CBO 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] https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz016/5290485 MMN Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky992. https://academic.oup.com/nar/article/47/D1/D614/5146204 MMN 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. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty766/5087713 MMN 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. https://www.frontiersin.org/articles/10.3389/fphys.2018.00787/full MMN 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. https://www.frontiersin.org/articles/10.3389/fphys.2018.00680/full MMN 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. https://www.sciencedirect.com/science/article/pii/S2211339817300941 KNF 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 https://www.nature.com/articles/s41540-018-0059-y KNF 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. https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bby031/4992169?redirectedFrom=fulltext KNF 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. https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby024/4982567 KNF 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. https://academic.oup.com/database/article/doi/10.1093/database/bay036/4964960 MLN 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. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190812 CBO 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. https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30011-4 MLN 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. https://www.nature.com/articles/s41540-017-0038-8 MMN 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. https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbx163/4716963 REV 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. https://www.nature.com/articles/nmeth.4457 MLN 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. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4112-9 MLN 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. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005573 MMN 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. https://academic.oup.com/database/article/doi/10.1093/database/bax026/3098441 MMN 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. https://academic.oup.com/bioinformatics/article/33/14/2226/3059141 REV 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. https://www.bioscience.org/2017/v22/af/4571/fulltext.htm MLN Gorban A, Mirkes E, Zinovyev A. Robust principal graphs for data approximation. Archives of Data Science 2(1):1:16, 2017. https://arxiv.org/abs/1603.06828 CBO 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. http://clincancerres.aacrjournals.org/content/23/4/1001.long MLN 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. https://www.sciencedirect.com/science/article/pii/S0893608016301113 CBO 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. https://journal.r-project.org/archive/2016/RJ-2016-047/index.html MLN 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. https://www.frontiersin.org/articles/10.3389/fgene.2016.00018/full REV 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. 2016. Oncotarget 7(8):8613-8624. http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=6937&pubmed-linkout=1 MMN 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. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004571 MMN Kuperstein I, Robine S, Zinovyev A. Network biology elucidates metastatic colon cancer mechanisms. 2015. Cell Cycle 14(14):2189-90. https://www.tandfonline.com/doi/full/10.1080/15384101.2015.1060816?scroll=top&needAccess=true REV 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. https://www.sciencedirect.com/science/article/pii/S0006291X15301443?via%3Dihub KNF 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. https://www.nature.com/articles/oncsis201519 MMN 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. http://cancerres.aacrjournals.org/content/75/19/4042 REV Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling. 2015. Mathematical Modeling of Natural Phenomena 10(3), 186-205. https://www.mmnp-journal.org/articles/mmnp/abs/2015/03/mmnp201510p186/mmnp201510p186.html MLN 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. https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-015-0189-4 CBO 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. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S6-S4 MMN Calzone L, Barillot E, Zinovyev A. Predicting genetic interactions from Boolean models of biological networks. 2015. Integr Biol (Camb) 7(8), 921929. https://academic.oup.com/ib/article/7/8/921/5199157 MLN Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A. NaviCell Web Service for network-based data visualization. 2015. Nucleic Acids Res. 43(W1):W560W565 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv450 REV 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 https://academic.oup.com/mutage/article/30/2/191/1358326 MLN 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 https://www.cell.com/cell-reports/fulltext/S2211-1247(14)00904-8 BIO 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 https://www.nature.com/articles/ncomms6005 REV 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 https://www.researchgate.net/publication/263430999_Biological_network_modelling_and_precision_medicine_in_oncology MMN 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 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-100 MMN 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 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-100 MMN Vera-Licona P, Bonnet E, Barillot E, Zinovyev A. OCSANA: Optimal Combinations of Interventions from Network Analysis. 2013. Bioinformatics 15:29: 1571-1573 https://academic.oup.com/bioinformatics/article/29/12/1571/293094 MLN Mirkes EM, Zinovyev A, Gorban AN. Geometrical Complexity of Data Approximators. 2013. Advances in Computational Intelligence 7902:500-508. https://link.springer.com/chapter/10.1007/978-3-642-38679-4_50 MMN 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 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003016 MMN 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 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-18 MMN 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 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-13 MLN 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 https://www.sciencedirect.com/science/article/pii/S0006291X12023741 MLN Zinovyev A, Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:1471-1482 https://www.sciencedirect.com/science/article/pii/S0898122112007055 MMN 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) https://www.researchgate.net/publication/286505437_The_application_of_model_reduction_methods_to_the_construction_of_the_composite_model_of_apoptotic_pathways_In_Russian MLN 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449386/ MLN 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 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041770 REV Radulescu O, Gorban AN, Zinovyev A and Noel V. Reduction of dynamical biochemical reactions networks in computational biology. 2012. Frontiers in Genetics 3: 00131 https://www.frontiersin.org/articles/10.3389/fgene.2012.00131/full MMN 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 https://rnajournal.cshlp.org/content/18/9/1635.long CBO Martignetti L, Zinovyev A, Barillot E. Identification of shortened 3prime untranslated regions from expression arrays. 2012. Journal of Bioinformatics and Computational Biology 10:1241001 https://www.worldscientific.com/doi/abs/10.1142/S0219720012410016 CBO 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 https://www.mmnp-journal.org/articles/mmnp/abs/2012/01/mmnp201271p337/mmnp201271p337.html MLN 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 https://academic.oup.com/bioinformatics/article/27/2/268/285534 MLN 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 https://www.worldscientific.com/doi/abs/10.1142/S0129065710002383 MMN 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 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000702 MMN 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 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-13 MMN Gorban AN, Radulescu O, Zinovyev AY. Asymptotology of chemical reaction networks. 2010. Chemical Engineering Science 65, 2310-2324 https://www.sciencedirect.com/science/article/pii/S0009250909005995 REV Barillot E, Calzone L, Zinovyev A. Biologie des Systemes du Cancer. 2009. Med Sci (Paris). 2009 Jun-Jul;25(6-7):601-7 https://www.medecinesciences.org/en/articles/medsci/full_html/2009/08/medsci2009256-7p601/medsci2009256-7p601.html CBO 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 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004932 REV Aebersold R et al. Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research. 2009. Molecular Oncology 3(1): 9-17 https://febs.onlinelibrary.wiley.com/doi/full/10.1016/j.molonc.2008.11.003 MMN Radulescu O, Gorban A, Zinovyev A, Lilienbaum A. Robust simplifications of multiscale biochemical networks. 2008. BMC Systems Biology 2:86 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-2-86 MMN Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for using and analyzing biological networks. 2008. Bioinformatics 24(6):876-877 https://academic.oup.com/bioinformatics/article/24/6/876/192449 CBO Ahnert SE, Fink TMA and Zinovyev A. How much non-coding DNA do eukaryotes require?. 2008. Journal of Theoretical Biology 252(4):587-592 https://www.sciencedirect.com/science/article/pii/S002251930800057X?via%3Dihub KNF 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290939/ MLN Rapaport F, Zinovyev A, Dutreix M, Barillot E, Vert J.-P. Classification of microarray data using gene networks. 2007. BMC Bioinformatics 8:35 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-35 CBO Gorban A, Zinovyev A. The Mystery of Two Straight Lines in Bacterial Genome Statistics. 2007. Bulletin of Mathematical Biology 69: 2429-2442 https://link.springer.com/article/10.1007%2Fs11538-007-9229-6 MLN Gorban A, Sumner N, Zinovyev A. Topological grammars for data approximation. 2007. Applied Mathematics Letters 20(4), 382-386 https://www.sciencedirect.com/science/article/pii/S0893965906001856 MMN Gorban A, Karlin I, Zinovyev A. Invariant grids: method of complexity reduction in reaction networks. 2005. ComPlexUs 2004-05;2:110-127 https://pdfs.semanticscholar.org/1e20/144f07c071ac4672b8438fe6dbddab9dfad0.pdf MLN Gorban A, Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. 2005. Computing 75, 359 -379 https://link.springer.com/article/10.1007/s00607-005-0122-6 CBO 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 https://www.sciencedirect.com/science/article/pii/S0378437105000828 CBO 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 http://www.bioinfo.de/isb/2005/05/0025/main.html CBO 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 https://academic.oup.com/mbe/article/22/3/547/1075922 MMN Gorban A, Karlin I, Zinovyev A. Constructive Methods of Invariant Manifolds for Kinetic Problems. 2004. Physics Reports 396, 197-403 https://www.sciencedirect.com/science/article/abs/pii/S0370157304001334 MMN Gorban A, Karlin I, Zinovyev A. Invariant grids for reaction kinetics. 2004. Physica A, V.333, pp.106-154 https://www.sciencedirect.com/science/article/pii/S0378437103009701 CBO Gorban A, Zinovyev A, Popova T. Seven clusters in genomic triplet distributions. 2003. In Silico Biology. V.3, 0039 https://content.iospress.com/articles/in-silico-biology/isb00110 CBO Carbone A, Zinovyev A, Kepes F. Codon Adaptation Index as a measure of dominating codon bias. 2003. Bioinformatics. 19(13), 2005-2015 https://www.ncbi.nlm.nih.gov/pubmed/14594704 CBO Zinovyev A, Gorban A.N, Popova T. Self-Organizing Approach for Automated Gene Identification. 2003. Open Systems and Information Dynamics 10(4), 321-333 https://link.springer.com/article/10.1023/B:OPSY.0000009554.93005.f6 MLN Gorban AN, Zinovyev A.Yu. Pitenko A.A. Visualization of data: Method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.19-30. MLN Zinovyev AYu, Pitenko AA, Popova TG. Practical applications of the method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.31-39. MLN Gorban AN, 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. MLN 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 http://cogprints.org/3088/ MLN 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.