Updated on 19 June 2020
||Current research interests
Born September 23, 1974
in Krasnoyarsk, USSR (Russia)
Institut Curie, Service Bioinformatique
26 rue d'Ulm, F75248, Paris, France.
E-mail: andrei . zinovyev at curie . fr
Researcher Id: B-4715-2010
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
PRAIRIE Intedisciplinary chair
- 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
- 1998-2001 - Post graduate, Institute of Computational Modeling, Krasnoyarsk, Russia
- 1991-1997 - Master's diploma with distinction (highest grade in all disciplines), Krasnoyarsk State University (Physical Department), chair of theoretical physics, cosmology
- September 2019-present- Interdisciplinary chair at Paris Artificial Intelligence Research Institute
- January 2005-present - scientific coordinator of "Computational Systems Biology of Cancer" team, permanent researcher at Institut Curie in Paris, INSERM U900
- December 2001-December 2004 - postdoc, involved in the project "Functional Genomics" (Institut des Hautes Etudes Scientifiques, France)
- February-October 2000 - Project leader of ecological data analysis, sponsored by Krasnoyarsk Regional Scientific Fund
- 1998-2001 - PhD student (computer science). Institute of Computational Modeling, Russian Academy of Sciences, Siberian Branch
- 1993-1999 - Developer/Researcher. Siberian Institute of Gydrotechny and Melioration, Russia
- 1993-1997 - Graduate student. Research work in the theory of gravitation and cosmology
- May 2002 - May 2003 - Project leader, creation of a parallelized bioinformatics platform Plug&Blast for a cluster of processors
- May-December 2001 - Principal software developer, creation of an information system for automated access
to world-wide patent databases (SIT project), 'SibTeCom' Company, Krasnoyarsk, Russia
- 1997-2001 - principal software developer. Creation of a book-keeping system for a commercial computer company (KomPAK, Krasnoyarsk, Russia)
- January-June 2000 - computer consultant, 'Electrosvyaz' company, Krasnoyarsk, Russia
- October-December 2016,2017 – organization of the “Mathematical modeling of biological systems” pre-doctoral 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.
- 2012-now - internal teaching program of Institut Curie, modules related to analysis of high-throughput data in the context of biological networks.
- May 2011 - 40-hours course on computational systems biology, as a part of PhD program in Bioinformatics at Kazakh National University after Al-Farabi, Almaty, Kazakhstan.
- 2009-now - short course "Modeling and integrating high-throughput 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
- 2014: "Thought Leader Award" by Agilent, as a part of the team
- 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 2006-November 2009), 400KEuros
- ISC MATBRAC: Mathematical theory of biological robustness with experimental applications in cancer systems biology - (November 2006-November 2009), 6KEuros
- Plug&Blast: Creation of a commercial parallel platform for bioinformatics computations - (May 2002-May 2003)
- As coordinator of Institut Curie or the systems biology team participation:
- iPaediatricCure EU Horizon-2020: large-scale Horizon-2020 project on application of cloud-based data science approach to improving treatment of paediatric cancers (January 2019-January 2023), 15Meuros
- IMMUCAN EU IMI: large-scale academy-industrial EU IMI project on molecular profiling tumor microenvironment (April 2019-April 2023), 36Meuros
- ITMO Cancer: non-coding RNA in cancerology: Using an integrative strategy to decipher miRNAs function in Pediatric Brain Tumor, (November 2018-November 2021), 613kEuros
- MOSAIC ITMO Cancer SysBio program: MOdeling Single cell vAriability In Cancer progression and treatment (2014-2017), 500kEuros
- APLIGOOGLE CNRS MASTODON project: Appliation of Google Matrix approach for analysis of large networks (2016), 40kEuros
- PANMETHYLOME Canceropole Emergence: Large-scale 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) (2015-2016), 50kEuros
- PIC3i Tumor microenvironment (Institut Curie internal project): Global view of CAF heterogeneity and functions in Tumorigenesis (2015-2018)
- 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 (2013-2016), 400kEuros
- EU FP7 APO-SYS: Apoptosis Systems Biology Applied to Cancer and AIDS - (December 2008-December 2011), 11MEuros
- EU FP7 ASSET: Analysing and Stryking the Sensitivities of Embryonal Tumours - (November 2010-November 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 (2013-2016), 100KEuros
- INVADE: Mathematical modeling of early tumour invasion (December 2012-December 2015), 1000KEuros
- CoMET: Modeling cell communication networks in breast cancer (2014-2017), 1000KEuros
- InCA SybEwing: Systems Biology of Ewing's sarcoma - (December 2009-December 2012), 500KEuros
- As participant:
- PerMedCOE EU Horizon-2020: Center of Excellence in Personalized Medicine (2020-2023), 5 Meuros
- PanNet EU TRANSCAN-2: Predictive models of therapy response in pancreatic neuroendocrine tumors (2019-2022), 1.1Meuros
- PRECISE EU Horizon-2020: Personalized Enginge for Cancer Integrative Study and Evaluation (2015-2018), 3Meuros
- COLOSYS EU EracoSysMed: A systems approach to preventing drug resistance in colon cancer (2015-2018), 1.8MEuros
- PSL Institute for Data Science: Big Data PSL Research University project: creating a cross-disciplinary and cross-institutional virtual hub of research and education, the PSL Institute for Data Science (PIDS) - (2016-2018), 100kEuros
- M5 ITMO Cancer SysBio program: Mathematical Modeling of Molecular Mechanisms involved in Medulloblastoma progression - (2015-2018), 400KEuros
- ANR CALAMAR: Compositional modelling and Analysis of LArge MoleculAr Regulatory networks - application to the control of human cell proliferation. - (October 2008-October 2011), 400KEuros
- EU FP6 ESBIC-D: European Systems Biology Initiative combating complex diseases. - (January 2005-January 2008)
- Member of scientific organizing comitee of 2nd International Curie course on Computational Systems Biology of Cancer (Promises of Artificial Intelligence), Paris, September 2019.
- 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 ECCB-2018, Athens, September 2018.
- Member of scientific organizing comitee of BioNetVisA workshop at BC2-2017, Basel, Septmeter 2017.
- Member of scientific organizing comitee of BioNetVisA workshop at ECCB-2016, Barcelona, July 2016.
- Member of scientific organizing comitee of BioNetVisA workshop at ICSB-2015, Singapore, November 2015.
- Member of organizing comitee of Model Reduction across disciplines-2014
- Member of programming commitee of SASB-2014
- Member of scientific organizing comitee of BioNetVisA workshop at ECCB-2014, Strasbourg, September 2014.
- Member of programming commitee of ECCB-2014, Strasbourg, September 2014.
- Member of programming commitee of ECCB-2012, Basel, September 2012.
- Member of programming commitee of ECCB-2010, Ghent, October 2010.
- Member of organizing commitee of "Principal manifolds-2006", Leicester, UK, 2006.
- Member of organizing commitee of "Geometry of Genome", Leicester, UK, 2005.
See my Publons profile.
- Physical Biology
- Nature Communications
- Genome Research
- BMC Genomics
- PLoS Computational biology
- 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
- Discrete Applied Mathematics
- Computational Statistics and Data Analysis
PhD theses (co-)supervision:
- Jonathan Bac, "Machine learning methods and tools to tackle the complexity of high-dimensional single cell datasets", 2019-2022
- Nicolas Sompairac, "Statistical modeling of tumor/microenvironment ecosystem to advance diagnostic and treatment", 2018-2021
- Alexey Guerassimov, "Kinetic model of regulation of translation in eukaryotic cells", 2016-2018 (not finished)
- Urszula Czerwinska, "Deconvolution of cell and environment specific signals and their interactions from complex mixtures in biological samples", 2015-2018
- Marine Le Morvan, "Search for cancer driver mutations using mutation, expression data and biological networks", 2014-2017
- Geraldine Cellier, "Multiscale modeling of early invasion of tumour cell into surrounding tissues", 2012-2015
- Ulykbek Kairov, "Analysis of microarray data for searching genetic markers in cancer" (Kazhakstan), 2009-2012
- Elena Kutumova, "Application of model reduction methods for constructing a composite model of apoptosis signaling" (Russia), 2009-2012
- Anne Biton, "Geometrical analysis of pathway deregulations in bladder cancer", 2008-2011.
- 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:
- Francisco Avila Cobos, "Addressing challenges in transcriptome annotationand cell-type heterogeneity through integration ofomics datasets and computational deconvolution", Ghent, June 2020.
- Natalia Rubanova, "MasterPATH: network analysis of functional genomics screening data", Paris, February 2018
- Christophe Becavin, "Dimensionality reduction and pathway network analysis of transcriptome data: Application to T-cell 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 ECCB-2018, 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, Bures-sur-Yvette
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. IHP-Curie 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, 24-26 January 2018.
Nontrivial geometry of omics data used for obtaining insights into biology. Curie-IHES-IHP 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 pan-cancer 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 ', Curie-SBI workshop, 7 December 2016, Tokyo, Japan
Detecting non-trivial geometrical data structures in cancer omics data', 7 November 2016, Invited talk at the Mathematical Biology seminar of Institut des Hautes Études Scientifiques, Bures-sur-Yvette.
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. Mini-simposium 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 bio-informaticien. 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 pan-cancer deconvolution of tumoral transcriptomes, 17 July 2015, Moscow Conference on Computational Molecular Biology (MCCMB-2015), Russia
Towards mathematical modelling of the signalling network downstream of EWS/FLI-1, ASSET-ENCCA Ewing meeting, Paris, 15-16 June 2015
Atlas of Cancer Signaling Network and NaviCell: Google Maps of cancer biology", Invited talk, The Genome Analysis Center, Norwich, 21 May 201
Pan-cancer 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, 19-22 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 cancer-related 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 Biology-2013, Copenhagen, 2 September 2013.
Mechanisms of genetic interactions and cancer treatment, Moscow Conference on Computational Molecular Biology-2013, 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 Meta-Analysis 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 disease-2011, Manchester, 14-18 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.
High-throughput sequencing for better understanding cancer: ChIP-Seq technology for studying Ewing's sarcoma. 19 May 2011. BioTech center seminar, Astana, Kazakhstan.
BioUML: a plug-in 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 Singalomics-2011, Luxembourg, 26-28 January 2011.
Non-linear principal manifolds for bioinformatics applications. ERCIM conference, London, UK, 9-12 December 2010.
Mathematical modeling of cell life and death in cancer. Invited talk at International Conference on Systems Biology (ICSB-2010), 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.
Chip-Seq technology for studying Ewing's sarcoma. "Bioinformatics after Next Generation Sequencing" French-Russian 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 High-Throughput Data: From Principal Trees To Spectral Filtering On Graphs. Moscow Conference on Computational Molecular Biology-2009, 20-25 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 high-throughput data for systems biology. Invited talk at Systems Biology for Medical Applications Summer School 29 Sept-03 Oct 2008, Tenerife, Spain.
BiNoM: a tool for manipulating and analysis of biological networks. Invited talk at International Conference on Systems Biology Workshop 'Web-services 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 non-coding 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. EAST-SCOPE conference, 3-4 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 BGRS-2006 (July 16-22, 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.
- 20-27 March 2017. Visiting Cancer Science Institute, National University of Singapore.
- 05-15 December 2016. 'Exploration Japan' visit sponsored by the French embassy in Japan.
- 10-16 October 2013. French delegation to Seatle, USA, invited by the governor of Washington state.
- 21-24 September 2010. Bioinformatics Center of Jena University, Germany.
- 23-31 August 2008. University of Leicester, UK.
- 20-31 March 2007. The Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), New-Jersey, 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
Publications (see the complete list of my citations in Google Scholar):
- 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.
- 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
- 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
- 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.
- 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.
- 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.
- 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.
- 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.; Harel-Bellan, A.; Morozova, N.; Pritchard, L.), Series: Springer Proceedings in Mathematics, Vol. 15. 2012. Springer. pp. 191-206
- 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., Berg-Schlosser, 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: 97-128
- 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.
- Articles in peer-reviewed journals (*equal contribution, +corresponding author, ^co-last authorship):
(see also the list of my articles in Pubmed database)
- 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
- 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
- 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.
- 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
- 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.
- 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.
- 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
- Bac J, Zinovyev A. Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets. Front Neurorobot 2020;13:110.
- 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.
- 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
- 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
- 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.
- 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.
- 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
- 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
- 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.
- 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.
- 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
- 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
- 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.
- 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
- 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.
- 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, 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.
- 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.
- 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
- 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. Community-driven 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., 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.
- 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 post-mortem analyses. Nat Methods 14(10):937-938. 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 Cancer-relevant 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 multi-level omics data. Database (Oxford) 1-11. 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 22:1774-1791. 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., 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.
- 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.
- 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.
- 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):2189-90.
- 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.
- 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 Co-Occurring Genetic Alterations in Bladder Tumorigenesis. 2015. Cancer Res. 75(19):4042-52.
- Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling. Mathematical Modeling of Natural Phenomena 10(3), 186-205.
- 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.
- 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 network-based 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):191-204.
- 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.
- 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.
- 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.
- 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.
- 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.
- Vera-Licona P, Bonnet E, Barillot E, Zinovyev A. OCSANA: Optimal Combinations of Interventions from Network Analysis. 2013. Bioinformatics 15:29: 1571-1573.
- Mirkes EM., Zinovyev A., Gorban AN. Geometrical Complexity of Data Approximators. 2013. Advances in Computational Intelligence 7902:500-508.
- 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.
- 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 NF-kappaB 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), 1182-1187.
- Zinovyev A. and Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:1471-1482.
- 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).
- 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.
- 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
- 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., Harel-Bellan 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 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
- 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.
- 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.
- 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.
- 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.
- Gorban AN, Radulescu O, Zinovyev AY. Asymptotology of chemical reaction networks. 2010. Chemical Engineering Science 65, 2310-2324.
- Barillot E., Calzone L., Zinovyev A. Biologie des Systemes du Cancer. 2009. Med Sci (Paris). 2009 Jun-Jul;25(6-7):601-7.
- 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.
- Aebersold, R. et al., Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research. 2009. Molecular Oncology 3(1): 9-17.
- 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):876-877
- 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.
- 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: 2429-2442.
- Gorban A., Sumner N., Zinovyev A. Topological grammars for data approximation. 2007. Applied Mathematics Letters 20(4), 382-386.
- Gorban A., Karlin I., Zinovyev A. Invariant grids: method of complexity reduction in reaction networks. 2005. ComPlexUs 2004-05;2:110-127.
- 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 7-cluster structure of 143 complete bacterial genomic sequences. 2005. Physica A 353, 365-387
- 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
- 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.
- Gorban A., Karlin I., Zinovyev A. Constructive Methods of Invariant Manifolds for Kinetic Problems. 2004. Physics Reports 396, pp.197-403.
- Gorban A., Karlin I., Zinovyev A. Invariant grids for reaction kinetics. 2004. Physica A, V.333, pp.106-154.
- 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.2005-2015.
- 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.
- Gorban A.N., Zinovyev A.Yu. Pitenko A.A.Visualization of data. Method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.19-30.
- 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.
- 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.
- 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.
- 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.
- Peer-reviewed proceedings of conferences:
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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
- 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 20-24, 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 "NeuroInformatics-2001". Moscow, 2001. Part 1. P. 47-54.
- 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.
- 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
'Neuroinformatics and its applications'. Krasnoyarsk: KGTU, 2001. P.76-79.
- 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.
- 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.
- 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.
- 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.73-76.
- Preprints (also see the list in arXiv):
- Czerwinska U., Calzone L., Barillot E., Zinovyev A. DeDaL: Cytoscape 3.0 app for producing and morphing data-driven and structure-driven network layouts. 2015. http://arxiv.org/abs/1501.06101
- Gorban A., Pitenko A., Zinovyev A. ViDaExpert: user-friendly 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 web-based 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., Harel-Belan A. Mathematical modeling of microRNA-mediated mechanisms of translation repression. http://arxiv.org/abs/1202.1243
- Gorban A.N., Zinovyev A., Morozova N., Harel-Bellan A. Modeling coupled transcription, translation and degradation and miRNA-based 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., Berg-Schlosser, 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., Harel-Bellan 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 non-coding RNA. 2006. http://arxiv.org/abs/q-bio.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 7-cluster 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. Self-organizing Approach for Automated Gene Identification in Whole Genomes // http://xxx.lanl.gov/abs/physics/0108016.
- Nonlinear dimensionality reduction
- Elastic map
- Elastic map (in Russian)
- Principal component analysis (in Russian)
- Alexander Gorban (also, in Russian)