Nicolas Vergne Publications

Accueil
CV
Publications
Enseignements

Articles

  • Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences. N. Vergne. Statistical Applications in Genetics and Molecular Biology 7 2008. [HAL]
  • Poisson approximation for search of rare words in DNA sequences. N. Vergne and M. Abadi. ALEA 4 2008. [HAL]
  • Sharp error for point-wise Poisson approximations in mixing processes. M. Abadi and N. Vergne. Nonlinearity 21 2008. [HAL]
  • Sharp error terms for return time statistics under mixing conditions. M. Abadi and N. Vergne. Journal of Theoretical Probability 22 2009. [HAL]
  • Coalescent-based DNA barcoding: multilocus analysis and robustness. O. David, C. Larédo, R. Leblois, B. Schaeffer and N. Vergne . Journal of Computational Biology 19 2012. [HAL]
  • Value of ultrasonography as a marker of early response to abatacept in patients with rheumatoid arthritis and an inadequate response to methotrexate: results from the APPRAISE study. M.V.C Nguyen & al. Annals of the Rheumatic Diseases 2016. [HAL]
  • Pre-silencing of genes involved in the electron transport chain (ETC) pathway is associated with responsiveness to abatacept in rheumatoid arthritis. C. Derambure, G. Dzangue-Tchoupou, C. Bérard, N. Vergne, M. Hiron M D'agostino, P. Musette, O. Vittecoq and T. Lequerré. Arthritis Research and Therapy 19 2017. [HAL]
  • Comparative in depth RNA sequencing of P. tricornutum’s morphotypes reveals specific features of the oval morphotype. C. Ovide, M.C. Kiefer-Meyer, C. Berard, N. Vergne, T. Lecroq, C. Plasson, C. Burel, S.Bernard, A. Driouich, P.Lerouge, I. Tournier, H. Dauchel, M. Bardor. Scientific Reports, Nature Publishing Group. 8 2018. [HAL]
  • Reliability and survival analysis for drifting Markov models: modeling and estimation. V.S. Barbu and N. Vergne. Methodology and Computing in Applied Probability, Springer Verlag. 2018. [HAL]
  • SMM: An R Package for Estimation and Simulation of Discrete-time semi-Markov Models. V.S. Barbu C. Bérard, D. Cellier, M. Sautreuil and N. Vergne. The R Journal. 2018. [HAL]
  • Improving Bioinformatics Prediction of microRNA Targets by Ranks Aggregation.  A. Quillet, C. Saad , G. Ferry, Y. Anouar , N. Vergne, T. Lecroq, C. Dubessy. Frontiers in Genetics. 2020. [HAL]
  • Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers. P.J. V. & al. BMC Bioinformatics. 2021. [HAL]
  • Bayesian Information Criterion for Fitting the Optimum Order of Markov Chain Models: Methodology and Application to Air Pollution Data. Y. Alyousifi, K. Ibrahim, M.Othmam, W.Z.W. Zin, N. Vergne, A. Al-Yaari. Mathematics. 2022. [HAL]
  • Narrowing the coordination solution space during motor learning standardizes individual patterns of search strategy but diversifies learning rates. J. Komar, L. Seifert, N. Vergne, K. Newell. Scientific Reports. 2023. [HAL] 
  • smmR: A Semi-Markov R package. V.S. Barbu, F. Lecocq, C. Lothodé, N. Vergne. Journal of Open Source Software. 2023. [HAL]
  • Unveiling the Persistent Dynamics of Visual-Motor Skill via Drifting Markov Modeling. E.N. Kalligeris, V.S. Barbu, G. Hacques, L. Seifert, N. Vergne. Nonlinear Dynamics, Psychology, and Life Sciences. 2024. [HAL]
  • dsmmR: Estimation and Simulation of Drifting Semi-Markov Models. V.S. Barbu, I. Mavrogiannis, N. Vergne. Journal of Open Source Software. 2024. [HAL]

 

Chapitres d'ouvrages

  • Monochain HSMM. A comprehensive guide to HSMM: Theory, software, and advanced extensions. J.-B. Durand, A. Franc, N. Peyrard, N. Vergne and I. Votsi. 2026. [HAL]
  • Review of HSMM R and Python softwares. A comprehensive guide to HSMM: Theory, software, and advanced extensions. C. Bérard, M.-J. Cros, J.-B. Durand, C. Lothodé, S. Plancade, R. Trepos, N. Vergne. 2026. [HAL]
  • Parametric estimation of censored semi-Markov chains. Stochastic Modeling and Statistical Methods. V. S. Barbu, F. Lecocq, N. Vergne. 2025. [HAL]
  • The application of drifting Markov modeling to dynamics skill acquisition. Stochastic Modeling and Statistical Methods. L. Seifert, E.-N. Kalligeris, J. Komar, G. Hacques, V. S. Barbu, N. Vergne. 2025. [HAL]

 

Ouvrages édités

  • Statistical Topics and Stochastic Models for Dependent Data - Applications in Reliability, Survival Analysis and Related Fields. V.S Barbu, N. Vergne. 2020. [HAL]

 

Conférences, colloques, séminaires

  • Les modèles de Markov régulés pour l'étude de séquences biologiques : Dérive polynomiale et applications. N. Vergne. 6èmes Journée Jeunes Chercheurs en Biométrie. Septembre 2006, à Villejuif.
  • Chaînes de Markov régulées pour l'analyse de séquences biologiques. N. Vergne. Séminaire de l'Unité MIA-Jouy (INRA). Octobre 2008, à Jouy-en-Josas.
  • Chaînes de Markov régulées pour l'analyse de séquences biologiques. N. Vergne. Séminaire Marin Mersenne - Samos, Mathématiques des Systèmes Complexes. Octobre 2008, Université Paris I.
  • Poisson approximation for search of rare words in DNA sequences. Workshop on "Hitting, returning and matching in dynamical systems, information theory and mathematical biology". N. Vergne. 2008. [HAL]
  • Error Rates of Phylogenetic and supervised Classification Algorithms in DNA Barcoding. Third International Barcode of Life Conference. C. Larédo, N. Vergne, F. Austerlitz, O. David, B. Schaeffer, et al. 2009. [HAL]
  • Error rates in phylogenetic and supervised classification algorithms in DNA Barcoding. Third International Barcode of Life Conference. C. Laredo, F. Austerlitz, O. David, B. Schaeffer, K. Bleakley, et al. 2009. [HAL]
  • Représentation des données praomys à l'aide des cartes autoorganisées. Projet IFORA, Colloque final de restitution. M. Olteanu, N. Vergne, B. Schaeffer, O. David, C. Laredo. 2010. [HAL]
  • Taux d’erreurs des méthodes phylogénétiques et des méthodes statistiques de classification pour le Barcode ADN. Projet IFORA. C. Laredo, B. Schaeffer, N. Vergne, O. David, F. Austerlitz, et al. 2010. [HAL]
  • Towards a better understanding of Phaeodactylum tricornutum’s morphogenesis. . Bardor, C. Bérard, H. Dauchel, M.C. Kiefer-Meyer, T. Lecroq, P. Lerouge, C. Ovide, W. Tair, I. Tournier and N. Vergne. Plant Genomics Congress. 13-14 May 2013, London Heathow, UK.
  • Elucidation of the morphogenesis mechanisms in the diatom P. tricornutum using RNA sequencing technology. 17ième Journées de l’Ecole Doctorale NBISE. C. Ovide, M.-C. Kiefer-Meyer, W. Tair, C. Bérard, N. Vergne, et al. 2014. [HAL]
  • Etude des mécanismes de morphogenèse chez la diatomée modèle Phaeodactylum tricornutum par séquençage d’ARN à haut débit (RNA-Seq). Journées phycologiques de France. C. Ovide, M.-C. Kiefer-Meyer, C. Bérard, N. Vergne, T. Lecroq, et al. 2015. [HAL]
  • RNA Sequencing technology will help deciphering the morphogenesis mechanisms in the model diatom Phaeodactylum tricornutum. Journée scientifique du GRR-IRIB. C. Ovide, M.-C. Kiefer-Meyer, C. Bérard, N. Vergne, T. Lecroq, et al. 2015. [HAL]
  • Rendre compte de la dynamique de l’activité des élèves en course d’orientation: application de modèles de Markov dérivant aux données d’expérience. 16ème congrès de l’Association des Chercheurs en Activité physique et Sportive. C. Jourand, J. Komar, A. D., N. Vergne, R. Thouvarecq. 2015. [HAL]
  • Drifting Markov models applied in reliability theory and survival analysis. JDS. V. S. Barbu, N. Vergne. 2017. [HAL]
  • Estimation paramétrique des chaînes semi-markoviennes pour des données censurées. JDS. V. S. Barbu, C. Bérard, D. Cellier, M. Sautreuil, N. Vergne. 2017. [HAL]
  • Reliability and survival analysis for drifting Markov models: modelling and estimation. Mathematical Methods in Reliability. V. S. Barbu, N. Vergne. 2017. [HAL]
  • Drifting Markov and semi-Markov models: modeling, estimation and applications. STODEP. N. Vergne, V. S. Barbu. 2018. [HAL]
  • DRIMM'R and WebDRIMM: an R package and a web interface for drifting Markov model estimation and reliability. JDS. V. S. Barbu, G. Brelurut, A. Gilles, A. Lefebvre, V. Mataigne, et al. 2018. [HAL]
  • Modèle de mélange binomial négatif bivarié pour l'analyse de données RNA-Seq. JDS. M. Sautreuil, C. Bérard, G. Chagny, A. Channarond, A. Roche, et al. 2018. [HAL]
  • mCNA : a new methodology to improve high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers. JOBIM. P.-J. Viailly, A. Abdel Sater, H. Dauchel, A. Celebi, C. Bérard, et al. 2019. [HAL]
  • Modeling and estimation by means of drifting Markov and semi-Markov chains. Quantitative Methods for Intangibles Evaluation. V. S. Barbu, N. Vergne. 2019. [HAL]
  • Amélioration de la prédiction bioinformatique des cibles des microARN par l'agrégation des rangs : application au phéochromocytome, une tumeur neuroendocrine. Réunion thématique de l'axe 1 du Cancéropôle Nord-Ouest. A. Quillet, I. Drissa, C. Saad, G. Ferry, N. Vergne, et al. 2021. [HAL]
  • Drifting Semi-Markov Models: Estimation and Simulation through the dsmmR package. The 23rd Conference of the Romanian Society of Probability and Statistics. V. S. Barbu, N. Vergne, I. Mavrogiannis. 2022. [HAL]
  • smmR: an R package for Simulation, Estimation and Reliability of Semi-Markov. The 23rd Conference of the Romanian Society of Probability and Statistics. V. S. Barbu, N. Vergne, F. Lecocq, C. Lothodé. 2022. [HAL]
  • dsmmR: Estimation and simulation of Drifting Semi-Markov Models. Statistical Modeling with Applications. I. Mavrogiannis, V. S. Barbu, N. Vergne. 2022. [HAL]
  • Different types of Markovian models and applications. Biomath Conference. N. Vergne, V. S. Barbu, I. Mavrogiannis, L. Seifert. 2023. [HAL]
  • Different types of Markovian models and applications in swimming and climbing. Summer School "ComplexSportsData". V. Barbu, E.-N. Kalligeris, G. Hacques, J. Komar, I. Mavrogiannis, et al. 2023. [HAL]
  • Modèles dérivants semi-markoviens : estimation, simulation et utilisation à travers le package dsmmR. Processus markoviens, semi-markoviens et leurs applications. N. Vergne, V. S. Barbu, I. Mavrogiannis. 2023. [HAL]
  • Différents types de modèles markoviens et applications en natation et escalade. Ecole thématique : analyse de données sportives complexes. N. Vergne. 2023. [HAL]
  • Graph representation learning and semantic distribution: application to omic expression data. JOBIM 2024. I. André, S. Abdeddaim, N. Vergne, L. F. Soualmia. 2024. [HAL]
  • Drifting Markov models in learning of climbing. 18th International Joint Conference CFE-CMStatistics. N. Vergne, E.-N. Kalligeris, V. S. Barbu, G. Hacques, L. Seifert. 2024. [HAL]
  • Modèles de Markov dérivants pour l'apprentissage de l'escalade. 55ièmes Journées de Statistique de la SFDS. E.-N. Kalligeris, V. S. Barbu, G. Hacques, L. Seifert, N. Vergne. 2024. [HAL]
  • Review of HSMM R and Python software. MaSeMo : Markov, Semi-Markov Models and Associated Fields. C. Bérard, M.-J. Cros, J.-B. Durand, C. Lothodé, S. Plancade, et al. 2025. [HAL]
  • Parameter Estimation and State Inference in Hidden Drifting Markov Models. MaSeMo : Markov, Semi-Markov Models and Associated Fields (from Theory to Application and back). A. L. Tehungue, V. S. Barbu, N. Vergne. 2025. [HAL]
  • Différents types de modèles markoviens et applications en natation et escalade. Gestion et Analyse des données Sportives (GAS'25). N. Vergne. 2025. [HAL]
  • Application of Drifting Markov Models to Dynamics Skill Acquisition. 56ème Journées de Statistique de la SFDS. V. S. Barbu, E.-N. Kalligeris, G. Hacques, L. Seifert, N. Vergne. 2025. [HAL]
  • Modelling and estimation of censored semi-Markov chains. 56ièmes Journées de Statistique de la SFDS. V. S. Barbu, N. Vergne. 2025. [HAL]
  • Hidden Drifting Markov Models: Theory, Inference, and Simulation-Based Evaluation. Statistical Modeling with Application (StatMode 2025). A. L. Tehungue, V. S. Barbu, N. Vergne. 2025. [HAL]

 

Posters

  • Les chaînes de Markov régulées. JOBIM. N. Vergne. 2005. [HAL]
  • Drifting Markov models. ECCB. N. Vergne. 2005. [HAL]
  • RNA-seq : a new tool to study Phaeodactylum tricornutum morphogenesis. 2nd Journée de l’Institut de Recherche et d’Innovation Biomédicale. C. Ovide, M.-C. Kiefer-Meyer, W. Tair, C. Bérard, N. Vergne, et al. 2013. [HAL]
  • Towards a better understanding of Phaeodactylum tricornutum’s morphogenesis. Plant Genomics Congress. M.-C. Kiefer-Meyer, C. Ovide, W. Tair, C. Bérard, N. Vergne, et al. 2013. [HAL]
  • Towards a better understanding of Phaeodactylum tricornutum’s morphogenesis. EMBO Workshop, The Molecular Life of Diatoms. C. Ovide, M.-C. Kiefer-Meyer, W. Tair, C. Bérard, N. Vergne, et al. 2013. [HAL]
  • Elucidation of the morphogenesis mechanisms in the diatom P. tricornutum using RNA sequencing technology. 17ième Journées de l’Ecole Doctorale NBISE. C. Ovide, M.-C. Kiefer-Meyer, W. Tair, C. Bérard, N. Vergne, et al. 2014. [HAL]
  • GC-VC/DGE : a user-friendly web application for Going over Concordance across results from NGS bioinformatics analytic pipelines. ECCB. C. Cabot, M. Mélissa, C. Saad, A. Renaux, A. Bertrand, et al. 2014. [HAL]
  • Bivariate Negative Binomial Mixture Model for the analysis of RNA-seq data. JOBIM. M. Sautreuil, N. Vergne, A. Channarond, A. Roche, G. Chagny, et al. 2017. [HAL]
  • Rôle des microARN dans l’hypersécrétion de catécholamines par les phéochromocytomes. Réunion Thématique de l'Axe 1 du Cancéropôle Nord-Ouest. I. Drissa, A. Quillet, M.-C. Tellier, D. Cartier, C. Bérard, et al. 2020. [HAL]
  • miRabel, un outil web pour la prédiction efficace des cibles des microARN en santé humaine. Les Rencontres Santé Numérique. A. Quillet, C. Saad, G. Ferry, I. Zerdane, M. Salhi, et al. 2022. [HAL]

 

Logiciels

  • R package SMM, Simulation and Estimation of Multi-State Discrete-Time Semi-Markov and Markov Models. Software. V. S. Barbu, C. Bérard, M. Sautreuil, D. Cellier, N. Vergne. 2017. [HAL]
  • R package smmR: Simulation, Estimation and Reliability of Semi-Markov Models. Software. V. S. Barbu, N. Vergne, F. Lecocq, C. Lothodé. 2021. [HAL]
  • drimmR: Estimation, Simulation and Reliability of Drifting Markov Models. Software. V. S. Barbu, G. Brelurut, A. Gilles, A. Lefebvre, C. Lothodé, et al. 2021. [HAL]
  • dsmmR: Estimation and Simulation of Drifting Semi-Markov Models. Software. V. Barbu, I. Mavrogiannis, N. Vergne. 2023. [HAL]