Andrei Yu. Zinovyev

87 papers B 9Journal 73Unranked 5
YearRankTypeTitle / Venue / Authors
2024 J jnl
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.
Innokentiy Kastalskiy, Andrei Yu. Zinovyev, Evgeny M. Mirkes, Victor B. Kazantsev, Alexander N. Gorban
2024 J jnl
scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics.
PLoS Comput. Biol.
Gustavo Magaña López, Laurence Calzone, Andrei Yu. Zinovyev, Loïc Paulevé
2023 J jnl
Domain Adaptation Principal Component Analysis: Base Linear Method for Learning with Out-of-Distribution Data.
Entropy
Evgeny M. Mirkes, Jonathan Bac, Aziz Fouché, Sergey V. Stasenko, Andrei Yu. Zinovyev, Alexander N. Gorban
2023 J jnl
Exploring the impact of social stress on the adaptive dynamics of COVID-19: Typing the behavior of naïve populations faced with epidemics.
CoRR
Innokentiy Kastalskiy, Andrei Yu. Zinovyev, Evgeny M. Mirkes, Victor B. Kazantsev, Alexander N. Gorban
2023 J jnl
Multiscale model of the different modes of cancer cell invasion.
Bioinform.
Marco Ruscone, Arnau Montagud, Philippe Chavrier, Olivier Destaing, Isabelle Bonnet, Andrei Yu. Zinovyev, Emmanuel Barillot, Vincent Noël, Laurence Calzone
2023 J jnl
Omics data integration in computational biology viewed through the prism of machine learning paradigms.
Frontiers Bioinform.
Aziz Fouché, Andrei Yu. Zinovyev
2022 J jnl
BIODICA: a computational environment for Independent Component Analysis of omics data.
Bioinform.
Nicolas Captier, Jane Merlevede, Askhat Molkenov, Ainur Seisenova, Altynbek Zhubanchaliyev, Petr V. Nazarov, Emmanuel Barillot, Ulykbek Kairov, Andrei Yu. Zinovyev
2022 J jnl
Coloring Panchromatic Nighttime Satellite Images: Comparing the Performance of Several Machine Learning Methods.
IEEE Trans. Geosci. Remote. Sens.
Natalya A. Rybnikova, Boris A. Portnov, Evgeny M. Mirkes, Andrei Yu. Zinovyev, Anna Brook, Alexander N. Gorban
2022 J jnl
Domain Adaptation Principal Component Analysis: base linear method for learning with out-of-distribution data.
CoRR
Evgeny M. Mirkes, Jonathan Bac, Aziz Fouché, Sergey V. Stasenko, Andrei Yu. Zinovyev, Alexander N. Gorban
2022 J jnl
Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data.
Bioinform.
Elise Amblard, Jonathan Bac, Alexander Chervov, Vassili Soumelis, Andrei Yu. Zinovyev
2022 B conf
Quasi-orthogonality and intrinsic dimensions as measures of learning and generalisation.
IJCNN
Qinghua Zhou, Alexander N. Gorban, Evgeny M. Mirkes, Jonathan Bac, Andrei Yu. Zinovyev, Ivan Yu. Tyukin
2022 J jnl
Quasi-orthogonality and intrinsic dimensions as measures of learning and generalisation.
CoRR
Qinghua Zhou, Alexander N. Gorban, Evgeny M. Mirkes, Jonathan Bac, Andrei Yu. Zinovyev, Ivan Yu. Tyukin
2021 B conf
Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees.
IJCNN
Alexander Chervov, Andrei Yu. Zinovyev
2021 — conf
LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales.
CMSB
Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Yu. Zinovyev, Ovidiu Radulescu
2021 J jnl
Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation.
Entropy
Jonathan Bac, Evgeny M. Mirkes, Alexander N. Gorban, Ivan Tyukin, Andrei Yu. Zinovyev
2021 J jnl
Scikit-dimension: a Python package for intrinsic dimension estimation.
CoRR
Jonathan Bac, Evgeny M. Mirkes, Alexander N. Gorban, Ivan Tyukin, Andrei Yu. Zinovyev
2020 J jnl
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.
PLoS Comput. Biol.
Andrei Yu. Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky
2020 J jnl
Exact solving and sensitivity analysis of stochastic continuous time Boolean models.
BMC Bioinform.
Mihály Koltai, Vincent Noel, Andrei Yu. Zinovyev, Laurence Calzone, Emmanuel Barillot
2020 B conf
Local intrinsic dimensionality estimators based on concentration of measure.
IJCNN
Jonathan Bac, Andrei Yu. Zinovyev
2020 J jnl
Local intrinsic dimensionality estimators based on concentration of measure.
CoRR
Jonathan Bac, Andrei Yu. Zinovyev
2020 J jnl
Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets.
Entropy
Alexander Chervov, Jonathan Bac, Andrei Yu. Zinovyev
2020 J jnl
Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph.
Entropy
Luca Albergante, Evgeny M. Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev
2020 — conf
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision.
CMSB
Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Yu. Zinovyev, Loïc Paulevé
2020 J jnl
Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data.
CoRR
Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban, Andrei Yu. Zinovyev
2020 J jnl
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.
Bioinform.
Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev
2020 J jnl
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.
Bioinform.
Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev
2019 J jnl
Application of Atlas of Cancer Signalling Network in preclinical studies.
Briefings Bioinform.
L. Cristobal Monraz Gomez, Maria Kondratova, Jean-Marie Ravel, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
2019 J jnl
Assessing reproducibility of matrix factorization methods in independent transcriptomes.
Bioinform.
Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Yu. Zinovyev
2019 J jnl
Community-driven roadmap for integrated disease maps.
Briefings Bioinform.
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
2019 J jnl
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.
Briefings Bioinform.
Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone
2019 B conf
Estimating the effective dimension of large biological datasets using Fisher separability analysis.
IJCNN
Luca Albergante, Jonathan Bac, Andrei Yu. Zinovyev
2019 J jnl
Estimating the effective dimension of large biological datasets using Fisher separability analysis.
CoRR
Luca Albergante, Jonathan Bac, Andrei Yu. Zinovyev
2019 J jnl
Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets.
Frontiers Neurorobotics
Jonathan Bac, Andrei Yu. Zinovyev
2019 J jnl
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.
BMC Bioinform.
Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein
2019 J jnl
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.
Bioinform.
Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone
2019 B conf
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming.
ICTAI
Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Yu. Zinovyev
2019 J jnl
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming.
CoRR
Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Yu. Zinovyev
2019 J jnl
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.
Nucleic Acids Res.
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
2018 — conf
Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals.
LVA/ICA
Urszula Czerwinska, Laura Cantini, Ulykbek Kairov, Emmanuel Barillot, Andrei Yu. Zinovyev
2018 B conf
Data analysis with arbitrary error measures approximated by piece-wise quadratic PQSQ functions.
IJCNN
Alexander N. Gorban, Evgeny M. Mirkes, Andrei Yu. Zinovyev
2018 J jnl
Robust and scalable learning of data manifolds with complex topologies via ElPiGraph.
CoRR
Luca Albergante, Evgeny M. Mirkes, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev
2018 J jnl
Signalling maps in cancer research: construction and data analysis.
Database J. Biol. Databases Curation
Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
2017 J jnl
MaBoSS 2.0: an environment for stochastic Boolean modeling.
Bioinform.
Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone
2017 J jnl
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.
Database J. Biol. Databases Curation
Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
2017 J jnl
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis.
PLoS Comput. Biol.
Marine Le Morvan, Andrei Yu. Zinovyev, Jean-Philippe Vert
2016 J jnl
Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages.
R J.
Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Yu. Zinovyev, Eric Bonnet
2016 J jnl
Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning.
Neural Networks
Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev
2016 J jnl
Piece-wise quadratic lego set for constructing arbitrary error potentials and their fast optimization.
CoRR
Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev
2016 J jnl
Robust principal graphs for data approximation.
CoRR
Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev
2015 J jnl
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.
BMC Syst. Biol.
Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev
2015 B conf
Fast and user-friendly non-linear principal manifold learning by method of elastic maps.
DSAA
Alexander N. Gorban, Andrei Yu. Zinovyev
2015 J jnl
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.
PLoS Comput. Biol.
David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone
2015 J jnl
NaviCell Web Service for network-based data visualization.
Nucleic Acids Res.
Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Yu. Zinovyev
2014 J jnl
ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data.
CoRR
Alexander N. Gorban, Alexander Pitenko, Andrei Yu. Zinovyev
2013 J jnl
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
BMC Syst. Biol.
Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Yu. Zinovyev
2013 J jnl
Blind source separation methods for deconvolution of complex signals in cancer biology
CoRR
Andrei Yu. Zinovyev, Ulykbek Kairov, Tatiana Karpenyuk, Erlan Ramanculov
2013 J jnl
Data complexity measured by principal graphs.
Comput. Math. Appl.
Andrei Yu. Zinovyev, Evgeny M. Mirkes
2013 — conf
Geometrical Complexity of Data Approximators.
IWANN (1)
Evgeny M. Mirkes, Andrei Yu. Zinovyev, Alexander N. Gorban
2013 J jnl
Geometrical complexity of data approximators
CoRR
Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, Alexander N. Gorban
2013 J jnl
Model composition through model reduction: a combined model of CD95 and NF-κ.
BMC Syst. Biol.
Elena Kutumova, Andrei Yu. Zinovyev, Ruslan N. Sharipov, Fedor A. Kolpakov
2013 J jnl
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.
BMC Syst. Biol.
Inna Kuperstein, David P. A. Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev
2013 J jnl
OCSANA: optimal combinations of interventions from network analysis.
Bioinform.
Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev
2013 J jnl
Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps.
PLoS Comput. Biol.
Andrei Yu. Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer
2012 J jnl
Data complexity measured by principal graphs
CoRR
Andrei Yu. Zinovyev, Evgeny M. Mirkes
2012 J jnl
Identification of Shortened 3′ untranslated Regions from Expression Arrays.
J. Bioinform. Comput. Biol.
Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot
2011 J jnl
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
Bioinform.
Valentina Boeva, Andrei Yu. Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
2010 J jnl
Data visualization in political and social sciences
CoRR
Andrei Yu. Zinovyev
2010 J jnl
Dynamical modeling of microRNA action on the protein translation process.
BMC Syst. Biol.
Andrei Yu. Zinovyev, Nadya Morozova, Nora Nonne, Emmanuel Barillot, Annick Harel-Bellan, Alexander N. Gorban
2010 J jnl
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement.
PLoS Comput. Biol.
Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev
2010 J jnl
Nonlinear Quality of Life Index
CoRR
Andrei Yu. Zinovyev, Alexander N. Gorban
2010 J jnl
Principal Manifolds and Graphs in Practice: from Molecular Biology to Dynamical Systems.
Int. J. Neural Syst.
Alexander N. Gorban, Andrei Yu. Zinovyev
2010 J jnl
Principal manifolds and graphs in practice: from molecular biology to dynamical systems
CoRR
Alexander N. Gorban, Andrei Yu. Zinovyev
2009 — conf
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks.
AIAI (Workshops)
Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Yu. Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu
2008 J jnl
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
Bioinform.
Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot
2008 J jnl
Principal Graphs and Manifolds
CoRR
Alexander N. Gorban, Andrei Yu. Zinovyev
2008 J jnl
Robust simplifications of multiscale biochemical networks.
BMC Syst. Biol.
Ovidiu Radulescu, Alexander N. Gorban, Andrei Yu. Zinovyev, Alain Lilienbaum
2007 B conf
Branching Principal Components: Elastic Graphs, Topological Grammars and Metro Maps.
IJCNN
Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev
2007 J jnl
Classification of microarray data using gene networks.
BMC Bioinform.
Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert
2007 J jnl
Topological grammars for data approximation.
Appl. Math. Lett.
Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev
2006 J jnl
Topological Grammars for Data Approximation
CoRR
Alexander N. Gorban, Neil R. Sumner, Andrei Yu. Zinovyev
2005 J jnl
Elastic Principal Graphs and Manifolds and their Practical Applications.
Computing
Alexander N. Gorban, Andrei Yu. Zinovyev
2005 J jnl
Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences.
Silico Biol.
Alexander N. Gorban, Tatyana G. Popova, Andrei Yu. Zinovyev
2003 B conf
Application of the method of elastic maps in analysis of genetic texts.
IJCNN
Alexander N. Gorban, Andrei Yu. Zinovyev, Donald C. Wunsch
2003 J jnl
Codon adaptation index as a measure of dominating codon bias.
Bioinform.
Alessandra Carbone, Andrei Yu. Zinovyev, François Képès
2003 J jnl
Self-Organizing Approach for Automated Gene Identification.
Open Syst. Inf. Dyn.
Andrei Yu. Zinovyev, Alexander N. Gorban, Tatyana G. Popova
2003 J jnl
Seven clusters in genomic triplet distributions
CoRR
Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova
2003 J jnl
Seven clusters in genomic triplet distributions.
Silico Biol.
Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova