My publications (sorted by date)

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

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

2021

Petrizzelli M, Merlevede J, Zinovyev A. Systems Biology Analysis for Ewing Sarcoma. Methods Mol Biol. 2021;2226:303-333.

2020

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.

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 (Basel). 2020. 22(3):296

Chervov A, Bac J, Zinovyev A. Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets. Entropy (Basel). 2020. 22(11):1274

Golovenkin SE, Bac J, Chervov A, Mirkes EM, Orlova YV, Barillot E, Gorban AN, Zinovyev A. Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data. Gigascience. 2020. 9(11):giaa128

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

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

Balaur I, Roy R, Mazein A, Karaca G, Dogrusoz U, Barillot E, Zinovyev A. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. 2020. Bioinformatics, 36(19):4975

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

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

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. 2020. PLoS Computational Biology, 16(2):e1007652

Peer-reviewed conference proceedings

Chevalier S, Noel V, Calzone L, Zinovyev A, Pauleve L. Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision 18th International Conference on Computational Methods in Systems Biology (CMSB), 2020, Online, Germany. pp.193-209

Bac J, Zinovyev A. Local intrinsic dimensionality estimators based on concentration of measure. Proceedings of International Joint Conference on Neural Networks, Glasgow, UK, 19-24 July 2020.

Peer-reviewed chapters

Monraz LCG, Kondratova M, Sompairac N, Lonjou C, Ravel JM, Barillot E, Zinovyev A, Kuperstein I. (2020). Atlas of Cancer Signaling Network: A resource of multi-scale biological maps to study disease mechanisms. In Systems Medicine: Integrative Qualitative and Computational Approaches. Elsevier

2019

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.

Peer-reviewed conference proceedings

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.

Unpublished preprints

2018

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.

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.

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.

Peer-reviewed conference proceedings

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.

2017

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.

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.

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.

2016

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, Calzone L, Bonnet E, Barillot E, Zinovyev A. ROMA: Representation and Quantification of Module Activity from Target Expression Data. Front Genet. 2016. 7:18.

2015

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. 2015. 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.

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

Peer-reviewed conference proceedings

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

2014

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

Unpublished preprints

2013

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

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

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

Peer-reviewed chapters

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

2012

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 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 AN, Harel-Bellan A. Kinetic signatures of microRNA modes of action. 2012. RNA 18(9): 032284

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

Unpublished preprints

2011

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

2010

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

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

Unpublished preprints

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

2009

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

Peer-reviewed chapters

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.

2008

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 SE, Fink TMA and Zinovyev A. 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

Peer-reviewed chapters

Gorban AN, Sumner NR, Zinovyev A. 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

2007

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 AN, Sumner NR, Zinovyev A. Branching principal components: elastic graphs, topological grammars and metro map. Proceedings of International Joint Conference on Neural Networks, Florida, USA, August 12-17, 2007.

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.

Earlier publications

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. 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

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

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

Gorban AN, Zinovyev AYu, Pitenko AA. Visualization of data using method of elastic maps (in Russian). Informatsionnie technologii. Mashinostrornie Publ, Moscow, 2000. N6, P.26-35.

Peer-reviewed conference proceedings

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

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

Unpublished preprints

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