Andrei Zinovyev

Andrei Zinovyev

PhD, Principal scientist, scientific coordinator of a research group

Personal dataCurrent positions
Born September 23, 1974 in Krasnoyarsk, USSR (Russia)
Mailing address:
Evotec, isR&D, 195 Rte d’Espagne, 31100, Toulouse, France.
E-mail: andrey.zinovyev@evotec.com
WWW: https://andreizinovyev.site
Languages: English (fluent), French (fluent), Russian (native)		Principal Scientist and group leader at Evotec, in silico R&D department, Toulouse, France

Scientific coordinator and co-lead of Computational Systems Biology of Cancer team in CANCER AND GENOME: BIOINFORMATICS, BIOSTATISTICS AND EPIDEMIOLOGY OF COMPLEX SYSTEMS INSERM unit
Institut Curie / Inserm Unit 900 / Ecoles des Mines

Chair at Paris Artificial Intelligence Research Institute (PRAIRIE)

Research interests

Education

Experience

Academic science

Industry

Teaching

Awards

Grants and projects

Development of scientific software

Conference and workshop committees and organization

  1. Organizer of the workshop Complex and simple multidimensional real-life datasets, 1 December 2021
  2. Member of organizing committee of SinCellMod-2020: Single cell data in network modeling, Online meeting, 1-2 December 2020
  3. Member of scientific organizing committee of 1,2,3,4th International Curie course on Computational Systems Biology of Cancer (Multi-omics data analysis), Paris, September 2018-2021.
  4. Member of scientific organizing committee of BioNetVisA workshop (ECCB, BC2, ICSB host), 2014-2021
  5. Member of organizing committee of Model Reduction across disciplines-2014
  6. Member of programming committee of SASB-2014, ECCB-2014, ECCB-2012, ECCB-2010, Ghent, October 2010.
  7. Member of organizing committee of “Principal manifolds-2006”, Leicester, UK, 2006.
  8. Member of organizing committee of “Geometry of Genome”, Leicester, UK, 2005.

Peer-Reviewing activities (see my Publons profile)

Physical Biology, PNAS, Nature Communications, Genome Research, BMC Genomics, RNA, PLoS Computational biology, Bioinformatics, npj Systems Biology and Applications, BMC Systems Biology, Journal of Theoretical Biology, BMC Bioinformatics, Physical Reviews E, International Journal of Neural Systems, Computers and Mathematics with Applications, American Journal of Political Science, Mathematics and Computers in Simulation, Pattern Recognition Letters, BioSystems, Discrete Applied Mathematics, Computational Statistics and Data Analysis, IEEE Transactions on pattern analysis and machine intelligence

PhD theses (co-)supervision:

  1. Loic Chadoutaud, “Spatial and Temporal Heterogeneity of single cell transcriptomics data”, 2021-2024
  2. Aziz Fouche, “Integration of multi-level single cell molecular data to unravel the mechanisms of oncogene activation effect on cellular phenotypes”, 2020-2023
  3. Marco Ruscone, “ Modélisation multi-échelle de la progression du cancer”, 2021-2024
  4. Jaydutt Bhalshankar, “Analyse bioinformatique intégrative de l’hétérogénéité intratumorale génétique dans le neuroblastome à un niveau cellule unique”, 2020-2023
  5. Jonathan Bac, “Machine learning methods and tools to tackle the complexity of high-dimensional single cell datasets”, 2019-2022
  6. Stephanie Chevalier “Automatically design Boolean networks from static and dynamical knowledge on a biological system, to model processes such as cell differentiation”, 2019-2022
  7. Nicolas Sompairac, “Statistical modeling of tumor/microenvironment ecosystem to advance diagnostic and treatment”, 2018-2021
  8. Alexey Guerassimov, “Kinetic model of regulation of translation in eukaryotic cells”, 2016-2018 (not finished)
  9. Urszula Czerwinska, “Deconvolution of cell and environment specific signals and their interactions from complex mixtures in biological samples”, 2015-2018
  10. Marine Le Morvan, “Search for cancer driver mutations using mutation, expression data and biological networks”, 2014-2017
  11. Geraldine Cellier, “Multiscale modeling of early invasion of tumour cell into surrounding tissues”, 2012-2015
  12. Ulykbek Kairov, “Analysis of microarray data for searching genetic markers in cancer” (Kazhakstan), 2009-2012
  13. Elena Kutumova, “Application of model reduction methods for constructing a composite model of apoptosis signaling” (Russia), 2009-2012
  14. Anne Biton, “Geometrical analysis of pathway deregulations in bladder cancer”, 2008-2011.
  15. Franck Rapaport, “Integration of gene expression data and gene regulatory networks for the study of cancers”, 2005-2008.

Participation in PhD theses jury as a referee

  1. Francisco Avila Cobos, “Addressing challenges in transcriptome annotationand cell-type heterogeneity through integration ofomics datasets and computational deconvolution”, Ghent, June 2020.
  2. Natalia Rubanova, “MasterPATH: network analysis of functional genomics screening data”, Paris, February 2018
  3. Christophe Becavin, “Dimensionality reduction and pathway network analysis of transcriptome data: Application to T-cell characterization”, Paris, December 2010.
  4. Michel Journee, “Geometric algorithms for component analysis with a view to gene expression data analysis”, Liege, June 2009.
  5. Nora Nonne, “Etude de l’action des microARN : mecanismes et cibles”, Paris, November, 2009.

Publications (see the complete list of my citations in Google Scholar)

Books

  1. Barillot E., Calzone L., Hupe P., Vert J.-P., Zinovyev A. Computational Systems Biology of Cancer . Chapman & Hall, CRC Mathematical & Computational Biology, 2012, 452 p.
  2. Gorban A, Kegl B, Wunch D, Zinovyev A. (eds.) Principal Manifolds for Data Visualisation and Dimension Reduction. 2008. Lecture Notes in Computational Science and Engeneering 58, p.340.
  3. Zinovyev A. Visualization of Multidimensional Data (in Russian). Krasnoyasrk: KGTU Publ., 2000, 168 p.

Articles in peer-reviewed journals (* equal contribution, + corresponding author, ^ co-last authorship)

see also the list of my articles in Pubmed

  1. Zinovyev A, Sadovsky M, Calzone L, Fouché A, Groeneveld CS, Chervov A, Barillot E, Gorban AN. Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches. Front Mol Biosci, 2022, https://doi.org/10.3389/fmolb.2021.793912.
  2. Amblard E, Bac J, Chervov A, Soumelis V, Zinovyev A. Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data. Bioinformatics. 2021 Nov 23:btab795.
  3. Noël V, Ruscone M, Stoll G, Viara E, Zinovyev A, Barillot E, Calzone L. WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically. Front Mol Biosci. 2021 Nov 15;8:754444.
  4. Bac J, Mirkes EM, Gorban AN, Tyukin I, Zinovyev A. Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation. Entropy (Basel). 2021 Oct 19;23(10):1368.
  5. Zinovyev A. Adaptation through the lens of single-cell multi-omics data: Comment on “Dynamic and thermodynamic models of adaptation” by A.N. Gorban et al. Phys Life Rev. 2021 Sep;38:132-134. doi: 10.1016/j.plrev.2021.05.004.
  6. Rybnikova N, Portnov BA, Mirkes EM, Zinovyev A, Brook A, Gorban AN. Coloring Panchromatic Nighttime Satellite Images: Comparing the Performance of Several Machine Learning Methods. IEEE Transactions on Geoscience and Remote Sensing 2021, In press
  7. Kuksin M, Morel D, Aglave M, Danlos F-X, Marabelle A, Zinovyev A, Gautheret D, Verlingue L. Applications of single-cell and bulk RNA sequencing in onco-immunology. European Journal of Cancer 2021, 149:193-210
  8. Nunez-Carpintero, M Petrizzelli, A Zinovyev, D Cirillo, A Valencia. The multilayer community structure of medulloblastoma. iScience 2021, 24(4):102365
  9. Kondratova M, Barillot E, Zinovyev A, Calzone L. Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response. Cancers 2020, 12(12):3600
  10. Chervov A, Zinovyev A. Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets. Entropy 2020, 22(11):1274
  11. Golovenkin S, Bac J, Chervov A, Mirkes E, Orlova Y, Barillot E, Gorban A, Zinovyev A. Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data. GigaScience 2020, 9(11)
  12. Koltai M, Noel V, Zinovyev A, Calzone L, Barillot E. Exact solving and sensitivity analysis of stochastic continuous time Boolean models. BMC Bioinformatics 2020;21(1):241
  13. Kieffer Y, Hocine HR, Gentric G, et al. Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer. Cancer Discov 2020;CD-19-1384
  14. Ravel JM, Monraz Gomez LC, Sompairac N, Calzone L, Zhivotovsky B, Kroemer G, Barillot E, Zinovyev A, Kuperstein I. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. Cancers (Basel) 2020;12(4):990.
  15. Albergante L, Mirkes E, Bac J, Chen H, Martin A, Faure L, Barillot E, Pinello L, Gorban A, Zinovyev A. Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. Entropy 2020, 22, 296
  16. Zinovyev A, Czerwinska U, Cantini L, Barillot E, Frahm KM, Shepelyansky DL. Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PLoS Comput Biol 2020;16(2):e1007652.
  17. Aynaud MM, Mirabeau O, Gruel N, Grossetete S, Boeva V, Durand S, Surdez D, Saulnier O, Zaidi S, Gribkova S, Fouche A, Kairov U, Raynal V, Tirode F, Grunewald TGP, Bohec M, Baulande S, Janoueix-Lerosey I, Vert JP, Barillot E, Delattre O, Zinovyev A. Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. Cell Reports 2020;30(6):1767-1779.e6.
  18. Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS, Papaleo E. Interpreting pathways to discover cancer driver genes with Moonlight. 2020. Nature Communications 11(1):69
  19. Bac J, Zinovyev A. Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets. Front Neurorobot 2020;13:110.
  20. Balaur I, Roy L, Mazein A, Karaca SG, Dogrusoz U, Barillot E, Zinovyev A. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinformatics 2020;36(8):2620-2622.
  21. Kondratova M, Czerwinska U, Sompairac N, Amigorena SD, Soumelis V, Barillot E, Zinovyev A, Kuperstein I. A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures. 2019. Nature Communications 10(1):4808
  22. 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
  23. Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A. Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets. 2019. Int J Mol Sci 20(18). pii: E4414.
  24. Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L. Molecular Inverse Comorbidity between Alzheimers Disease and Lung Cancer: New Insights from Matrix Factorization. 2019. Int J Mol Sci 20(13). pii: E3114.
  25. Gorban AN, Harel-Bellan A, Morozova N, Zinovyev A. Basic, simple and extendable kinetic model of protein synthesis. 2019. Mathematical Biosciences and Engineering 16 (6), 6602-6622
  26. Cantini L, Kairov U, de Reynies A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes. 2019. Bioinformatics 35(21):4307-4313
  27. Sompairac N, Modamio J, Barillot E, Fleming RMT, Zinovyev A, Kuperstein I. Metabolic and signalling network map integration: application to cross-talk studies and omics data analysis in cancer. 2019. BMC Bioinformatics 20(Suppl 4):140.
  28. Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan G-C, Pinello L. Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data with STREAM. 2019. Nature Communications 10:1903.
  29. Heirendt L, Arreckx S, Pfau T, et al. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. 2019. Nature Protocols 14(3):639-702
  30. 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
  31. 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.
  32. Letort G, Montagud A, Stoll G, Heiland R, Barillot E, Macklin P, Zinovyev A, Calzone L. PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. 2019. Bioinformatics 35(7):1188-1196
  33. 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.
  34. Levy N, Naldi A, Hernandez C, Stoll G, Thieffry D, Zinovyev A, Calzone L, Paulevé L. Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). 2018. Front Physiol 9:787.
  35. 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.
  36. Calzone L, Barillot E, Zinovyev A. Logical versus kinetic modeling of biological networks: applications in cancer research. Current Opinion in Chemical Engineering 21, 22-31.
  37. 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. NPJ systems biology and applications 4 (1), 21
  38. Monraz Gomez LC, Kondratova M, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. Application of Atlas of Cancer Signalling Network in preclinical studies. Brief Bioinform. 2018 May 3.
  39. Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novere N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R. Community-driven roadmap for integrated disease maps. Brief Bioinform. 2018 Apr 23.
  40. Kondratova M, Sompairac N, Barillot E, Zinovyev A, Kuperstein I. Signalling maps in cancer research: construction and data analysis. Database (Oxford). 2018 Jan 1;2018.
  41. Lages J., Shepelyansky D., Zinovyev A. Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks. 2018. PLoS One 13(1):e0190812.
  42. 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.
  43. Cantini L, Calzone L, Martignetti L, Rydenfelt M, Blüthgen N, Barillot E, Zinovyev A. Classification of gene signatures for their information value and functional redundancy. NPJ Syst Biol Appl. 4:2. 2017.
  44. Montagud A, Traynard P, Martignetti L, Bonnet E, Barillot E, Zinovyev A, Calzone L. Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Brief Bioinform. doi: 10.1093/bib/bbx163. 2017.
  45. Azencott CA, Aittokallio T, Roy S; DREAM Idea Challenge Consortium, Norman T, Friend S, Stolovitzky G, Goldenberg A. The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nat Methods 14(10):937-938. 2017.
  46. Kairov U, Cantini L, Greco A, Molkenov A, Czerwinska U, Barillot E, Zinovyev A. Determining the optimal number of independent components for reproducible transcriptomic data analysis. BMC Genomics 18(1):712. 2017.
  47. Le Morvan M, Zinovyev A, Vert JP. NetNorM: Capturing Cancer-relevant Information in Somatic Exome Mutation Data with Gene Networks for Cancer Stratification and Prognosis. PLoS Computational Biology 13(6):e1005573. 2017.
  48. Dorel M, Viara E, Barillot E, Zinovyev A^ and Kuperstein I^. NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. Database (Oxford) 1-11. 2017.
  49. Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L. MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinformatics: btx123. 2017.
  50. Cantini L, Caselle M, Forget A, Zinovyev A, Barillot E, Martignetti L. A review of computational approaches for the detection of microRNAs involved in cancer. Frontiers in Biosciences 22:1774-1791. 2017.
  51. Gorban A., Mirkes E., Zinovyev A. Robust principal graphs for data approximation. Archives of Data Science 2(1):1:16, 2017.
  52. 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.
  53. Gorban AN, Mirkes EM, Zinovyev A. Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning. Neural Netw. 2016, 84:28-38.
  54. Deveau P., Barillot E., Boeva V., Zinovyev A., Bonnet E. Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. R journal 2016, 8:293-306.
  55. Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A. ROMA: Representation and Quantification of Module Activity from Target Expression Data. Front Genet. 2016. 7:18.
  56. Kovar H., et al (46 authors). The second European interdisciplinary Ewing sarcoma research summit - A joint effort to deconstructing the multiple layers of a complex disease. Oncotarget, in press.
  57. Cohen PAD, Martignetti L, Robine S., Barillot E., Zinovyev A.^, Calzone L.^ Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. 2015. PLoS Computational Biology 11(11):e1004571.
  58. Kuperstein I, Robine S, Zinovyev A. Network biology elucidates metastatic colon cancer mechanisms. 2015. Cell Cycle 14(14):2189-90.
  59. Dorel M, Barillot E, Zinovyev A, Kuperstein I. Network-based approaches for drug response prediction and targeted therapy development in cancer. 2015. Biochem Biophys Res Commun. 464(2):386-91.
  60. Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. 2015. Oncogenesis 4:e160.
  61. Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L. A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis. 2015. Cancer Res. 75(19):4042-52.
  62. Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling. Mathematical Modeling of Natural Phenomena 10(3), 186-205.
  63. Czerwinska U, Calzone L, Barillot E, Zinovyev A. DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. 2015. BMC Syst Biol. 14;9:46.
  64. Martignetti L, Tesson B, Almeida A, Zinovyev A, Tucker GC, Dubois T, Barillot E. Detection of miRNA regulatory effect on triple negative breast cancer transcriptome. BMC Genomics 2015;16:S4.
  65. Calzone L, Barillot E, Zinovyev A. Predicting genetic interactions from Boolean models of biological networks. Integr Biol (Camb) 2015 May 11. [Epub ahead of print]
  66. Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A. NaviCell Web Service for network-based data visualization. Nucleic Acids Res. 2015 May 9. pii: gkv450. [Epub ahead of print]
  67. Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A^, Barillot E^. The shortest path is not the one you know: application of biological network resources in precision oncology research. 2015. Mutagenesis 30(2):191-204.
  68. 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.
  69. 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.
  70. Calzone L, Kuperstein I, Cohen D, Grieco L, Bonnet E, Servant N, Hupe P, Zinovyev A^, Barillot E.^ Biological network modelling and precision medicine in oncology [in French]. 2014. Bull Cancer. 101(S1):18-21.
  71. Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. 2013. BMC Syst Biol 7(1):100.
  72. Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A^, Delattre O^. Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis. 2013. Nucleic Acids Res., 41(19):8853-71.
  73. Vera-Licona P, Bonnet E, Barillot E, Zinovyev A. OCSANA: Optimal Combinations of Interventions from Network Analysis. 2013. Bioinformatics 15:29: 1571-1573.
  74. Mirkes EM., Zinovyev A., Gorban AN. Geometrical Complexity of Data Approximators. 2013. Advances in Computational Intelligence 7902:500-508.
  75. Zinovyev A, Kuperstein I, Barillot E, Heyer W-D. Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps. 2013. PLoS Comput Biol 9(4): e1003016.
  76. Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. 2013. BMC Syst Biol. 7(1):18.
  77. Kutumova E, Zinovyev A, Sharipov R, Kolpakov F. Model composition through model reduction: a combined model of CD95 and NF-kappaB signaling pathways. 2013. BMC Syst Biol. 7(1):13.
  78. Zinovyev A., Kairov U., Karpenyuk T., Ramanculov E. Blind Source Separation Methods For Deconvolution Of Complex Signals In Cancer Biology. 2013. Biochemical and Biophysical Research Communications 430(3), 1182-1187.
  79. Zinovyev A. and Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:1471-1482.
  80. 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).
  81. Kairov U., Karpenyuk T., Ramanculov E., Zinovyev A. Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures. 2012. Bioinformation 18(6):773-776.
  82. Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A. Antagonism Pattern Detection between MicroRNA and Target Expression in Ewing’s Sarcoma. 2012. PLoS One 7(7):e41770
  83. Radulescu O, Gorban AN, Zinovyev A and Noel V. Reduction of dynamical biochemical reactions networks in computational biology. 2012. Frontiers in Genetics 3: 00131.
  84. Morozova N., Zinovyev A., Nonne N., Pritchard L.-L., Gorban A.N., Harel-Bellan A. Kinetic signatures of microRNA modes of action. 2012. RNA 18(9): 032284.
  85. Martignetti L., Zinovyev A., Barillot E. Identification of shortened 3’ untranslated regions from expression arrays. 2012. Journal of Bioinformatics and Computational Biology 10:1241001.
  86. Pinna G., Zinovyev A., Araujo N., Morozova N. and Harel-Bellan A. Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells. 2012. Mathematical Modelling of Natural Phenomena 7(01):337-368
  87. Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. 2011. Bioinformatics 27(2):268-269.
  88. Gorban A.N., Zinovyev A. 2010. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. Int J Neural Syst 20(3):219-32.
  89. Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A. 2010. Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol 5;6(3):e1000702.
  90. Zinovyev A, Morozova N, Nonne N, Barillot E, Harel-Bellan A, Gorban AN. Dynamical modeling of microRNA action on the protein translation process. 2010. BMC Systems Biology 4:13.
  91. Gorban AN, Radulescu O, Zinovyev AY. Asymptotology of chemical reaction networks. 2010. Chemical Engineering Science 65, 2310-2324.
  92. Barillot E., Calzone L., Zinovyev A. Biologie des Systemes du Cancer. 2009. Med Sci (Paris). 2009 Jun-Jul;25(6-7):601-7.
  93. Guillon N, Tirode F, Boeva V, Zinovyev A, Barillot E, Delattre O. The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. 2009. PLoS ONE 4(3):e4932.
  94. Aebersold, R. et al., Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research. 2009. Molecular Oncology 3(1): 9-17.
  95. Radulescu O., Gorban A., Zinovyev A., Lilienbaum A. Robust simplifications of multiscale biochemical networks. 2008. BMC Systems Biology 2:86.
  96. Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for using and analyzing biological networks. 2008. Bioinformatics 24(6):876-877
  97. Ahnert S.E, Fink T.M.A and Zinovyev A. 2008. How much non-coding DNA do eukaryotes require? 2008. Journal of Theoretical Biology 252(4):587-592.
  98. Calzone L., Gelay A., Zinovyev A.*+, Radvanyi F., Barillot E. A comprehensive modular map of molecular interactions in RB/E2F pathway. 2008. Molecular Systems Biology 4:174 doi:10.1038/msb.2008.7
  99. Rapaport F., Zinovyev A., Dutreix M., Barillot E., Vert J.-P. Classification of microarray data using gene networks. 2007. BMC Bioinformatics 8:35.
  100. Gorban A., Zinovyev A. The Mystery of Two Straight Lines in Bacterial Genome Statistics. 2007. Bulletin of Mathematical Biology 69: 2429-2442.
  101. Gorban A., Sumner N., Zinovyev A. Topological grammars for data approximation. 2007. Applied Mathematics Letters 20(4), 382-386.
  102. Gorban A., Karlin I., Zinovyev A. Invariant grids: method of complexity reduction in reaction networks. 2005. ComPlexUs 2004-05;2:110-127.
  103. Gorban A., Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. 2005. Computing 75,359 -379
  104. Gorban A., Popova T., Zinovyev A. Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences. 2005. Physica A 353, 365-387
  105. Gorban A., Popova T., Zinovyev A. Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. 2005. In Silico Biology 5, 0025
  106. Carbone A., Kepes F., Zinovyev A. Codon bias signatures, organisation of microorganisms in codon space and lifestyle. 2005. Mol.Biol.Evol. 22(3):547-561.
  107. Gorban A., Karlin I., Zinovyev A. Constructive Methods of Invariant Manifolds for Kinetic Problems. 2004. Physics Reports 396, pp.197-403.
  108. Gorban A., Karlin I., Zinovyev A. Invariant grids for reaction kinetics. 2004. Physica A, V.333, pp.106-154.
  109. Gorban A., Zinovyev A., Popova T. Seven clusters in genomic triplet distributions. 2003. In Silico Biology. V.3, 0039.
  110. Carbone A., Zinovyev A., Kepes F. Codon Adaptation Index as a measure of dominating codon bias. 2003. Bioinformatics. 19, N13, p.2005-2015.
  111. Zinovyev A., Gorban A.N., Popova T. Self-Organizing Approach for Automated Gene Identification. 2003. Open Systems and Information Dynamics 10 (4). p.321-333.
  112. Gorban A.N., Zinovyev A.Yu. Pitenko A.A.Visualization of data. Method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.19-30.
  113. Zinovyev A.Yu., Pitenko A.A. Popova T.G. Practical applications of the method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.31-39.
  114. Gorban A.N., Pitenko A.A., Zinov’ev A.Y., Wunsch D.C. Vizualization of any data using elastic map method. Smart Engineering System Design. 2001, V.11, p. 363-368.
  115. Gorban A.N., Zinovyev A. Yu. Method of Elastic Maps and its Applications in Data Visualization and Data Modeling. International Journal of Computing Anticipatory Systems, CHAOS. 2001. V. 12. PP. 353-369.
  116. Gorban A.N., Zinovyev A.Yu., Pitenko A.A. Visualization of data using method of elastic maps (in Russian). Informatsionnie technologii. ‘Mashinostrornie’ Publ., Moscow, 2000. N6, P.26-35

Chapters

  1. Petrizzelli M, Merlevede J, Zinovyev A. Systems biology analysis for Ewing sarcoma. In ‘Ewing Sarcoma: Methods and Protocols (Methods in Molecular Biology)’ (ed. by F. Cidre-Aranaz, T. Gruenewald). 2020, Springer US
  2. Gomez LCM, Kondratova M, Sompairac N, Lonjou C, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. Atlas of Cancer Signaling Network: A resource of multi-scale biological maps to study disease mechanisms. In ‘Reference Module in Biomedical Sciences’, 2020
  3. Czerwinska U, Sompairac N, Zinovyev A. Deconvolution of heterogeneous cancer omics data. In Computational Systems Biology Approaches in Cancer Research (ed. by I.Kuperstein and E.Barilot), 2019
  4. Kondratova M, Barillot E, Zinovyev A, Kuperstein I. Knowledge formalization and high-throughput data visualization using signaling network maps. In ‘Bio-Molecular Modeling’ book, Austin Publishing group, 2017.
  5. Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. Practical Use of BiNoM: A Biological Network Manager Software. Methods Mol Biol. 2013;1021:127-46.
  6. Cohen D, Kuperstein I, Barillot E, Zinovyev A, Calzone L. From a biological hypothesis to the construction of a mathematical model. Methods Mol Biol. 2013;1021:107-25.
  7. Zinovyev A, Morozova N, Gorban A, Harel-Belan A. Mathematical modeling of microRNA-mediated mechanisms of translation repression. In MiRNA Cancer Regulation: Advanced Concepts, Bioinformatics and Systems Biology Tools (ed. Schmitz U, Wolkenhauer O, Vera J), Springer, 2013. pp. 189-224.
  8. Calzone L., Zinovyev A., Zhivotovsky B. Understanding Different Types of Cell Death Using Systems Biology. In Systems Biology of Apoptosis (ed. by Lavrik, I.), 2012, Springer. 203 p.
  9. Zinovyev A, Calzone L, Tournier L, Fourquet S and Barillot E. How cell decides between life and death: mathematical modeling of epigenetic landscapes of cellular fates. In Patterns formation in Morphogenesis (ed. by Capasso, V.; Gromov, M.; Harel-Bellan, A.; Morozova, N.; Pritchard, L.), Series: Springer Proceedings in Mathematics, Vol. 15. 2012. Springer. pp. 191-206
  10. Zinovyev A., Fourquet S., Tournier L., Calzone L. and Barillot E. Cell death and life in cancer: mathematical modeling of cell fate decisions. In Advances in Experimental Medicine and Biology, Vol. 736 (Goryanin, I. and Goryachev A., eds.), Springer, 2012, 682p.
  11. Zinovyev A. Data visualization in political and social sciences. Article in International Encyclopedia of Political Science (eds. Badie, B., Berg-Schlosser, D., Morlino, L. A.), SAGE Publications, 2011.
  12. Gorban AN and Zinovyev AY. Principal Graphs and Manifolds. In Handbook of Research on Machine Learning Applications and Trends: Algorithms, Methods and Techniques (eds. Olivas E.S., Guererro J.D.M., Sober M.M., Benedito J.R.M., Lopes A.J.S.). Information Science Reference, September 4, 2009.
  13. Gorban A and Zinovyev A. Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization. 2008. Lecture Notes in Computational Science and Engeneering 58: 97-128
  14. Gorban A, Sumner N, Zinovyev A. Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes. 2008. Lecture Notes in Computational Science and Engeneering 58: 223-240.

Peer-reviewed proceedings of conferences

  1. Buffard M., Desoeuvres A., Naldi A., Requilé C., Zinovyev A., Radulescu O. (2021) LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. In: Cinquemani E., Paulevé 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
  2. Chervov A., Zinovyev A. Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees. Proceedings of International Joint Conference on Neural Networks, Online, 18-22 July 2021.
  3. Bac J, Zinovyev A. Local intrinsic dimensionality estimators based on concentration of measure. Proceedings of International Joint Conference on Neural Networks, UK, Glasgow, 18-24 July 2020.
  4. Albergante A, Bac J, Zinovyev A. Estimating the effective dimension of large biological datasets using Fisher separability analysis. Proceedings of International Joint Conference on Neural Networks, Budapest, Hungary, 14-17 July 2019.
  5. Chevalier S, Froidevaux C, Pauleve L, Zinovyev A. Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. Proceedings of 31st International Conference on Tools with Artificial Intelligence, 2019, Portland, Oregon, United States.
  6. 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.
  7. Gorban A.N., Mirkes E. and Zinovyev A. Data analysis with arbitrary error measures approximated by piece-wise quadratic PQSQ functions. Proceedings of International Joint Conference on Neural Networks, Rio, Brazil, 8-13 July 2018.
  8. Gorban A.N. and Zinovyev A. Fast and user-friendly non-linear principal manifold learning by method of elastic maps. Proceedings of IEEE DSAA-2015 conference, 06-09/10/2015, Paris, France.
  9. Gorban A.N., Mirkes E.M., Zinovyev A. Robust principal graphs for data approximation. Proceedings of European Conference on Data Analysis-2015, 2-4/9/2015, Colchester, UK.
  10. Mirkes E.M., Zinovyev A., Gorban A.N. Geometrical complexity of data approximators. Proceedings of IWANN-2013, Puerto de la Cruz, 12-14 June 2013.
  11. Kuperstein I.; Vera-Licona P.; Zinovyev A.; et al. Integrated cell cycle and DNA repair signalling network modelling for identification of key molecular regulators in basal-like breast cancer. 2010. 21st Meeting of the European-Association-for-Cancer-Research Location: Oslo, NORWAY Date: JUN 26-29, 2010
  12. Stoll G.; Surdez D.; Tirode F.; et al. Ewing sarcoma network model through EWS-FLI1 signaling. 21st Meeting of the European-Association-for-Cancer-Research Location: Oslo, NORWAY Date: JUN 26-29, 2010
  13. Radulescu O., Zinovyev A., Lilienbaum A. Model reduction and model comparison for NFkB signalling In Proceedings of Foundations of Systems Biology in Engineering, September 2007, Stuttgart, Germany.
  14. Gorban A., Sumner N., Zinovyev A. Branching principal components: elastic graphs, topological grammars and metro maps In Proceedings of International Joint Conference on Neural Networks, August 2007, Orlando, USA.
  15. Radulescu O., Gorban A., Vakulenko S., Zinovyev A. Hierarchies and modules in complex biological systems. In Proceedings of European Conference on Complex Systems, September 2006, Oxford, UK.
  16. Gorban A.N., Zinovyev A.Y., Wunsch D.C. Application of The Method of Elastic Maps In Analysis of Genetic Texts. Proc. International Joint Conference on Neural Networks (IJCNN), Portland, Oregon, July 20-24, 2003.
  17. Alexander Gorban, A. Pitenko, A. Zinovyev, and Donald Wunsch. Visualization of Any Data with Elastic Map Method. Proc. Artificial Neural Networks in Engineering, St. Louis, MO, November, 2001.
  18. Zinovyev A.Yu. Method of constructing elastic manifolds. Proc. of National scientific conference “NeuroInformatics-2001”. Moscow, 2001. Part 1. P. 47-54.
  19. Zinovyev A.Yu., Pitenko A.A. Application of the method of elastic maps to visualization of economical indicators. Proc. of National scientific conference “NeuroInformatics-2001”. Moscow, 2001. Part 2. P. 244-249.
  20. Zinovyev A.Yu., Pitenko A.A. Method of elastic maps for data visualization and its implementation in the computer program ViDaExpert 1.0. Proc. of IX National scientific conference ‘Neuroinformatics and its applications’. Krasnoyarsk: KGTU, 2001. P.76-79.
  21. Zinovyev A.Yu., Popova T.G. Visualization of triplet distributions in coding and non-coding regions of DNA. Proc. of IX National scientific conference ‘Neuroinformatics and its applications’. Krasnoyarsk: KGTU, 2001. P.80-84.
  22. Zinovyev A.Yu., Pitenko A.A. A system of data visualization (project description). Proc. of National scientific conference “NeuroInformatics-2000”. Moscow, 2000. Part 1. P. 75-80.
  23. Zinovyev A.Yu., Pitenko A.A., Rossiev A. Projecting of multidimensional data onto two-dimensional surface. Proc. of National scientific conference “NeuroInformatics-2000”. Moscow, 2000. Part 1. P. 80-88.
  24. Zinovyev A.Yu., Pitenko A.A. Cartography of any data. Proc. of International student conference ‘Student i tehnicheskiy progress’. Novosibirsk: NSU, 2000. P. 38.
  25. Zinovyev A.Yu., Pitenko A.A. Technology of data visualization using elastic maps method. Proc. of VIII National scientific conference ‘Neuroinformatics and its applications’. Krasnoyarsk: KGTU, 2000. P.73-76.

Preprints

See the list in arXiv and bioRxiv

Invited talks and special sessions

Visiting

  1. 20-27 March 2017. Visiting Cancer Science Institute, National University of Singapore.
  2. 05-15 December 2016. ‘Exploration Japan’ visit sponsored by the French embassy in Japan.
  3. 10-16 October 2013. French delegation to Seatle, USA, invited by the governor of Washington state.
  4. 21-24 September 2010. Bioinformatics Center of Jena University, Germany.
  5. 23-31 August 2008. University of Leicester, UK.
  6. 20-31 March 2007. The Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), New-Jersey, USA.