Andrei Yu. Zinovyev

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 47

Top Topics

Intrinsic Dimension

Factorization Methods

Computational Biology

Top Venues

Publications

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 (2024)
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 (2023)
Aziz Fouché, Andrei Yu. Zinovyev
Omics data integration in computational biology viewed through the prism of machine learning paradigms. Frontiers Bioinform. 3 (2023)
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) (2023)
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) (2022)
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 (2022)
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)
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) (2022)
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 (2022)
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 (2022)
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)
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) (2021)
Jonathan Bac, Evgeny M. Mirkes, Alexander N. Gorban, Ivan Tyukin, Andrei Yu. Zinovyev
Scikit-dimension: a Python package for intrinsic dimension estimation. CoRR (2021)
Alexander Chervov, Andrei Yu. Zinovyev
Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees. IJCNN (2021)
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) (2020)
Alexander Chervov, Jonathan Bac, Andrei Yu. Zinovyev
Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets. Entropy 22 (11) (2020)
Jonathan Bac, Andrei Yu. Zinovyev
Local intrinsic dimensionality estimators based on concentration of measure. CoRR (2020)
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) (2020)
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)
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)
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) (2020)
Jonathan Bac, Andrei Yu. Zinovyev
Local intrinsic dimensionality estimators based on concentration of measure. IJCNN (2020)
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) (2020)
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 (2020)
Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Yu. Zinovyev
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. CoRR (2019)
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) (2019)
Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Yu. Zinovyev
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. ICTAI (2019)
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. (4) (2019)
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) (2019)
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) (2019)
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) (2019)
Luca Albergante, Jonathan Bac, Andrei Yu. Zinovyev
Estimating the effective dimension of large biological datasets using Fisher separability analysis. IJCNN (2019)
Luca Albergante, Jonathan Bac, Andrei Yu. Zinovyev
Estimating the effective dimension of large biological datasets using Fisher separability analysis. CoRR (2019)
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, 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) (2019)
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) (2019)
Jonathan Bac, Andrei Yu. Zinovyev
Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets. Frontiers Neurorobotics 13 (2019)
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)
Alexander N. Gorban, Evgeny M. Mirkes, Andrei Yu. Zinovyev
Data analysis with arbitrary error measures approximated by piece-wise quadratic PQSQ functions. IJCNN (2018)
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 (2018)
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 (2018)
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)
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) (2017)
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 (2017)
Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev
Piece-wise quadratic lego set for constructing arbitrary error potentials and their fast optimization. CoRR (2016)
Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev
Robust principal graphs for data approximation. CoRR (2016)
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) (2016)
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 (2016)
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 (2015)
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)
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) (2015)
Alexander N. Gorban, Andrei Yu. Zinovyev
Fast and user-friendly non-linear principal manifold learning by method of elastic maps. DSAA (2015)
Alexander N. Gorban, Alexander Pitenko, Andrei Yu. Zinovyev
ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data. CoRR (2014)
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 (2013)
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)
Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev
OCSANA: optimal combinations of interventions from network analysis. Bioinform. 29 (12) (2013)
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 (2013)
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 (2013)
Andrei Yu. Zinovyev, Evgeny M. Mirkes
Data complexity measured by principal graphs. Comput. Math. Appl. 65 (10) (2013)
Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, Alexander N. Gorban
Geometrical complexity of data approximators CoRR (2013)
Evgeny M. Mirkes, Andrei Yu. Zinovyev, Alexander N. Gorban
Geometrical Complexity of Data Approximators. IWANN (1) (2013)
Andrei Yu. Zinovyev, Ulykbek Kairov, Tatiana Karpenyuk, Erlan Ramanculov
Blind source separation methods for deconvolution of complex signals in cancer biology CoRR (2013)
Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot
Identification of Shortened 3′ untranslated Regions from Expression Arrays. J. Bioinform. Comput. Biol. 10 (2) (2012)
Andrei Yu. Zinovyev, Evgeny M. Mirkes
Data complexity measured by principal graphs CoRR (2012)
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) (2011)
Andrei Yu. Zinovyev
Data visualization in political and social sciences CoRR (2010)
Andrei Yu. Zinovyev, Alexander N. Gorban
Nonlinear Quality of Life Index CoRR (2010)
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)
Alexander N. Gorban, Andrei Yu. Zinovyev
Principal manifolds and graphs in practice: from molecular biology to dynamical systems CoRR (2010)
Alexander N. Gorban, Andrei Yu. Zinovyev
Principal Manifolds and Graphs in Practice: from Molecular Biology to Dynamical Systems. Int. J. Neural Syst. 20 (3) (2010)
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 (2010)
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)
Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinform. 24 (6) (2008)
Alexander N. Gorban, Andrei Yu. Zinovyev
Principal Graphs and Manifolds CoRR (2008)
Ovidiu Radulescu, Alexander N. Gorban, Andrei Yu. Zinovyev, Alain Lilienbaum
Robust simplifications of multiscale biochemical networks. BMC Syst. Biol. 2 (2008)
Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev
Branching Principal Components: Elastic Graphs, Topological Grammars and Metro Maps. IJCNN (2007)
Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert
Classification of microarray data using gene networks. BMC Bioinform. 8 (2007)
Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev
Topological grammars for data approximation. Appl. Math. Lett. 20 (4) (2007)
Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev
Topological Grammars for Data Approximation CoRR (2006)
Alexander N. Gorban, Andrei Yu. Zinovyev
Elastic Principal Graphs and Manifolds and their Practical Applications. Computing 75 (4) (2005)
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) (2005)
Alessandra Carbone, Andrei Yu. Zinovyev, François Képès
Codon adaptation index as a measure of dominating codon bias. Bioinform. 19 (16) (2003)
Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova
Seven clusters in genomic triplet distributions. Silico Biol. 3 (4) (2003)
Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova
Seven clusters in genomic triplet distributions CoRR (2003)
Andrei Yu. Zinovyev, Alexander N. Gorban, Tatyana G. Popova
Self-Organizing Approach for Automated Gene Identification. Open Syst. Inf. Dyn. 10 (4) (2003)