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Cell Death and Life in Cancer: Mathematical Modeling of Cell Fate Decisions

 Andrei Zinovyev , Simon Fourquet , Laurent Tournier , Laurence Calzone , Emmanuel Barillot
Advances in Experimental Medicine and Biology, 2012, 736, pp.261 - 274. ⟨10.1007/978-1-4419-7210-1_15⟩
Article dans une revue hal-02653014v1

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

 Laurent Heirendt , Sylvain Arreckx , Thomas Pfau , Sebastián Mendoza , Anne Richelle , et al.
Nature Protocols, 2019, 14 (3), pp.639-702. ⟨10.1038/s41596-018-0098-2⟩
Article dans une revue hal-03211136v1

Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches

 Andrei Zinovyev , Michail Sadovsky , Laurence Calzone , Aziz Fouché , Clarice Groeneveld , et al.
2021
Pré-publication, Document de travail hal-03445160v1

Unsupervised weights selection for optimal transport based dataset integration

 Aziz Fouche , Andrei Zinovyev
2021
Pré-publication, Document de travail hal-03226629v1
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LNetReduce: tool for reducing linear dynamic networks with separated time scales

 Marion Buffard , Aurélien Desoeuvres , Aurélien Naldi , Clément Requilé , Andrei Zinovyev , et al.
Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. ⟨10.1007/978-3-030-85633-5_15⟩
Communication dans un congrès hal-03226633v1
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Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

 Nicolas Sompairac , Petr V Nazarov , Urszula Czerwinska , Laura Cantini , Anne Biton , et al.
International Journal of Molecular Sciences, 2019, 20 (18), pp.4414. ⟨10.3390/ijms20184414⟩
Article dans une revue hal-02343412v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

 Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Article dans une revue hal-01794294v2
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Determining the optimal number of independent components for reproducible transcriptomic data analysis

 Ulykbek Kairov , Laura Cantini , Alessandro Greco , Askhat Molkenov , Urszula Czerwinska , et al.
BMC Genomics, 2017, 18 (1), pp.712. ⟨10.1186/s12864-017-4112-9⟩
Article dans une revue inserm-02064099v1

Classification of gene signatures for their information value and functional redundancy

 Laura Cantini , Laurence Calzone , Loredana Martignetti , Mattias Rydenfelt , Nils Blüthgen , et al.
npj Systems Biology and Applications, 2018, 4 (1), ⟨10.1038/s41540-017-0038-8⟩
Article dans une revue hal-02129604v1
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Spectral analysis of gene expression profiles using gene networks

 Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
2006
Pré-publication, Document de travail hal-00021785v1

Classification of microarray data using gene networks.

 Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
BMC Bioinformatics, 2007, 8, pp.35. ⟨10.1186/1471-2105-8-35⟩
Article dans une revue hal-00433577v1

A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis.

 Elisabeth Remy , Sandra Rebouissou , Claudine Chaouiya , Andrei Zinovyev , François Radvanyi , et al.
Cancer Research, 2015, 75 (19), pp.4042-52
Article dans une revue hal-01285974v1

Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees

 Alexander Chervov , Andrei Zinovyev
2021 International Joint Conference on Neural Networks (IJCNN), Jul 2021, Shenzhen, France. pp.1-9, ⟨10.1109/IJCNN52387.2021.9534249⟩
Communication dans un congrès hal-03445139v1

Robust simplifications of multiscale biochemical networks

 Ovidiu Radulescu , Alexander N. Gorban , Andrei Zinovyev , Alain Lilienbaum
BMC Systems Biology, 2008, 2:86
Article dans une revue inria-00331212v1
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Local intrinsic dimensionality estimators based on concentration of measure

 Jonathan Bac , Andrei Zinovyev
2020 International Joint Conference on Neural Networks (IJCNN), Jul 2020, Glasgow, United Kingdom. pp.1-8, ⟨10.1109/IJCNN48605.2020.9207096⟩
Communication dans un congrès hal-02972293v1
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Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer

 Yann Kieffer , Hocine Rachid Hocine , Géraldine Gentric , Floriane Pelon , Charles Bernard , et al.
Cancer Discovery, 2020, 10 (9), pp.1330-1351. ⟨10.1158/2159-8290.CD-19-1384⟩
Article dans une revue hal-02890211v1

Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer

 Laura Cantini , Gloria Bertoli , Claudia Cava , Thierry Dubois , Andrei Zinovyev , et al.
Nucleic Acids Research, 2019, 47 (5), pp.2205-2215. ⟨10.1093/nar/gkz016⟩
Article dans une revue hal-02129600v1

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks

 Sylvain Blachon , Gautier Stoll , Carito Guziolowski , Andrei Zinovyev , Emmanuel Barillot , et al.
AIAI 2009 Workshop -- Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Apr 2009, Thessalonik, Greece. pp.72-87
Communication dans un congrès inria-00429801v1
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Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

 Maia Chanrion , Inna Kuperstein , Cédric Barrière , Fatima El Marjou , David Cohen , et al.
Nature Communications, 2014, 5, pp.5005. ⟨10.1038/ncomms6005⟩
Article dans une revue hal-01712223v1
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Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data

 Sergey E Golovenkin , Jonathan Bac , Alexander Chervov , Evgeny M Mirkes , Yuliya V Orlova , et al.
GigaScience, 2020, 9 (11), pp.giaa128. ⟨10.1093/gigascience/giaa128⟩
Article dans une revue hal-02972281v1
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NetNorM: capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis

 Marine Le Morvan , Andrei Zinovyev , Jean-Philippe Vert
2016
Pré-publication, Document de travail hal-01341856v2
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Exact solving and sensitivity analysis of stochastic continuous time Boolean models

 Mihály Koltai , Vincent Noël , Andrei Zinovyev , Laurence Calzone , Emmanuel Barillot
BMC Bioinformatics, 2020, 21 (1), pp.241. ⟨10.1186/s12859-020-03548-9⟩
Article dans une revue inserm-02971389v1
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Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer: New Insights from Matrix Factorization

 Alessandro Greco , Jon Sanchez Valle , Vera Pancaldi , Anaïs Baudot , Emmanuel Barillot , et al.
International Journal of Molecular Sciences, 2019, 20 (13), pp.3114. ⟨10.3390/ijms20133114⟩
Article dans une revue hal-02277045v2
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Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming

 Stéphanie Chevalier , Christine Froidevaux , Loïc Paulevé , Andrei Zinovyev
2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), 2019, Portland, Oregon, United States. ⟨10.1109/ICTAI.2019.00014⟩
Communication dans un congrès hal-02276921v2
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ROMA: Representation and Quantification of Module Activity from Target Expression Data

 Loredana Martignetti , Laurence Calzone , Eric Bonnet , Emmanuel Barillot , Andrei Zinovyev
Frontiers in Genetics, 2016, 7, ⟨10.3389/fgene.2016.00018⟩
Article dans une revue hal-04407412v1
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Interpreting pathways to discover cancer driver genes with Moonlight

 Antonio Colaprico , Catharina Olsen , Matthew Bailey , Gabriel Odom , Thilde Terkelsen , et al.
Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-019-13803-0⟩
Article dans une revue hal-03001026v1

Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets

 Alexander Chervov , Jonathan Bac , Andrei Zinovyev
Entropy, 2020, 22 (11), pp.1274. ⟨10.3390/e22111274⟩
Article dans une revue hal-03007469v1
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Systems Biology Analysis for Ewing Sarcoma

 Marianyela Petrizzelli , Jane Merlevede , Andrei Zinovyev
Ewing Sarcoma Methods and Protocols, 2226, pp.303-333, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1020-6_23⟩
Chapitre d'ouvrage hal-03168235v1
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Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

 Nicolas Sompairac , Jennifer Modamio , Emmanuel Barillot , Ronan M T Fleming , Andrei Zinovyev , et al.
BMC Bioinformatics, 2019, 20 (S4), pp.140. ⟨10.1186/s12859-019-2682-z⟩
Article dans une revue inserm-02289698v1
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NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

 Inna Kuperstein , David Cohen , Stuart Pook , Eric Viara , Laurence Calzone , et al.
BMC Systems Biology, 2013, 7 (1), pp.100. ⟨10.1186/1752-0509-7-100⟩
Article dans une revue inserm-00872428v1
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