My publications (sorted by topics)

You can also find my articles on my Google Scholar profile.

*, ^ - stands for joint first or senior authorship.

Topics

Machine Learning - Knowledge formalization
Modeling biological networks - Computational biology
Reviews

Machine learning methods and applications

Cantini L, Kairov U, de Reynies A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes. 2019. Bioinformatics, btz225

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.

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.

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.

Gorban A, Mirkes E, Zinovyev A. Robust principal graphs for data approximation. Archives of Data Science 2(1):1:16, 2017.

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.

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.

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

Zinovyev A. and Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:1471-1482.

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

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. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. 2010. Int J Neural Syst 20(3):219-32

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, Sumner N, Zinovyev A. Topological grammars for data approximation. 2007. Applied Mathematics Letters 20(4), 382-386

Gorban A, Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. 2005. Computing 75, 359 -379

Zinovyev A, Gorban A.N, Popova T. Self-Organizing Approach for Automated Gene Identification. 2003. Open Systems and Information Dynamics 10(4), 321-333

Gorban AN, Zinovyev AYu. Method of Elastic Maps and its Applications in Data Visualization and Data Modeling. 2001. International Journal of Computing Anticipatory Systems, CHAOS 12, 353-369

Peer-reviewed conference papers

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.

Gorban AN, Mirkes E, 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.

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 AN, Pitenko A, Zinovyev A. ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data. Proceedings of IEEE International Conference on Data Science and Advanced Analytics (DSAA), Paris, 19-21 October 2015

Gorban AN, Mirkes EM, Zinovyev A. Robust principal graphs for data approximation. Proceedings of European Conference on Data Analysis-2015, 2-4/9/2015, Colchester, UK

Gorban AN, Zinovyev A, Wunsch D. Application of the method of elastic maps in analysis of genetic texts. Proceedings of the International Joint Conference on Neural Networks, Portland, 20-24 July 2003

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

Peer-reviewed chapters

Mirkes EM, Zinovyev A, Gorban AN. Geometrical Complexity of Data Approximators. 2013. Advances in Computational Intelligence 7902:500-508.

Gorban AN, Zinovyev A. Principal Graphs and Manifolds. In Handbook of Research on Machine Learning Applications and Trends: Algorithms, Methods and Techniques, Information Science Reference, 2009. 28-59.

Gorban AN, Sumner NR, Zinovyev A. PCA Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes. In Principal Manifolds for Data Visualization and Dimension Reduction, Lecture Notes in Computational Science and Engineering 58, Springer, Berlin - Heidelberg, 2008, 219-237

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

Gorban AN, Zinovyev A. PCA and K-Means decipher genome. In Principal Manifolds for Data Visualization and Dimension Reduction, Lecture Notes in Computational Science and Engineering 58, Springer, Berlin - Heidelberg, 2008, 307-323

Unpublished preprints

Nazarov PL, Wienecke-Baldacchino AK, Zinovyev A, Czerwinska U, Muller A, Nashan D, Dittmar G, Azuaje F, Kreis S. Independent component analysis provides clinically relevant insights into the biology of melanoma patients. 2018. Biorxiv preprint 10.1101/395145v1

Albergante A, Mirkes EM, Chen H, Martin A, Faure L, Barillot E, Pinello L, Gorban AN, Zinovyev A. Robust And Scalable Learning Of Complex Dataset Topologies Via Elpigraph. 2018. Arxiv preprint 1804.07580.

Colaprico A, Olsen C, Cava C, Terkelsen T, Silva TC, Olsen A, Cantini L, Bertoli G, Zinovyev A, Barillot E, Castiglioni I, Noushmehr H, Papaleo E, Bontempi G. Moonlight: a tool for biological interpretation and driver genes discovery. 2018. Biorxiv preprint 10.1101/265322v1

Zinovyev A, Gorban AN. Nonlinear Quality of Life Index. 2010. Arxiv preprint 1008.4063

Zinovyev A. Data visualization in political and social sciences. 2010. Arxiv preprint 1008.1188

Gorban AN, Zinovyev A. Elastic principal manifolds and their practical applications. 2004. Arxiv preprint cond-mat/0405648.

Knowledge formalization in biology

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

Monraz Gomez LC, Kondratova M, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. Application of Atlas of Cancer Signalling Network in preclinical studies. Brief Bioinformatics. 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 Bioinformatics. 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.

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.

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

Mathematical modeling of biological networks

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.

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

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. 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, 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. 2018. Current Opinion in Chemical Engineering 21, 22-31.

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.

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. 2017. Bioinformatics 33(14):2226-2228.

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.

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.

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

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

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)

Morozova N*, Zinovyev A*, Nonne N, Pritchard L-L, Gorban AN, Harel-Bellan A. Kinetic signatures of microRNA modes of action. 2012. RNA 18(9): 032284

Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A. Mathematical modelling of cell-fate decision in response to death receptor engagement. 2010. 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

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

Gorban A, Karlin I, Zinovyev A. Invariant grids: method of complexity reduction in reaction networks. 2005. ComPlexUs 2004-05;2:110-127

Gorban A, Karlin I, Zinovyev A. Constructive Methods of Invariant Manifolds for Kinetic Problems. 2004. Physics Reports 396, 197-403

Gorban A, Karlin I, Zinovyev A. Invariant grids for reaction kinetics. 2004. Physica A, V.333, pp.106-154

Peer-reviewed conference papers

Radulescu O, Zinovyev A, Lilienbaum A. Model reduction and model comparison for NFkB signalling. Proceedings of Foundations of Systems Biology in Engineering, September 2007, Stuttgart, Germany.

Radulescu O, Gorban A, Vakulenko S, Zinovyev A. Hierarchies and modules in complex biological systems. Proceedings of European Conference on Complex Systems, September 2006, Oxford, UK

Unpublished preprints

Gorban AN, Harel-Bellan A, Morozova N, Zinovyev A. Basic and simple mathematical model of coupled transcription, translation and degradation. 2012. Arxiv preprint 1204.5941

Computational biology methods and applications

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]

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.

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.

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.

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, Zinovyev A, Barillot E. Identification of shortened 3prime untranslated regions from expression arrays. 2012. Journal of Bioinformatics and Computational Biology 10:1241001

Pinna G, Zinovyev A, Araujo N, Morozova N, 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

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

Ahnert SE, Fink TMA and Zinovyev A. How much non-coding DNA do eukaryotes require?. 2008. Journal of Theoretical Biology 252(4):587-592

Gorban A, Zinovyev A. The Mystery of Two Straight Lines in Bacterial Genome Statistics. 2007. Bulletin of Mathematical Biology 69: 2429-2442

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, 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(13), 2005-2015

Reviews

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.

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.

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.

Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling. 2015. Mathematical Modeling of Natural Phenomena 10(3), 186-205.

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

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

Radulescu O, Gorban AN, Zinovyev A and Noel V. Reduction of dynamical biochemical reactions networks in computational biology. 2012. Frontiers in Genetics 3: 00131

Barillot E, Calzone L, Zinovyev A. Biologie des Systemes du Cancer. 2009. Med Sci (Paris). 2009 Jun-Jul;25(6-7):601-7

Aebersold R et al. Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research. 2009. Molecular Oncology 3(1): 9-17