Andrei Zinovyev

Andrei Zinovyev

PhD, Principal scientist, scientific coordinator of a research group

Posts by Collection

portfolio

publications

Visualization of Any Data with Elastic Map Method

Published in , 1900

Recommended citation: Gorban AN, Pitenko A, Zinovyev A, Wunsch D. Visualization of Any Data with Elastic Map Method. Proceedings of Artificial Neural Networks in Engineering, St. Louis, MO, November, 2001

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Published in , 1900

Recommended citation: Gorban AN, Zinovyev A. Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization. In Principal Manifolds for Data Visualization and Dimension Reduction, Lecture Notes in Computational Science and Engineering 58, Springer, Berlin - Heidelberg, 2008, 96-130 https://arxiv.org/abs/0801.0168

[Application of model reduction methods for constructing a composite model of apoptosis signaling]

Published in , 1900

Recommended citation: Kutumova E.O, Zinovyev A, Sharipov R.N, Kolpakov F.A. [Application of model reduction methods for constructing a composite model of apoptosis signaling]. 2012. Math. Biol. i Bioinformatika 7(2):572-588 (In Russian) https://www.researchgate.net/publication/286505437_The_application_of_model_reduction_methods_to_the_construction_of_the_composite_model_of_apoptotic_pathways_In_Russian

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

Published in , 1900

Recommended citation: Chanrion M, Kuperstein I, Barriere C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Bieche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Ne P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A^, Robine S.^. Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. 2014. Nature Communications, 5:5005 https://www.nature.com/articles/ncomms6005

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

Published in , 1900

Recommended citation: Biton A, Bernard-Pierrot I, Lou Y, Krucker C, Chapeaublanc E, Rubio Perez C, Lopez Bigas N, Kamoun A, Neuzillet Y, Gestraud P, Grieco G, Rebouissou S, de Reynies A, Benhamou S, Lebret T, Southgate J, Barillot E, Allory Y, Zinovyev A.^, Radvanyi F^. Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. 2014. Cell Reports 9(4), 1235-1245 https://www.cell.com/cell-reports/fulltext/S2211-1247(14)00904-8

Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of AsiDNA and PARP inhibitors

Published in , 1900

Recommended citation: Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun J.-S, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M. Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of AsiDNA and PARP inhibitors. 2016. Clinical Cancer Research, pii: clincanres.1193.2016. http://clincancerres.aacrjournals.org/content/23/4/1001.long

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific And Reproducible Immune-related Signals

Published in , 1900

Recommended citation: Czerwinska U, Cantini L, Kairov U, Barillot E, Zinovyev A. Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific And Reproducible Immune-related Signals. Proceedings of International Conference on Latent Variable Analysis and Signal Separation, Surrey, UK, 2-6 July 2018. https://link.springer.com/chapter/10.1007/978-3-319-93764-9_46

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients.

Published in , 1900

Recommended citation: Nazarov PL, Wienecke-Baldacchino AK, Zinovyev A, Czerwinska U, Muller A, Nashan D, Dittmar G, Azuaje F, Kreis S. Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients.. 2019. BMC Medical Genomics, 12(1):132. https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0578-4

Fibroblast heterogeneity and immunosuppressive environment in human breast cancer

Published in , 1900

Recommended citation: Costa A, Kieffer Y, Scholer-Dahirel A, Pelon F, Bourachot B, Cardon M, Sirven P, Magagna I, Fuhrmann L, Bernard C, Bonneau C, Kondratova M, Kuperstein I, Zinovyev A, Givel A.-M, Parrini M.-C, Soumelis V, Vincent-Salomon A, Mechta-Grigoriou F. Fibroblast heterogeneity and immunosuppressive environment in human breast cancer. 2018. Cancer Cell 33(3):463-479.e10. https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30011-4

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Published in , 1900

Recommended citation: Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novere N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. 2018. NPJ systems biology and applications 4 (1), 21 https://www.nature.com/articles/s41540-018-0059-y

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Published in , 1900

Recommended citation: Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, Paulevé L. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. 2018. Front Physiol 9:680. https://www.frontiersin.org/articles/10.3389/fphys.2018.00680/full

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Published in , 1900

Recommended citation: Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. 2019. Nucleic Acids Res. 47(D1):D614-D624. https://academic.oup.com/nar/article/47/D1/D614/5146204

Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution

Published in , 1900

Recommended citation: Aynaud M-M, Mirabeau O, Gruel N, Grossetete S, Boeva V, Durand S, Surdez D, Saulnier O, Zaidi S, Gribkova S, Kairov U, Raynal V, Tirode F, Grunewald TGP, Bohec M, Baulande S, Janoueix-Lerosey I, Vert J-P, Barillot E, Delattre O, Zinovyev A. Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution. 2020. Cell Reports, 30(6):1767-1779.e6 https://linkinghub.elsevier.com/retrieve/pii/S2211-1247(20)30074-7

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

Published in , 1900

Recommended citation: Cantini L, Bertoli G, Cava C, Dubois T, Zinovyev A, Caselle M, Castiglioni I, Barillot E, Martignetti L. Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer. 2019. Nucleic Acids Res. 47(5):2205-2215 https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz016/5290485

ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma

Published in , 1900

Recommended citation: Srivastava S, Belugali Nataraj N, Sekar A, Bornstein-Ovits C, Ghosh S, Drago-Garcia D, Roth L, Romaniello D, Marrocco I, Gilad Y, Lauriola M, Rotkopf R, Kimchi A, Mirabeau O, Surdez D, Zinovyev A, Dellattre O, Kovar H, Amit I, Yarden Y. ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma. 2019. Cell Reports, 29, Issue 1, p104-117.e4 https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31150-7

Single-Cell Analysis Reveals Fibroblast Clusters Linked to Immunotherapy Resistance in Cancer

Published in , 1900

Recommended citation: Kieffer Y, Hocine HR, Gentric G, Pelon F, Bernard C, Bourachot B, Lameiras S, Albergante L, Bonneau C, Guyard A, Tarte K, Zinovyev A, Baulande S, Zalcman G, Vincent-Salomon A, Mechta-Grigoriou F. Single-Cell Analysis Reveals Fibroblast Clusters Linked to Immunotherapy Resistance in Cancer. Cancer Discov. 2020 Sep;10(9):1330-1351 https://cancerdiscovery.aacrjournals.org/content/10/9/1330.long

LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales

Published in , 1900

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Recommended citation: Buffard M., Desoeuvres A., Naldi A., Requilé C., Zinovyev A., Radulescu O. LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. In: Cinquemani E., Pauleve L. (eds) Computational Methods in Systems Biology. CMSB 2021. Lecture Notes in Computer Science, vol 12881. Springer, Cham. https://doi.org/10.1007/978-3-030-85633-5_15 https://pastel.archives-ouvertes.fr/PRAIRIE-IA/hal-03226633v1

talks

teaching

Basic introduction into Windows and Microsoft Office tools

Open free course, Krasnoyarsk State Technical University, 1900

In 1998-1999 I participated in creation of a free and open to public intensive 2 weeks introductory course on the basic use of Windows operating system and Microsoft Office tools. Various modifications of the course were adapted to students, general public, children (including 8-10 years old).

Computational Systems Biology of Cancer

PhD course, Alma Ata University, 1900

As a part of joint Kazakhstan-France PhD program, I developed and delivered a 40-hours course on Computational Systems Biology of Cancer, covering many aspects of technology, data analysis, machine learning techniques, mathematical modeling of networks in cancer research. The course included approximately 15 hours of intensive hands-on sessions.

Omics Data Analysis and Medical Applications

Professional course, Skoltech University, 1900

In July 2015, I was as principal organizer, developer and lecturer of 7-days intensive course Omics Data Analysis and Medical Applications aimed at professional bioinformaticians and PhD students. The course covered a wide range of topics in application and analysis of omics data in various diseases including cancer. Theoretical lectures were accompanied by hands-on sessions.

Mathematical modeling of biological systems

Pre-doctoral course, Universite Paris, Institute of Technology and Innovation, 1900

In 2016 and 2017 I was a co-organizer and lecturer of 80 hours teaching module “Mathematical Modeling of Biological Systems” as a part of the pre-doctoral training program at PSL-ITI. The course covered a wide range of topics related to application of mathematical modeling (in wide sense) to understand biology. My lectures in the course were devoted to application of machine learning in cancer research. In 2018, I organized a limited edition of this module, with only few lectures.

International Curie Course on Computational Systems Biology of Cancer

PhD students, Institut Curie, 1900

I co-organize and give lectures at yearly International Curie Course on Computational Systems Biology of Cancer. In 2018, I gave a short course on application of machine learning for characterizing tumor microenvironment. The 2019 edition of International Curie course on computational biology will be devoted to single-cell data analysis. The 2020 edition of International Curie course will focus on application of machine learning and artificial intelligence in biology of cancer.

Participation in teaching courses as invited lecturer

---, Various venues, 1900

I constantly participate as invited lecturer in courses and summer schools organized worldwide. For example, I participated in the thematic school Analysis of Cancer genome (2015) and in the Genopole Summer School on Bioinformatic and Biostatistic tools in medical genomics in 2018. My topics are various, including data visualization, some aspects of machine learning for biomedical applications, mathematical modeling in biology and introductory lectures into systems biology and cancer bioinformatics.