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-02089501 v2
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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-01608245 v1
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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-01167837 v2
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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-01474524 v1
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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-01426652 v1

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-02049895 v1
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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-01938697 v1
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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-01280238 v1
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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-01416841 v1

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-02045097 v1
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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-02045124 v1

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-00965711 v1
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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-01636872 v1

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-00698365 v1

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-00539318 v1

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-00391483 v1
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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-02658961 v1

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-00428390 v1
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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-00319296 v1

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-00428182 v1

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-00428131 v1

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-00428088 v1

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-02654141 v1

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-00427880 v1

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-00428049 v1

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-00427936 v1

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-00427832 v1

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-04849520 v1

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-02793574 v1

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-02793581 v1

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-02742012 v1

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-01079947 v1

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-02069363 v1

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-03811607 v1
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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-02473919 v1

Calcul parallèle avec R

Vincent Miele , Violaine Louvet
EDP sciences, 2016, 978-2-7598-2060-3
Ouvrages hal-02090003 v1