

CURRICULUM VITAE
Andrei Zinovyev
Updated on 29 January 2019 
Personal data 
Current research interests 
Current status 
Born September 23, 1974
in Krasnoyarsk, USSR (Russia)
Mailing address:
Institut Curie, Service Bioinformatique
26 rue d'Ulm, F75248, Paris, France.
Tel: (33)156246989
Email: andrei . zinovyev at curie . fr
WWW: https://auranic.github.io
GitHub: auranic
ResearchGate: Andrei_Zinovyev
Researcher Id: B47152010
Languages: English (fluent), French (fluent), Russian (native)

Machine Learning for biological and healthcare problems
Latent spaces and structures in big data point clouds
Cancer systems biology
Model and dimension reduction in complex systems

Senior researcher at Institut Curie, Paris, France
Scientific coordinator of
Computational Systems Biology of Cancer team
in Bioinformatics, biostatistics, epidemiology and computational systems biology of cancer unit
Institut Curie / Inserm Unit 900 / Ecoles des Mines

Education:
 2014: Habilitation thesis (HDR, Habilitation à diriger des recherches) in Biology, Department of Biology of École Normale Supérieure
Thesis title: Dealing with complexity of biological systems: from data to models
 2001: PhD in Computer Science, Krasnoyarsk State University:
Thesis title: Method of Elastic Maps for Data Visualization: Algorithms, Software and Applications in Bioinformatics
Scientific advisor: Professor Alexander N. Gorban
 19982001  Post graduate, Institute of Computational Modeling, Krasnoyarsk, Russia
 19911997  Master's diploma with distinction (highest grade in all disciplines), Krasnoyarsk State University (Physical Department), chair of theoretical physics, cosmology
Experience:
 Science
 January 2005present  scientific coordinator of "Computational Systems Biology of Cancer" team, permanent researcher at Institut Curie in Paris, INSERM U900
 December 2001December 2004  postdoc, involved in the project "Functional Genomics" (Institut des Hautes Etudes Scientifiques, France)
 FebruaryOctober 2000  Project leader of ecological data analysis, sponsored by Krasnoyarsk Regional Scientific Fund
 19982001  PhD student (computer science). Institute of Computational Modeling, Russian Academy of Sciences, Siberian Branch
 19931999  Developer/Researcher. Siberian Institute of Gydrotechny and Melioration, Russia
 19931997  Graduate student. Research work in the theory of gravitation and cosmology
 Industry
 May 2002  May 2003  Project leader, creation of a parallelized bioinformatics platform Plug&Blast for a cluster of processors
 MayDecember 2001  Principal software developer, creation of an information system for automated access
to worldwide patent databases (SIT project), 'SibTeCom' Company, Krasnoyarsk, Russia
 19972001  principal software developer. Creation of a bookkeeping system for a commercial computer company (KomPAK, Krasnoyarsk, Russia)
 JanuaryJune 2000  computer consultant, 'Electrosvyaz' company, Krasnoyarsk, Russia
 Teaching
 OctoberDecember 2016,2017 – organization of the “Mathematical modeling of biological systems” predoctoral teaching course at University Paris Sciences et Lettres, Institut de Technologie et d'Innovation.
 November 2015  participation in the course Analysis fof cancer genome, Rosay sur Lieure Eure, France.
 July 2015  organization of 7 day course "Omics Data Analysis and Medical Applications" for professional bioinformaticians and PhD students, Skoltech, Moscow, Russia.
 2012now  internal teaching program of Institut Curie, modules related to analysis of highthroughput data in the context of biological networks.
 May 2011  40hours course on computational systems biology, as a part of PhD program in Bioinformatics at Kazakh National University after AlFarabi, Almaty, Kazakhstan.
 2009now  short course "Modeling and integrating highthroughput data in cancer research" at Ecole normale superieure as a part of "Biology of cellular systems" Master 2 course, Paris, France.
 April and June 2008  teaching sessions on analysis of biological networks for INSERM Workshop 184 "Modélisation et analyse statistique des réseaux biologiques".
 November 1998  July 1999  lecturer of informatics, Krasnoyarsk State Technical University, Russia
Awards:
 2014: "Thought Leader Award" by Agilent
 2005: "Lobry's prize" for the best presentation at "Geometry of Genome: Unravelling of Structures Hidden in Genomic Sequences" conference.
 2001: Personal grant from the Fund of Russian Academy of Science for young researchers
 2001: Special prize from Institute of Computational Modeling, Krasnoyarsk, Russia for fast (in two years)
Ph.D. thesis accomplishement
 1992, 1993: Special prize for talented students
 1994, 1995: Soros student (two years).
Grants and projects:
 As the principal coordinator of a project:
 ANR SITCON: Modeling Signal Transduction Induced By A Chimeric Oncogene  (November 2006November 2009), 400KEuros
 ISC MATBRAC: Mathematical theory of biological robustness with experimental applications in cancer systems biology  (November 2006November 2009), 6KEuros
 Plug&Blast: Creation of a commercial parallel platform for bioinformatics computations  (May 2002May 2003)
 As coordinator of Institut Curie or the systems biology team participation:
 iPaediatricCure EU Horizon2020: largescale Horizon2020 project on application of cloudbased data science approach to improving treatment of paediatric cancers (January 2019January 2023), 15Meuros
 IMMUCAN EU IMI: largescale academyindustrial EU IMI project on molecular profiling tumor microenvironment (April 2019April 2023), 36Meuros
 ITMO Cancer: noncoding RNA in cancerology: Using an integrative strategy to decipher miRNAs function in Pediatric Brain Tumor, (November 2018November 2021), 613kEuros
 iPaediatricCure: largescale EU Horizon2020 project on application of cloudbased data science approach to improving treatment of paediatric cancers (January 2019January 2023), 15Meuros
 MOSAIC ITMO Cancer SysBio program: MOdeling Single cell vAriability In Cancer progression and treatment (20142017), 500kEuros
 APLIGOOGLE CNRS MASTODON project: Appliation of Google Matrix approach for analysis of large networks (2016), 40kEuros
 PANMETHYLOME Canceropole Emergence: Largescale analysis of DNA methylation data, using blind signal deconvolution statistical techniques, with aim to determin signatures based on DNA methylation patterns of exposure to certain environmental factors (such as smoking) (20152016), 50kEuros
 PIC3i Tumor microenvironment (Institut Curie internal project): Global view of CAF heterogeneity and functions in Tumorigenesis (20152018)
 Agilent Thought Leader Award: developing a database of cellular signaling pathways and a visualization tool to help the pharmaceutical industry develop more effective cancer treatments (20132016), 400kEuros
 EU FP7 APOSYS: Apoptosis Systems Biology Applied to Cancer and AIDS  (December 2008December 2011), 11MEuros
 EU FP7 ASSET: Analysing and Stryking the Sensitivities of Embryonal Tumours  (November 2010November 2013), 11MEuros
 As coordinator of big parts of a project (i.e., workpackages):
 PIC SysBio (Institut Curie internal project): Genetic Interactions in DNA repair pathways and cancer (20132016), 100KEuros
 INVADE: Mathematical modeling of early tumour invasion (December 2012December 2015), 1000KEuros
 CoMET: Modeling cell communication networks in breast cancer (20142017), 1000KEuros
 InCA SybEwing: Systems Biology of Ewing's sarcoma  (December 2009December 2012), 500KEuros
 As participant:
 PanNet EU TRANSCAN2: Predictive models of therapy response in pancreatic neuroendocrine tumors (20192022), 1.1Meuros
 PRECISE EU Horizon2020: Personalized Enginge for Cancer Integrative Study and Evaluation (20152018), 3Meuros
 COLOSYS EU EracoSysMed: A systems approach to preventing drug resistance in colon cancer (20152018), 1.8MEuros
 PSL Institute for Data Science: Big Data PSL Research University project: creating a crossdisciplinary and crossinstitutional virtual hub of research and education, the PSL Institute for Data Science (PIDS)  (20162018), 100kEuros
 M5 ITMO Cancer SysBio program: Mathematical Modeling of Molecular Mechanisms involved in Medulloblastoma progression  (20152018), 400KEuros
 ANR CALAMAR: Compositional modelling and Analysis of LArge MoleculAr Regulatory networks  application to the control of human cell proliferation.  (October 2008October 2011), 400KEuros
 EU FP6 ESBICD: European Systems Biology Initiative combating complex diseases.  (January 2005January 2008)
Conference committees:
 Member of scientific organizing comitee of 2nd International Curie course on Computational Systems Biology of Cancer (Single Cell data analysis), Paris, September 2019.
 Member of scientific organizing comitee of 1st International Curie course on Computational Systems Biology of Cancer, Paris, September 2018.
 Member of scientific organizing comitee of BioNetVisA workshop at ECCB2018, Athens, September 2018.
 Member of scientific organizing comitee of BioNetVisA workshop at BC22017, Basel, Septmeter 2017.
 Member of scientific organizing comitee of BioNetVisA workshop at ECCB2016, Barcelona, July 2016.
 Member of scientific organizing comitee of BioNetVisA workshop at ICSB2015, Singapore, November 2015.
 Member of organizing comitee of Model Reduction across disciplines2014
 Member of programming commitee of SASB2014
 Member of scientific organizing comitee of BioNetVisA workshop at ECCB2014, Strasbourg, September 2014.
 Member of programming commitee of ECCB2014, Strasbourg, September 2014.
 Member of programming commitee of ECCB2012, Basel, September 2012.
 Member of programming commitee of ECCB2010, Ghent, October 2010.
 Member of organizing commitee of "Principal manifolds2006", Leicester, UK, 2006.
 Member of organizing commitee of "Geometry of Genome", Leicester, UK, 2005.
PeerReviewing activities:
See my Publons profile.
 Physical Biology
 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
PhD theses (co)supervision:
 Alexey Guerassimov, "Kinetic model of regulation of translation in eukaryotic cells", 20162018 (not finished)
 Urszula Czerwinska, "Deconvolution of cell and environment specific signals and their interactions from complex mixtures in biological samples", 20152018
 Marine Le Morvan, "Search for cancer driver mutations using mutation, expression data and biological networks", 20142017
 Geraldine Cellier, "Multiscale modeling of early invasion of tumour cell into surrounding tissues", 20122015
 Ulykbek Kairov, "Analysis of microarray data for searching genetic markers in cancer" (Kazhakstan), 20092012
 Elena Kutumova, "Application of model reduction methods for constructing a composite model of apoptosis signaling" (Russia), 20092012
 Anne Biton, "Geometrical analysis of pathway deregulations in bladder cancer", 20082011.
 Franck Rapaport, "Integration of gene expression data and gene regulatory networks for the study of cancers", 20052008.
Participation in PhD theses jury as a referee:
 Christophe Becavin, "Dimensionality reduction and pathway network analysis of transcriptome data: Application to Tcell characterization", Paris, December 2010.
 Michel Journee, "Geometric algorithms for component analysis with a view to gene expression data analysis", Liege, June 2009.
 Nora Nonne, "Etude de l'action des microARN : mecanismes et cibles", Paris, November, 2009.
Invited talks and special sessions:
Biological networks help unraveling tumoral heterogeneity at single cell level. Talk at BIONETVISA workshop at ECCB2018, 9 September 2018, Athens, Greece
Reduced Google Matrix approach for exploring biological networks. Invited talk at Google Matrix: theory and applications conference. 18 October 2018, IHES, BuressurYvette
Deconvolution of heterogeneous cancer omics data. Talk at 1st International Course on Computational Systems Biology of Cancer, Paris, 25 September 2018
Machine learning methods in molecular biology: unsupervised approach. Invited talk at Lobachevsky University, Nizhniy Novgorod, Russia,9 August 2018
Quantifying intratumoral heterogeneity at single cell level. Invited seminar for Lecture Series Translational Bioinformatics & Systems Biomedicine, Luxemburg Institute of Health, 26 June 2018
Modern Biomedical Omics Data Visualization. Genopole Summer School, Paris, 25 June 2018
Use of network propagation methods in cancer data analysis. Network Medicine workshop at Network Science conference, Paris, 22 May 2018
Independent Component Analysis unravels molecular mechanisms of Ewing sarcoma. IHPCurie seminar, Paris, 17 May 2018
Multiscale integrative modeling of early tumour invasion mechanisms. ITMO SysBio seminar, 26 February 2018
Single cell molecular pro?ling to understand cancerogenesis. Keynote talk at Workshop Computational Systems Biology for Cancer, Institut des Systèmes Complexes, Paris, 2426 January 2018.
Nontrivial geometry of omics data used for obtaining insights into biology. CurieIHESIHP seminar on mathematical biology, 20 February 2018.
InfoSigMap: Google Maps of informative gene signatures visualizes their compositional and functional redundancies in transcriptomic studies. Invited talk at Cancer Science Institute, Singapore, 21 March 2017.
Deconvoluting cancer omics data using independent component analysis. Institututional seminar of Luxembourg Institute of Health, 5 October 2017, Luxembourg
Disease maps for mathematical modeling: encyclopedia or blueprint? 2nd Disease Maps consortium meeting. 3 October 2017, Luxembourg
Network propagation for cancer data analysis. Invited talk at Interdisciplinary Signaling Workshop. 19 July 2017, Visegrad
Systems Biology as a field of science in the last and the future 15 years. Invited talk at DC Biol Labex course, 14 March 2017
The shortest path is not the one you know: application of biological networks in precision oncology research', Invited talk at Kyoto University, Ogata lab, 13 December 2016, Kyoto, Japan
Mathematical modeling of biological networks helps finding genetic determinants of metastatic colon cancer', Invited talk at Osaka University, Mariko Okada lab, 12 December 2016, Osaka, Japan.
Disentangling bladder cancer progression pathways by pancancer deconvolution of tumoral transcriptomes', Invited talk at RIKEN, Carnici lab, 6 December 2016, Yokohama, Japan
Detecting and exploiting nontrivial geometrical omics data structures for obtaining insights into cancer biology ', CurieSBI workshop, 7 December 2016, Tokyo, Japan
Detecting nontrivial geometrical data structures in cancer omics data', 7 November 2016, Invited talk at the Mathematical Biology seminar of Institut des Hautes Études Scientifiques, BuressurYvette.
Mathematical modeling of molecular pathways enabling tumor cell invasion and migration Conference "Mathematical modeling and cancer", 2 December 2015, Montpellier.
Identifying the Functional Interaction Between p53 and Notch pathways in Triggering Metastasis: From Maps to Data to Models. Minisimposium at Cancer Science Institute, Singapore, November 26, 2015.
Atlas of Cancer Signaling Network and NaviCell: Google Maps of cancer biology. 16th International Conference of Systems Biology, Singapore, November 25, 2015
Atlas of Cancer Signaling Network and NaviCell. 16th International Conference of Systems Biology (ICSB)BioNetVisA workshop, Singapore, November 25, 2015
Utilisation des outils génomiques dans la prise en charge des cancers du sein du point de vue du bioinformaticien. 37es Journées de la société française de sénologie et de pathologie mammaire, Bordeaux, 11 November 2015.
Gene Networks and Omics Data Visualization. Thematic School "Analysis of Tumoral Genome", 03 November 2015.
Blind source deconvolution of omics data in cancer studies. Institut Curie Research Center Scientific Day, 30 October 2015.
Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes. Selected talk, highlight track, ISMB 2015, Dublin, 13 July 2015
Modern methods for visualization and exploratory analysis of omics data, Omics data analysis in medicine summer school, 21 July 2015, Skolkovo, Russia
Mathematical modeling of biological processes using omics data, Omics data analysis in medicine summer school, 24 July 2015, Skolkovo, Russia
Revealing mechanisms of cancer progression by pancancer deconvolution of tumoral transcriptomes, 17 July 2015, Moscow Conference on Computational Molecular Biology (MCCMB2015), Russia
Towards mathematical modelling of the signalling network downstream of EWS/FLI1, ASSETENCCA Ewing meeting, Paris, 1516 June 2015
Atlas of Cancer Signaling Network and NaviCell: Google Maps of cancer biology", Invited talk, The Genome Analysis Center, Norwich, 21 May 201
Pancancer deconvolution of tumoral transcriptomes reveals new mechanisms of bladder cancerogenesis, 2nd International Conference on Personalized Medicine and Global Health, Astana, Kazakhstan, 13 May 2015
Mathematical modeling of biological networks helps finding genetic determinants of metastatic colon cancer. Invited talk at the seminar of Oncology department, Oxford University. 22 January 2015.
Fighting with complexity of biological systems, Model Reduction across disciplines, Leicester, UK, 1922 August 2014.
Mathematical aspects of cancer biology. Invited seminar at Vavilov Institute of General Genetics, Moscow, Russia, 22 January 2014.
Looking at Big Data in cancer biology: make it simple. Invited talk at University College of Cork, Ireland, 19 November 2013.
Mathematical modeling of cancerrelated molecular mechanisms. Invited talk at COMBINE2013. Institut Curie, Paris. 16 September 2013.
Computational analyses of synthetic lethality in DNA repair pathways with application to cancer treatment, International Conference of Systems Biology2013, Copenhagen, 2 September 2013.
Mechanisms of genetic interactions and cancer treatment, Moscow Conference on Computational Molecular Biology2013, Moscow, 28 July 2013.
Cancer biology questions asked in a mathematical language, Keynote talk at "Mathematics and Cancer biology" conference, Institut Curie, Paris, 12 June 2013
Kinetic signatures of miRNA modes of action, Invited talk at "Mechanisms of microRNA action" workshop, University of Leicester, Leicester, 7 November 2012.
Systems biology, treatment of cancer and the future of medicine. Invited talk given in Siberian Federal University, Krasnoyarsk, July 2012.
Network Interpretation And MetaAnalysis Of Independent Components Applied To Cancer Transcriptomes. Bioinformatics of Genome Regulation and Structure/Systems Biology' 2012. Novosibirsk, June 2012.
Synthetic lethality within one pathway: DNA repair and cancer treatment. Bioinformatics of Genome Regulation and Structure/Systems Biology' 2012. Novosibirsk, June 2012.
Modelling life and death cellular decisions in cancer. Dynamics of disease2011, Manchester, 1418 February 2011.
Mathematical modelling of cell death and life decisions in cancer. Invited talk at BioIntelligence consortium's simposium. 04 July 2011, Nice.
Model reduction for modeling in systems biology. 30 May 2011, Invited talk at Prof. Hans Westerhoff's group seminar. Faculty of Biology, Vrije Universiteit, Amsterdam.
Modelling life and death cellular decisions in cancer. 20 May 2011. BioTech center seminar, Astana, Kazakhstan.
Highthroughput sequencing for better understanding cancer: ChIPSeq technology for studying Ewing's sarcoma. 19 May 2011. BioTech center seminar, Astana, Kazakhstan.
BioUML: a plugin for model reduction. July 23rd 2011, MCCMB'11, Moscow, Russia.
Deciphering mechanisms of miRNA action on translation by mathematical modeling. July 24th 2011. MCCMB'11, Moscow, Russia.
Mathematical modeling of cellular decisions between life and death in cancer. Invited talk at Cell Singalomics2011, Luxembourg, 2628 January 2011.
Nonlinear principal manifolds for bioinformatics applications. ERCIM conference, London, UK, 912 December 2010.
Mathematical modeling of cell life and death in cancer. Invited talk at International Conference on Systems Biology (ICSB2010), 11 October 2010, Edinburgh, UK.
BiNoM  a Cytoscape plugin for analysis of biological networks using systems biology standards. Computational Modeling of Biological Networks (COMBINE) meeting. 08 October 2010, Edinburgh, UK.
Next generation sequencing for better understanding cancer. Invited talk at Seminar of the Bioinformatics Center of Jena University. 23 September 2010, Jena, Germany.
Dynamical modeling of microRNA mechanisms. 7th International conference on Bioinformatics of genome regulation and structure (BGRS'2010). June 2010, Novosibirsk, Russia.
ChipSeq technology for studying Ewing's sarcoma. "Bioinformatics after Next Generation Sequencing" FrenchRussian seminar, June 2010, Zvenigorod, Russia.
Dynamical modeling of microRNA effect on translation. 4th Joint Cold Spring Harbor/Wellcome Trust conference "Computational Cell Biology". February 2010, Hinxton, UK.
What in silico models can give to biology and clinics? Invited presentation at "Chez Claudius" meeting on 11 March 2010. Institut Curie, Paris, France.
Principal Manifolds And Graphs In Practice: From Molecular Biology To Dynamical Systems. Coping with Complexity: Model Reduction and Data Analysis" workshop at "Algorithms for Approximation VI", 1 September 2009, University of Cumbria, UK.
Finding Meaningfull Structures In HighThroughput Data: From Principal Trees To Spectral Filtering On Graphs. Moscow Conference on Computational Molecular Biology2009, 2025 July 2009, Moscow, Russia.
Robust simplifications of multiscale biochemical networks. International Conference of Intelligent Systems for Molecular Biology (ECCB/ISMB 2009) 1 July 2009, Stokholm, Sweden.
Unsupervised machine learning in the analysis of highthroughput data for systems biology. Invited talk at Systems Biology for Medical Applications Summer School 29 Sept03 Oct 2008, Tenerife, Spain.
BiNoM: a tool for manipulating and analysis of biological networks. Invited talk at International Conference on Systems Biology Workshop 'Webservices in Systems Biology'. 28 August 2008, Gotenborg, Sweden.
Method For Complexity Reduction And Model Comparison With Application To Nfkb Signalling. The Sixth International Conference on Bioinformatics of Genome Regulation and Structure. 24 July 2008, Russia, Novosibirsk, Russia.
How much noncoding DNA do eukaryotes require? Invited talk at Think Tank in Systems Biology "Statistical semantics of genomes: from sequence to function". 27 May 2008, Evry, France.
Projects and tools for systems biology at Curie Institute. EASTSCOPE conference, 34 December 2007, Moscow, Russia.
Frequency dictionaries and genome grammars. Invited talk at Repetitive DNA in the Genomic Era 14 Nov 2007, Leicester, UK.
Elastic principal graphs and topological grammars for data approximation. Bell Labs Research seminar, 23 March 2007, New Jersey, USA.
Ewing tumor as a model for systems biology. Journees Scientifiques et Medicales 2007. 9 Fevrier 2007, Paris.
Codons, Genes and Networks: multiple scales in genomic organization. Theoretical Approaches for Genome (10 Novembre 2006) Annecy, France.
Spectral analysis of gene expression profiles using gene networks. Bioinformatics of genome regulation and structure BGRS2006 (July 1622, 2006, Novosibirsk)
Elastic maps and its applications in bioinformatics. Principal manifolds for data cartography and dimension reduction. Leicester, UK. August, 2006.
Seven clusters and four types of symmetry in microbial genomes. Geometry of Genome: Unravelling of Structures Hidden in Genomic Sequences, Leicester, UK, 2005.
Codon bias vector field. Geometry of Genome: Unravelling of Structures Hidden in Genomic Sequences, Leicester, UK, 2005.
Elastic maps method and its applications in data visualization. VIII National scientific conference 'Neuroinformatics and its applications'. Krasnoyarsk, Russia, 2000.
Visiting:
 2027 March 2017. Visiting Cancer Science Institute, National University of Singapore.
 0515 December 2016. 'Exploration Japan' visit sponsored by the French embassy in Japan.
 1016 October 2013. French delegation to Seatle, USA, invited by the governor of Washington state.
 2124 September 2010. Bioinformatics Center of Jena University, Germany.
 2331 August 2008. University of Leicester, UK.
 2031 March 2007. The Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), NewJersey, USA.
Development of scientific software:
See my GitHub page and the list of the tools of
Computational Systems Biology of Cancer group at Institut Curie for many of which
I've contributed.
Publications (see the complete list of my citations in Google Scholar):
 Books:
 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.
 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.
 Zinovyev A. Visualization of Multidimensional Data (in Russian). Krasnoyasrk: KGTU Publ., 2000, 168 p.
 Chapters:
 Kondratova M, Barillot E, Zinovyev A, Kuperstein I. Knowledge formalization and highthroughput data visualization using signaling network maps. In 'BioMolecular Modeling' book, Austin Publishing group, 2017.
 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;1021:12746.
 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;1021:10725.
 Zinovyev A, Morozova N, Gorban A, HarelBelan A. Mathematical modeling of microRNAmediated 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. 189224.
 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.
 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.; HarelBellan, A.; Morozova, N.; Pritchard, L.), Series: Springer Proceedings in Mathematics, Vol. 15. 2012. Springer. pp. 191206
 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.
 Zinovyev A. Data visualization in political and social sciences. Article in International Encyclopedia of Political Science (eds. Badie, B., BergSchlosser, D., Morlino, L. A.), SAGE Publications, 2011.
 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.
 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: 97128
 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: 223240.
 Articles in peerreviewed journals (^{*}equal contribution, ^{+}corresponding author, ^{^}colast authorship):
(see also the list of my articles in Pubmed database)
 Heirendt L et al (54 authors). Creation and analysis of biochemical constraintbased models: the COBRA Toolbox v3.0. 2019. Nature Protocols, in press.
 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.. [Epub ahead of print]
 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. Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky992.
 Letort G, Montagud A, Stoll G, Heiland R, Barillot E, Macklin P, Zinovyev A, Calzone L. PhysiBoSS: a multiscale agentbased modelling framework integrating physical dimension and cell signalling. Bioinformatics. 2018 Aug 30. doi: 10.1093/bioinformatics/bty766.
 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.
 Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, CohenBoulakia S, Thieffry D, Paulevé L. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. 2018. Front Physiol 9:680.
 Calzone L, Barillot E, Zinovyev A. Logical versus kinetic modeling of biological networks: applications in cancer research. Current Opinion in Chemical Engineering 21, 2231.
 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: communitydriven comprehensive representation of disease mechanisms. NPJ systems biology and applications 4 (1), 21
 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.
 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. Communitydriven roadmap for integrated disease maps. Brief Bioinform. 2018 Apr 23.
 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.
 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.
 Costa A.,Kieffer Y., ScholerDahirel 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., VincentSalomon A., MechtaGrigoriou F. Fibroblast heterogeneity and immunosuppressive environment in human breast cancer. 2018. Cancer Cell 33(3):463479.e10.
 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.
 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.
 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 postmortem analyses. Nat Methods 14(10):937938. 2017.
 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.
 Le Morvan M, Zinovyev A, Vert JP. NetNorM: Capturing Cancerrelevant Information in Somatic Exome Mutation Data with Gene Networks for Cancer Stratification and Prognosis. PLoS Computational Biology 13(6):e1005573. 2017.
 Dorel M, Viara E, Barillot E, Zinovyev A^ and Kuperstein I^. NaviCom: a web application to create interactive molecular network portraits using multilevel omics data. Database (Oxford) 111. 2017.
 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.
 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 22:17741791. 2017.
 Gorban A., Mirkes E., Zinovyev A. Robust principal graphs for data approximation. Archives of Data Science 2(1):1:16, 2017.
 Jdey W., Thierry S., Russo C., Devun F., Al Abo M., NoguiezHellin 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.
 Gorban AN, Mirkes EM, Zinovyev A. Piecewise quadratic approximations of arbitrary error functions for fast and robust machine learning. Neural Netw. 2016, 84:2838.
 Deveau P., Barillot E., Boeva V., Zinovyev A., Bonnet E. Calculating Biological Module Enrichment or Depletion and Visualizing Data on Largescale Molecular Maps with ACSNMineR and RNaviCell Packages. R journal 2016, 8:293306.
 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.
 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.
 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.
 Kuperstein I, Robine S, Zinovyev A. Network biology elucidates metastatic colon cancer mechanisms. 2015. Cell Cycle 14(14):218990.
 Dorel M, Barillot E, Zinovyev A, Kuperstein I. Networkbased approaches for drug response prediction and targeted therapy development in cancer. 2015. Biochem Biophys Res Commun. 464(2):38691.
 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.
 Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L. A Modeling Approach to Explain Mutually Exclusive and CoOccurring Genetic Alterations in Bladder Tumorigenesis. 2015. Cancer Res. 75(19):404252.
 Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling. Mathematical Modeling of Natural Phenomena 10(3), 186205.
 Czerwinska U, Calzone L, Barillot E, Zinovyev A. DeDaL: Cytoscape 3 app for producing and morphing datadriven and structuredriven network layouts. 2015. BMC Syst Biol. 14;9:46.
 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.
 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]
 Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A. NaviCell Web Service for networkbased data visualization. Nucleic Acids Res. 2015 May 9. pii: gkv450. [Epub ahead of print]
 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):191204.
 Biton A., BernardPierrot 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), 12351245.
 Chanrion M, Kuperstein I, Barriere C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, PaulGilloteaux P, Bieche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, LegoixNe P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A^{^}, Robine S.^{^} Concomitant Notch activation and p53 deletion trigger epithelialtomesenchymal transition and metastasis in mouse gut. 2014. Nature Communications, 5:5005.
 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):1821.
 Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A. NaviCell: a webbased environment for navigation, curation and maintenance of large molecular interaction maps. 2013. BMC Syst Biol 7(1):100.
 Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A^{^}, Delattre O^{^}. Systems biology of Ewing sarcoma: a network model of EWSFLI1 effect on proliferation and apoptosis. 2013. Nucleic Acids Res., 41(19):885371.
 VeraLicona P, Bonnet E, Barillot E, Zinovyev A. OCSANA: Optimal Combinations of Interventions from Network Analysis. 2013. Bioinformatics 15:29: 15711573.
 Mirkes EM., Zinovyev A., Gorban AN. Geometrical Complexity of Data Approximators. 2013. Advances in Computational Intelligence 7902:500508.
 Zinovyev A, Kuperstein I, Barillot E, Heyer WD. Synthetic Lethality between Gene Defects Affecting a Single Nonessential Molecular Pathway with Reversible Steps. 2013. PLoS Comput Biol 9(4): e1003016.
 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.
 Kutumova E, Zinovyev A, Sharipov R, Kolpakov F. Model composition through model reduction: a combined model of CD95 and NFkappaB signaling pathways. 2013. BMC Syst Biol. 7(1):13.
 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), 11821187.
 Zinovyev A. and Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:14711482.
 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):572588 (In Russian).
 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):773776.
 Martignetti L, LaudDuval 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
 Radulescu O, Gorban AN, Zinovyev A and Noel V. Reduction of dynamical biochemical reactions networks in computational biology. 2012. Frontiers in Genetics 3: 00131.
 Morozova N.^{*}, Zinovyev A.^{*}, Nonne N., Pritchard L.L., Gorban A.N., HarelBellan A. Kinetic signatures of microRNA modes of action. 2012. RNA 18(9): 032284.
 Martignetti L., Zinovyev A., Barillot E. Identification of shortened 3' untranslated regions from expression arrays. 2012. Journal of Bioinformatics and Computational Biology 10:1241001.
 Pinna G., Zinovyev A., Araujo N., Morozova N. and HarelBellan A. Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells. 2012. Mathematical Modelling of Natural Phenomena 7(01):337368
 Boeva V, Zinovyev A, Bleakley K, Vert JP, JanoueixLerosey I, Delattre O, Barillot E. Controlfree calling of copy number alterations in deepsequencing data using GCcontent normalization. 2011. Bioinformatics 27(2):268269.
 Gorban A.N., Zinovyev A. 2010. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. Int J Neural Syst 20(3):21932.
 Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A. 2010. Mathematical modelling of cellfate decision in response to death receptor engagement. PLoS Comput Biol 5;6(3):e1000702.
 Zinovyev A, Morozova N, Nonne N, Barillot E, HarelBellan A, Gorban AN. Dynamical modeling of microRNA action on the protein translation process. 2010. BMC Systems Biology 4:13.
 Gorban AN, Radulescu O, Zinovyev AY. Asymptotology of chemical reaction networks. 2010. Chemical Engineering Science 65, 23102324.
 Barillot E., Calzone L., Zinovyev A. Biologie des Systemes du Cancer. 2009. Med Sci (Paris). 2009 JunJul;25(67):6017.
 Guillon N, Tirode F, Boeva V, Zinovyev A, Barillot E, Delattre O. The oncogenic EWSFLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. 2009. PLoS ONE 4(3):e4932.
 Aebersold, R. et al., Report on EUUSA Workshop: How Systems Biology Can Advance Cancer Research. 2009. Molecular Oncology 3(1): 917.
 Radulescu O., Gorban A., Zinovyev A., Lilienbaum A. Robust simplifications of multiscale biochemical networks. 2008. BMC Systems Biology 2:86.
 Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for using and analyzing biological networks. 2008. Bioinformatics 24(6):876877
 Ahnert S.E, Fink T.M.A and Zinovyev A. 2008. How much noncoding DNA do eukaryotes require? 2008. Journal of Theoretical Biology 252(4):587592.
 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
 Rapaport F., Zinovyev A., Dutreix M., Barillot E., Vert J.P. Classification of microarray data using gene networks. 2007.
BMC Bioinformatics 8:35.
 Gorban A., Zinovyev A. The Mystery of Two Straight Lines in Bacterial Genome Statistics. 2007. Bulletin of Mathematical Biology 69: 24292442.
 Gorban A., Sumner N., Zinovyev A. Topological grammars for data approximation. 2007. Applied Mathematics Letters 20(4), 382386.
 Gorban A., Karlin I., Zinovyev A. Invariant grids: method of complexity reduction in reaction networks. 2005. ComPlexUs 200405;2:110127.
 Gorban A., Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. 2005. Computing 75,359 379
 Gorban A., Popova T., Zinovyev A. Codon usage trajectories and 7cluster structure of 143 complete bacterial genomic sequences. 2005. Physica A 353, 365387
 Gorban A., Popova T., Zinovyev A. Four basic symmetry types in the universal 7cluster structure of microbial genomic sequences. 2005. In Silico Biology 5, 0025
 Carbone A., Kepes F., Zinovyev A. Codon bias signatures, organisation of microorganisms in codon space and lifestyle. 2005. Mol.Biol.Evol. 22(3):547561.
 Gorban A., Karlin I., Zinovyev A. Constructive Methods of Invariant Manifolds for Kinetic Problems. 2004. Physics Reports 396, pp.197403.
 Gorban A., Karlin I., Zinovyev A. Invariant grids for reaction kinetics. 2004. Physica A, V.333, pp.106154.
 Gorban A., Zinovyev A., Popova T. Seven clusters in genomic triplet distributions. 2003.
In Silico Biology. V.3, 0039.
 Carbone A., Zinovyev A., Kepes F. Codon Adaptation Index as a measure of dominating codon bias. 2003. Bioinformatics. 19, N13, p.20052015.
 Zinovyev A., Gorban A.N., Popova T. SelfOrganizing Approach for Automated Gene Identification. 2003. Open Systems and Information Dynamics
10 (4). p.321333.
 Gorban A.N., Zinovyev A.Yu. Pitenko A.A.Visualization of data. Method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.1930.
 Zinovyev A.Yu., Pitenko A.A. Popova T.G. Practical applications of the method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.3139.
 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. 363368.
 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. 353369.
 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.2635.
 Reviewed proceedings of conferences:
 Czerwinska U., Cantini L., Kairov U., Barillot E., Zinovyev A.Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific And Reproducible Immunerelated Signals. Proceedings of International Conference on Latent Variable Analysis and Signal Separation, Surrey, UK, 26 July 2018.
 Gorban A.N., Mirkes E. and Zinovyev A. Data analysis with arbitrary error measures approximated by piecewise quadratic PQSQ functions. Proceedings of International Joint Conference on Neural Networks, Rio, Brazil, 813 July 2018.
 Gorban A.N. and Zinovyev A. Fast and userfriendly nonlinear principal manifold learning by method of elastic maps. Proceedings of IEEE DSAA2015 conference, 0609/10/2015, Paris, France.
 Gorban A.N., Mirkes E.M., Zinovyev A. Robust principal graphs for data approximation. Proceedings of European Conference on Data Analysis2015, 24/9/2015, Colchester, UK.
 Mirkes E.M., Zinovyev A., Gorban A.N. Geometrical complexity of data approximators. Proceedings of IWANN2013, Puerto de la Cruz, 1214 June 2013.
 Kuperstein I.; VeraLicona P.; Zinovyev A.; et al. Integrated cell cycle and DNA repair signalling network modelling for identification of key molecular regulators in basallike breast cancer. 2010. 21st Meeting of the EuropeanAssociationforCancerResearch Location: Oslo, NORWAY Date: JUN 2629, 2010
 Stoll G.; Surdez D.; Tirode F.; et al. Ewing sarcoma network model through EWSFLI1 signaling. 21st Meeting of the EuropeanAssociationforCancerResearch Location: Oslo, NORWAY Date: JUN 2629, 2010
 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.
 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.
 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.
 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 2024, 2003.
 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.
 Zinovyev A.Yu. Method of constructing elastic manifolds. Proc. of National scientific
conference "NeuroInformatics2001". Moscow, 2001. Part 1. P. 4754.
 Zinovyev A.Yu., Pitenko A.A. Application of the method of elastic maps to visualization of economical indicators. Proc. of National scientific
conference "NeuroInformatics2001". Moscow, 2001. Part 2. P. 244249.
 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.7679.
 Zinovyev A.Yu., Popova T.G. Visualization of triplet distributions in coding and noncoding regions of DNA. Proc. of IX National
scientific conference 'Neuroinformatics and its applications'. Krasnoyarsk: KGTU, 2001. P.8084.
 Zinovyev A.Yu., Pitenko A.A. A system of data visualization (project description). Proc. of National scientific
conference "NeuroInformatics2000". Moscow, 2000. Part 1. P. 7580.
 Zinovyev A.Yu., Pitenko A.A., Rossiev A. Projecting of multidimensional data onto twodimensional
surface. Proc. of National scientific conference "NeuroInformatics2000". Moscow, 2000. Part 1. P. 8088.
 Zinovyev A.Yu., Pitenko A.A. Cartography of any data. Proc. of International student conference 'Student i tehnicheskiy progress'.
Novosibirsk: NSU, 2000. P. 38.
 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.7376.
 Preprints (also see the list in arXiv):
 Czerwinska U., Calzone L., Barillot E., Zinovyev A. DeDaL: Cytoscape 3.0 app for producing and morphing datadriven and structuredriven network layouts. 2015. http://arxiv.org/abs/1501.06101
 Gorban A., Pitenko A., Zinovyev A. ViDaExpert: userfriendly tool for nonlinear visualization and analysis of multidimensional vectorial data. http://arxiv.org/abs/1406.5550
 Zinovyev A. Dealing with complexity of biological systems: from data to models. http://arxiv.org/abs/1404.1626
 Mirkes E.M. , Zinovyev A., Gorban A.N. Geometrical complexity of data approximators. http://arxiv.org/abs/1302.2645
 Kuperstein I, Cohen DPA, Pook S, Calzone L, Barillot E, Zinovyev A. NaviCell: a webbased environment for navigation, curation and maintenance of large molecular interaction maps. http://arxiv.org/abs/1301.7618
 Radulescu O., Gorban A.N., Zinovyev A., Noel V. Reduction of dynamical biochemical reaction networks in computational biology. http://arxiv.org/abs/1205.2851
 Zinovyev A., Morozova N., Gorban A.N., HarelBelan A. Mathematical modeling of microRNAmediated mechanisms of translation repression. http://arxiv.org/abs/1202.1243
 Gorban A.N., Zinovyev A., Morozova N., HarelBellan A. Modeling coupled transcription, translation and degradation and miRNAbased regulation of this process. 2012. http://arxiv.org/abs/1204.5941
 Zinovyev A., Gorban A. Nonlinear Quality of Life Index. 2010. http://arxiv.org/abs/1008.4063
 Zinovyev A. Data visualization in political and social sciences. 2010. Entry in SAGE "International Encyclopedia of Political Science" (eds. Badie, B., BergSchlosser, D., Morlino, L. A.), 2011. http://arxiv.org/abs/1008.1188
 Gorban A., Zinovyev A. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. 2010. http://arxiv.org/abs/1001.1122
 Zinovyev A., Morozova N., Nonne N., Barillot E., HarelBellan A., Gorban A. Dynamical modeling of microRNA action on the protein translation process. 2010. http://arxiv.org/abs/0911.1797
 Gorban A., Zinovyev A. Principal Graphs and Manifolds. 2010. http://arxiv.org/abs/0809.0490
 Fink T., Zinovyev A., Ahnert S. Evidence for a parallel regulatory system in eukaryotes based on noncoding RNA. 2006. http://arxiv.org/abs/qbio.GN/0611047
 Gorban A., Sumner N., Zinovyev A. Topological grammars for data approximation // http://xxx.lanl.gov/abs/cs/0603090
 Gorban A., Popova T., Zinovyev A. Four basic symmetry types in the universal 7cluster structure of 143 complete bacterial genomic sequences. 2004. IHES Preprint. M/04/49.
 Zinovyev A. Method And Software For Fast Construction Of Principal Manifolds Approximations.  IHES Preprint, France, 2003.  M/03/61
 Gorban A., Zinovyev A., Popova T. Seven Clusters In Genomic Triplet Distributions.  IHES Preprint, France, 2003.  M/03/62
 Gorban A., Karlin I., Zinovyev A. Constructive Methods of Invariant Manifolds for Kinetic Problems.  IHES Preprint, France. 2003.  M/03/50
 Gorban A., Karlin I., Zinovyev A. Invariant grids for reaction kinetics.  IHES Preprint, France. 2003.  P/03/42
 Carbone A., Zinovyev A., Kepes F. Codon Adaptation Index as a measure of dominating codon bias.  IHES Preprint, France. 2002.  M/02/93
 Zinovyev A. Visualizing the spatial structure of triplet distributions in genetic texts.  IHES Preprint, France. 2002.  M/02/28.
 Von Hahn P., Khlebopros R., Zinovyev A., Timber yield and spatial trunks arrangement in artificial forests: experiments and modeling.  IHES Preprint, France. 2002.  M/02/67.
 Gorban A.N., Zinovyev A.Yu., Popova T.G. Statistical approaches to the automated gene identification without teacher // Institut des Hautes Etudes Scientiques.  IHES Preprint, France. 2001.  M/01/34.
 Gorban A.N., Zinovyev A.Yu. Visualization of data by method of elastic maps and its applications in genomics, economics and sociology // Institut des Hautes Etudes Scientiques.  IHES Preprint, France. 2001.  M/01/36.
 Gorban A.N., Zinovyev A.Yu, Popova T.G. Selforganizing Approach for Automated Gene Identification in Whole Genomes // http://xxx.lanl.gov/abs/physics/0108016.
 Wikipages:
 Nonlinear dimensionality reduction
 Elastic map
 Elastic map (in Russian)
 Principal component analysis (in Russian)
 Alexander Gorban (also, in Russian)

