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ORCIDAndrei Yu. Zinovyev
Person information
- affiliation: PSL Research University, Institut Curie, Paris, France
- affiliation: Lobachevsky University, Nizhny Novgorod, Russia
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2020 – today
- 2024
[j50]Innokentiy Kastalskiy
, Andrei Yu. Zinovyev, Evgeny M. Mirkes, Victor B. Kazantsev, Alexander N. Gorban:
Exploring the impact of social stress on the adaptive dynamics of COVID-19: Typing the behavior of naïve populations faced with epidemics. Commun. Nonlinear Sci. Numer. Simul. 132: 107906 (2024)- 2023
- [j49]Evgeny M. Mirkes, Jonathan Bac, Aziz Fouché, Sergey V. Stasenko, Andrei Yu. Zinovyev, Alexander N. Gorban:
Domain Adaptation Principal Component Analysis: Base Linear Method for Learning with Out-of-Distribution Data. Entropy 25(1): 33 (2023) - [j48]Aziz Fouché, Andrei Yu. Zinovyev:
Omics data integration in computational biology viewed through the prism of machine learning paradigms. Frontiers Bioinform. 3 (2023) - [i21]Innokentiy Kastalskiy, Andrei Yu. Zinovyev, Evgeny M. Mirkes, Victor B. Kazantsev, Alexander N. Gorban:
Exploring the impact of social stress on the adaptive dynamics of COVID-19: Typing the behavior of naïve populations faced with epidemics. CoRR abs/2311.13917 (2023) - 2022
- [j47]Elise Amblard, Jonathan Bac, Alexander Chervov, Vassili Soumelis, Andrei Yu. Zinovyev:
Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data. Bioinform. 38(4): 1045-1051 (2022) - [j46]Nicolas Captier, Jane Merlevede, Askhat Molkenov, Ainur Seisenova, Altynbek Zhubanchaliyev, Petr V. Nazarov, Emmanuel Barillot, Ulykbek Kairov, Andrei Yu. Zinovyev:
BIODICA: a computational environment for Independent Component Analysis of omics data. Bioinform. 38(10): 2963-2964 (2022) - [j45]Natalya A. Rybnikova, Boris A. Portnov, Evgeny M. Mirkes, Andrei Yu. Zinovyev, Anna Brook, Alexander N. Gorban:
Coloring Panchromatic Nighttime Satellite Images: Comparing the Performance of Several Machine Learning Methods. IEEE Trans. Geosci. Remote. Sens. 60: 1-15 (2022) - [c13]Qinghua Zhou, Alexander N. Gorban, Evgeny M. Mirkes, Jonathan Bac, Andrei Yu. Zinovyev, Ivan Yu. Tyukin:
Quasi-orthogonality and intrinsic dimensions as measures of learning and generalisation. IJCNN 2022: 1-8 - [i20]Qinghua Zhou, Alexander N. Gorban, Evgeny M. Mirkes, Jonathan Bac, Andrei Yu. Zinovyev, Ivan Yu. Tyukin:
Quasi-orthogonality and intrinsic dimensions as measures of learning and generalisation. CoRR abs/2203.16687 (2022) - [i19]Evgeny M. Mirkes, Jonathan Bac, Aziz Fouché, Sergey V. Stasenko, Andrei Yu. Zinovyev, Alexander N. Gorban:
Domain Adaptation Principal Component Analysis: base linear method for learning with out-of-distribution data. CoRR abs/2208.13290 (2022) - 2021
- [j44]Jonathan Bac, Evgeny M. Mirkes, Alexander N. Gorban, Ivan Tyukin, Andrei Yu. Zinovyev:
Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation. Entropy 23(10): 1368 (2021) - [c12]Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Yu. Zinovyev, Ovidiu Radulescu:
LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. CMSB 2021: 238-244 - [c11]Alexander Chervov, Andrei Yu. Zinovyev:
Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees. IJCNN 2021: 1-9 - [i18]Jonathan Bac, Evgeny M. Mirkes, Alexander N. Gorban, Ivan Tyukin, Andrei Yu. Zinovyev:
Scikit-dimension: a Python package for intrinsic dimension estimation. CoRR abs/2109.02596 (2021) - 2020
- [j43]Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36(8): 2620-2622 (2020) - [j42]Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36(19): 4975 (2020) - [j41]Mihály Koltai, Vincent Noel, Andrei Yu. Zinovyev, Laurence Calzone, Emmanuel Barillot:
Exact solving and sensitivity analysis of stochastic continuous time Boolean models. BMC Bioinform. 21(1): 241 (2020) - [j40]Luca Albergante, Evgeny M. Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev:
Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. Entropy 22(3): 296 (2020) - [j39]Alexander Chervov, Jonathan Bac, Andrei Yu. Zinovyev:
Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets. Entropy 22(11): 1274 (2020) - [j38]Andrei Yu. Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky:
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PLoS Comput. Biol. 16(2) (2020) - [c10]Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Yu. Zinovyev, Loïc Paulevé:
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. CMSB 2020: 193-209 - [c9]Jonathan Bac, Andrei Yu. Zinovyev:
Local intrinsic dimensionality estimators based on concentration of measure. IJCNN 2020: 1-8 - [i17]Jonathan Bac, Andrei Yu. Zinovyev:
Local intrinsic dimensionality estimators based on concentration of measure. CoRR abs/2001.11739 (2020) - [i16]Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban, Andrei Yu. Zinovyev:
Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data. CoRR abs/2007.03788 (2020)
2010 – 2019
- 2019
- [j37]Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider:
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20(2): 659-670 (2019) - [j36]L. Cristobal Monraz Gomez, Maria Kondratova, Jean-Marie Ravel, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein:
Application of Atlas of Cancer Signalling Network in preclinical studies. Briefings Bioinform. 20(2): 701-716 (2019) - [j35]Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone:
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Briefings Bioinform. 20(4): 1238-1249 (2019) - [j34]Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone:
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinform. 35(7): 1188-1196 (2019) - [j33]Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Yu. Zinovyev:
Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinform. 35(21): 4307-4313 (2019) - [j32]Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein:
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. BMC Bioinform. 20-S(4): 140:1-140:14 (2019) - [j31]Jonathan Bac, Andrei Yu. Zinovyev:
Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets. Frontiers Neurorobotics 13: 110 (2019) - [j30]Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Elisabeth Guerard, Nicolas Sompairac, German A. Preciat Gonzalez, Anna Dröfn Daníelsdóttir, Max Krecke, Diane Merten, Hulda S. Haraldsdóttir, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Dmitry A. Ravcheev, Swagatika Sahoo, Piotr Gawron, Lucia Friscioni, Beatriz Garcia Santa Cruz, Mabel Prendergast, Alberto Puente, Mariana Rodrigues, Akansha Roy, Mouss Rouquaya, Luca Wiltgen, Alise Zagare, Elisabeth John, Maren Krueger, Inna Kuperstein, Andrei Yu. Zinovyev, Reinhard Schneider, Ronan M. T. Fleming, Ines Thiele:
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 47(Database-Issue): D614-D624 (2019) - [c8]Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Yu. Zinovyev:
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. ICTAI 2019: 34-41 - [c7]Luca Albergante, Jonathan Bac, Andrei Yu. Zinovyev:
Estimating the effective dimension of large biological datasets using Fisher separability analysis. IJCNN 2019: 1-8 - [i15]Luca Albergante, Jonathan Bac, Andrei Yu. Zinovyev:
Estimating the effective dimension of large biological datasets using Fisher separability analysis. CoRR abs/1901.06328 (2019) - [i14]Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Yu. Zinovyev:
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. CoRR abs/1909.04309 (2019) - 2018
- [j29]Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein:
Signalling maps in cancer research: construction and data analysis. Database J. Biol. Databases Curation 2018: bay036 (2018) - [c6]Urszula Czerwinska, Laura Cantini, Ulykbek Kairov, Emmanuel Barillot, Andrei Yu. Zinovyev:
Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals. LVA/ICA 2018: 501-513 - [c5]Alexander N. Gorban, Evgeny M. Mirkes, Andrei Yu. Zinovyev:
Data analysis with arbitrary error measures approximated by piece-wise quadratic PQSQ functions. IJCNN 2018: 1-8 - [i13]Luca Albergante, Evgeny M. Mirkes, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev:
Robust and scalable learning of data manifolds with complex topologies via ElPiGraph. CoRR abs/1804.07580 (2018) - 2017
- [j28]Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein:
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. Database J. Biol. Databases Curation 2017: bax026 (2017) - [j27]Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone:
MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinform. 33(14): 2226-2228 (2017) - [j26]Marine Le Morvan, Andrei Yu. Zinovyev, Jean-Philippe Vert:
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PLoS Comput. Biol. 13(6) (2017) - 2016
- [j25]Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev:
Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning. Neural Networks 84: 28-38 (2016) - [j24]Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Yu. Zinovyev, Eric Bonnet:
Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. R J. 8(2): 293 (2016) - [i12]Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev:
Robust principal graphs for data approximation. CoRR abs/1603.06828 (2016) - [i11]Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev:
Piece-wise quadratic lego set for constructing arbitrary error potentials and their fast optimization. CoRR abs/1605.06276 (2016) - 2015
- [j23]Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev:
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. BMC Syst. Biol. 9: 46 (2015) - [j22]Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Yu. Zinovyev:
NaviCell Web Service for network-based data visualization. Nucleic Acids Res. 43(Webserver-Issue): W560-W565 (2015) - [j21]David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone:
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. PLoS Comput. Biol. 11(11) (2015) - [c4]Alexander N. Gorban, Andrei Yu. Zinovyev:
Fast and user-friendly non-linear principal manifold learning by method of elastic maps. DSAA 2015: 1-9 - 2014
- [i10]Alexander N. Gorban, Alexander Pitenko, Andrei Yu. Zinovyev:
ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data. CoRR abs/1406.5550 (2014) - 2013
- [j20]Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev:
OCSANA: optimal combinations of interventions from network analysis. Bioinform. 29(12): 1571-1573 (2013) - [j19]Elena Kutumova, Andrei Yu. Zinovyev, Ruslan N. Sharipov, Fedor A. Kolpakov:
Model composition through model reduction: a combined model of CD95 and NF-κ. BMC Syst. Biol. 7: 13 (2013) - [j18]Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Yu. Zinovyev:
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst. Biol. 7: 18 (2013) - [j17]Inna Kuperstein, David P. A. Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev:
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst. Biol. 7: 100 (2013) - [j16]Andrei Yu. Zinovyev, Evgeny M. Mirkes:
Data complexity measured by principal graphs. Comput. Math. Appl. 65(10): 1471-1482 (2013) - [j15]Andrei Yu. Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer:
Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps. PLoS Comput. Biol. 9(4) (2013) - [c3]Evgeny M. Mirkes, Andrei Yu. Zinovyev, Alexander N. Gorban:
Geometrical Complexity of Data Approximators. IWANN (1) 2013: 500-509 - [i9]Andrei Yu. Zinovyev, Ulykbek Kairov, Tatiana Karpenyuk, Erlan Ramanculov:
Blind source separation methods for deconvolution of complex signals in cancer biology. CoRR abs/1301.2634 (2013) - [i8]Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, Alexander N. Gorban:
Geometrical complexity of data approximators. CoRR abs/1302.2645 (2013) - 2012
- [j14]Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot:
Identification of Shortened 3′ untranslated Regions from Expression Arrays. J. Bioinform. Comput. Biol. 10(2) (2012) - [i7]Andrei Yu. Zinovyev, Evgeny M. Mirkes:
Data complexity measured by principal graphs. CoRR abs/1212.5841 (2012) - 2011
- [j13]Valentina Boeva, Andrei Yu. Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot:
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinform. 27(2): 268-269 (2011) - 2010
- [j12]Andrei Yu. Zinovyev, Nadya Morozova, Nora Nonne, Emmanuel Barillot, Annick Harel-Bellan, Alexander N. Gorban:
Dynamical modeling of microRNA action on the protein translation process. BMC Syst. Biol. 4: 13 (2010) - [j11]Alexander N. Gorban, Andrei Yu. Zinovyev:
Principal Manifolds and Graphs in Practice: from Molecular Biology to Dynamical Systems. Int. J. Neural Syst. 20(3): 219-232 (2010) - [j10]Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev:
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLoS Comput. Biol. 6(3) (2010) - [i6]Alexander N. Gorban, Andrei Yu. Zinovyev:
Principal manifolds and graphs in practice: from molecular biology to dynamical systems. CoRR abs/1001.1122 (2010) - [i5]Andrei Yu. Zinovyev:
Data visualization in political and social sciences. CoRR abs/1008.1188 (2010) - [i4]Andrei Yu. Zinovyev, Alexander N. Gorban:
Nonlinear Quality of Life Index. CoRR abs/1008.4063 (2010)
2000 – 2009
- 2009
- [c2]Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Yu. Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu:
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. AIAI Workshops 2009: 72-87 - 2008
- [j9]Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot:
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinform. 24(6): 876-877 (2008) - [j8]Ovidiu Radulescu, Alexander N. Gorban, Andrei Yu. Zinovyev, Alain Lilienbaum:
Robust simplifications of multiscale biochemical networks. BMC Syst. Biol. 2: 86 (2008) - [i3]Alexander N. Gorban, Andrei Yu. Zinovyev:
Principal Graphs and Manifolds. CoRR abs/0809.0490 (2008) - 2007
- [j7]Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev:
Topological grammars for data approximation. Appl. Math. Lett. 20(4): 382-386 (2007) - [j6]Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert:
Classification of microarray data using gene networks. BMC Bioinform. 8 (2007) - [c1]Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev:
Branching Principal Components: Elastic Graphs, Topological Grammars and Metro Maps. IJCNN 2007: 2586-2591 - 2006
- [i2]Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev:
Topological Grammars for Data Approximation. CoRR abs/cs/0603090 (2006) - 2005
- [j5]Alexander N. Gorban, Andrei Yu. Zinovyev:
Elastic Principal Graphs and Manifolds and their Practical Applications. Computing 75(4): 359-379 (2005) - [j4]Alexander N. Gorban, Tatyana G. Popova, Andrei Yu. Zinovyev:
Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. Silico Biol. 5(3): 265-282 (2005) - 2003
- [j3]Alessandra Carbone, Andrei Yu. Zinovyev, François Képès:
Codon adaptation index as a measure of dominating codon bias. Bioinform. 19(16): 2005-2015 (2003) - [j2]Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova:
Seven clusters in genomic triplet distributions. Silico Biol. 3(4): 471-482 (2003) - [j1]Andrei Yu. Zinovyev, Alexander N. Gorban, Tatyana G. Popova:
Self-Organizing Approach for Automated Gene Identification. Open Syst. Inf. Dyn. 10(4): 321-334 (2003) - [i1]Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova:
Seven clusters in genomic triplet distributions. CoRR cond-mat/0305681 (2003)
Coauthor Index
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