Application of the method of elastic maps in analysis of genetic texts. - Alexander N. Gorban; Andrei Yu. Zinovyev; Donald C. Wunsch (IJCNN, 2003)

Codon adaptation index as a measure of dominating codon bias. - Alessandra Carbone; Andrei Yu. Zinovyev; François Képès (Bioinform., 2003)

Seven clusters in genomic triplet distributions. - Alexander N. Gorban; Andrei Yu. Zinovyev; Tatyana G. Popova (Silico Biol., 2003)

Self-Organizing Approach for Automated Gene Identification. - Andrei Yu. Zinovyev; Alexander N. Gorban; Tatyana G. Popova (Open Syst. Inf. Dyn., 2003)

Elastic Principal Graphs and Manifolds and their Practical Applications. - Alexander N. Gorban; Andrei Yu. Zinovyev (Computing, 2005)

Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. - Alexander N. Gorban; Tatyana G. Popova; Andrei Yu. Zinovyev (Silico Biol., 2005)

Branching Principal Components: Elastic Graphs, Topological Grammars and Metro Maps. - Alexander N. Gorban; Neil R. Sumner; Andrei Yu. Zinovyev (IJCNN, 2007)

Topological grammars for data approximation. - Alexander N. Gorban; Neil R. Sumner; Andrei Yu. Zinovyev (Appl. Math. Lett., 2007)

Classification of microarray data using gene networks. - Franck Rapaport; Andrei Yu. Zinovyev; Marie Dutreix; Emmanuel Barillot; Jean-Philippe Vert (BMC Bioinform., 2007)

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. - Andrei Yu. Zinovyev; Eric Viara; Laurence Calzone; Emmanuel Barillot (Bioinform., 2008)

Robust simplifications of multiscale biochemical networks. - Ovidiu Radulescu; Alexander N. Gorban; Andrei Yu. Zinovyev; Alain Lilienbaum (BMC Syst. Biol., 2008)

Principal Graphs and Manifolds - Alexander N. Gorban; Andrei Yu. Zinovyev (CoRR, 2008)

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. - Sylvain Blachon; Gautier Stoll; Carito Guziolowski; Andrei Yu. Zinovyev; Emmanuel Barillot; Anne Siegel; Ovidiu Radulescu (AIAI (Workshops), 2009)

Dynamical modeling of microRNA action on the protein translation process. - Andrei Yu. Zinovyev; Nadya Morozova; Nora Nonne; Emmanuel Barillot; Annick Harel-Bellan; Alexander N. Gorban (BMC Syst. Biol., 2010)

Data visualization in political and social sciences - Andrei Yu. Zinovyev (CoRR, 2010)

Nonlinear Quality of Life Index - Andrei Yu. Zinovyev; Alexander N. Gorban (CoRR, 2010)

Principal Manifolds and Graphs in Practice: from Molecular Biology to Dynamical Systems. - Alexander N. Gorban; Andrei Yu. Zinovyev (Int. J. Neural Syst., 2010)

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. - Laurence Calzone; Laurent Tournier; Simon Fourquet; Denis Thieffry; Boris Zhivotovsky; Emmanuel Barillot; Andrei Yu. Zinovyev (PLoS Comput. Biol., 2010)

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. - Valentina Boeva; Andrei Yu. Zinovyev; Kevin Bleakley; Jean-Philippe Vert; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2011)

Identification of Shortened 3′ untranslated Regions from Expression Arrays. - Loredana Martignetti; Andrei Yu. Zinovyev; Emmanuel Barillot (J. Bioinform. Comput. Biol., 2012)

Geometrical Complexity of Data Approximators. - Evgeny M. Mirkes; Andrei Yu. Zinovyev; Alexander N. Gorban (IWANN (1), 2013)

OCSANA: optimal combinations of interventions from network analysis. - Paola Vera-Licona; Eric Bonnet; Emmanuel Barillot; Andrei Yu. Zinovyev (Bioinform., 2013)

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. - Eric Bonnet; Laurence Calzone; Daniel Rovera; Gautier Stoll; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2013)

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. - Inna Kuperstein; David P. A. Cohen; Stuart Pook; Eric Viara; Laurence Calzone; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2013)

Model composition through model reduction: a combined model of CD95 and NF-κ. - Elena Kutumova; Andrei Yu. Zinovyev; Ruslan N. Sharipov; Fedor A. Kolpakov (BMC Syst. Biol., 2013)

Data complexity measured by principal graphs. - Andrei Yu. Zinovyev; Evgeny M. Mirkes (Comput. Math. Appl., 2013)

Blind source separation methods for deconvolution of complex signals in cancer biology - Andrei Yu. Zinovyev; Ulykbek Kairov; Tatiana Karpenyuk; Erlan Ramanculov (CoRR, 2013)

Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps. - Andrei Yu. Zinovyev; Inna Kuperstein; Emmanuel Barillot; Wolf-Dietrich Heyer (PLoS Comput. Biol., 2013)

ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data. - Alexander N. Gorban; Alexander Pitenko; Andrei Yu. Zinovyev (CoRR, 2014)

Fast and user-friendly non-linear principal manifold learning by method of elastic maps. - Alexander N. Gorban; Andrei Yu. Zinovyev (DSAA, 2015)

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. - Urszula Czerwinska; Laurence Calzone; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2015)

NaviCell Web Service for network-based data visualization. - Eric Bonnet; Eric Viara; Inna Kuperstein; Laurence Calzone; David P. A. Cohen; Emmanuel Barillot; Andrei Yu. Zinovyev (Nucleic Acids Res., 2015)

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. - David P. A. Cohen; Loredana Martignetti; Sylvie Robine; Emmanuel Barillot; Andrei Yu. Zinovyev; Laurence Calzone (PLoS Comput. Biol., 2015)

Robust principal graphs for data approximation. - Alexander N. Gorban; Eugenij Moiseevich Mirkes; Andrei Yu. Zinovyev (CoRR, 2016)

Piece-wise quadratic lego set for constructing arbitrary error potentials and their fast optimization. - Alexander N. Gorban; Eugenij Moiseevich Mirkes; Andrei Yu. Zinovyev (CoRR, 2016)

Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning. - Alexander N. Gorban; Eugenij Moiseevich Mirkes; Andrei Yu. Zinovyev (Neural Networks, 2016)

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. - Paul Deveau; Emmanuel Barillot; Valentina Boeva; Andrei Yu. Zinovyev; Eric Bonnet (R J., 2016)

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. - Mathurin Dorel; Eric Viara; Emmanuel Barillot; Andrei Yu. Zinovyev; Inna Kuperstein (Database J. Biol. Databases Curation, 2017)

MaBoSS 2.0: an environment for stochastic Boolean modeling. - Gautier Stoll; Barthélémy Caron; Eric Viara; Aurélien Dugourd; Andrei Yu. Zinovyev; Aurélien Naldi; Guido Kroemer; Emmanuel Barillot; Laurence Calzone (Bioinform., 2017)

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. - Marine Le Morvan; Andrei Yu. Zinovyev; Jean-Philippe Vert (PLoS Comput. Biol., 2017)

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals. - Urszula Czerwinska; Laura Cantini; Ulykbek Kairov; Emmanuel Barillot; Andrei Yu. Zinovyev (LVA/ICA, 2018)

Data analysis with arbitrary error measures approximated by piece-wise quadratic PQSQ functions. - Alexander N. Gorban; Evgeny M. Mirkes; Andrei Yu. Zinovyev (IJCNN, 2018)

Signalling maps in cancer research: construction and data analysis. - Maria Kondratova; Nicolas Sompairac; Emmanuel Barillot; Andrei Yu. Zinovyev; Inna Kuperstein (Database J. Biol. Databases Curation, 2018)

Robust and scalable learning of data manifolds with complex topologies via ElPiGraph. - Luca Albergante; Evgeny M. Mirkes; Huidong Chen; Alexis Martin; Louis Faure; Emmanuel Barillot; Luca Pinello; Alexander N. Gorban; Andrei Yu. Zinovyev (CoRR, 2018)

Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. - Stéphanie Chevalier; Christine Froidevaux; Loïc Paulevé; Andrei Yu. Zinovyev (ICTAI, 2019)

Estimating the effective dimension of large biological datasets using Fisher separability analysis. - Luca Albergante; Jonathan Bac; Andrei Yu. Zinovyev (IJCNN, 2019)

Application of Atlas of Cancer Signalling Network in preclinical studies. - L. Cristobal Monraz Gomez; Maria Kondratova; Jean-Marie Ravel; Emmanuel Barillot; Andrei Yu. Zinovyev; Inna Kuperstein (Briefings Bioinform., 2019)

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. - Arnau Montagud; Pauline Traynard; Loredana Martignetti; Eric Bonnet; Emmanuel Barillot; Andrei Yu. Zinovyev; Laurence Calzone (Briefings Bioinform., 2019)

Community-driven roadmap for integrated disease maps. - 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; et al. (Briefings Bioinform., 2019)

Assessing reproducibility of matrix factorization methods in independent transcriptomes. - Laura Cantini; Ulykbek Kairov; Aurélien de Reyniès; Emmanuel Barillot; François Radvanyi; Andrei Yu. Zinovyev (Bioinform., 2019)

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. - Gaëlle Letort; Arnau Montagud; Gautier Stoll; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Andrei Yu. Zinovyev; Laurence Calzone (Bioinform., 2019)

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. - Nicolas Sompairac; Jennifer Modamio; Emmanuel Barillot; Ronan M. T. Fleming; Andrei Yu. Zinovyev; Inna Kuperstein (BMC Bioinform., 2019)

Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets. - Jonathan Bac; Andrei Yu. Zinovyev (Frontiers Neurorobotics, 2019)

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. - 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; et al. (Nucleic Acids Res., 2019)

Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. - Stéphanie Chevalier; Vincent Noël; Laurence Calzone; Andrei Yu. Zinovyev; Loïc Paulevé (CMSB, 2020)

Local intrinsic dimensionality estimators based on concentration of measure. - Jonathan Bac; Andrei Yu. Zinovyev (IJCNN, 2020)

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. - Irina Balaur; Ludovic Roy; Alexander Mazein; S. Gökberk Karaca; Ugur Dogrusoz; Emmanuel Barillot; Andrei Yu. Zinovyev (Bioinform., 2020)

Exact solving and sensitivity analysis of stochastic continuous time Boolean models. - Mihály Koltai; Vincent Noel; Andrei Yu. Zinovyev; Laurence Calzone; Emmanuel Barillot (BMC Bioinform., 2020)

Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data. - Sergey E. Golovenkin; Jonathan Bac; Alexander Chervov; Evgeny M. Mirkes; Yuliya V. Orlova; Emmanuel Barillot; Alexander N. Gorban; Andrei Yu. Zinovyev (CoRR, 2020)

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. - Luca Albergante; Evgeny M. Mirkes; Jonathan Bac; Huidong Chen; Alexis Martin; Louis Faure; Emmanuel Barillot; Luca Pinello; Alexander N. Gorban; Andrei Yu. Zinovyev (Entropy, 2020)

Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets. - Alexander Chervov; Jonathan Bac; Andrei Yu. Zinovyev (Entropy, 2020)

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. - Andrei Yu. Zinovyev; Urszula Czerwinska; Laura Cantini; Emmanuel Barillot; Klaus M. Frahm; Dima L. Shepelyansky (PLoS Comput. Biol., 2020)

LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. - Marion Buffard; Aurélien Desoeuvres; Aurélien Naldi; Clément Requilé; Andrei Yu. Zinovyev; Ovidiu Radulescu (CMSB, 2021)

Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees. - Alexander Chervov; Andrei Yu. Zinovyev (IJCNN, 2021)

Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation. - Jonathan Bac; Evgeny M. Mirkes; Alexander N. Gorban; Ivan Tyukin; Andrei Yu. Zinovyev (Entropy, 2021)

Quasi-orthogonality and intrinsic dimensions as measures of learning and generalisation. - Qinghua Zhou; Alexander N. Gorban; Evgeny M. Mirkes; Jonathan Bac; Andrei Yu. Zinovyev; Ivan Yu. Tyukin (IJCNN, 2022)

Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data. - Elise Amblard; Jonathan Bac; Alexander Chervov; Vassili Soumelis; Andrei Yu. Zinovyev (Bioinform., 2022)

BIODICA: a computational environment for Independent Component Analysis of omics data. - Nicolas Captier; Jane Merlevede; Askhat Molkenov; Ainur Seisenova; Altynbek Zhubanchaliyev; Petr V. Nazarov; Emmanuel Barillot; Ulykbek Kairov; Andrei Yu. Zinovyev (Bioinform., 2022)

Coloring Panchromatic Nighttime Satellite Images: Comparing the Performance of Several Machine Learning Methods. - Natalya A. Rybnikova; Boris A. Portnov; Evgeny M. Mirkes; Andrei Yu. Zinovyev; Anna Brook; Alexander N. Gorban (IEEE Trans. Geosci. Remote. Sens., 2022)

Domain Adaptation Principal Component Analysis: Base Linear Method for Learning with Out-of-Distribution Data. - Evgeny M. Mirkes; Jonathan Bac; Aziz Fouché; Sergey V. Stasenko; Andrei Yu. Zinovyev; Alexander N. Gorban (Entropy, 2023)

Omics data integration in computational biology viewed through the prism of machine learning paradigms. - Aziz Fouché; Andrei Yu. Zinovyev (Frontiers Bioinform., 2023)

Exploring the impact of social stress on the adaptive dynamics of COVID-19: Typing the behavior of naïve populations faced with epidemics. - Innokentiy Kastalskiy; Andrei Yu. Zinovyev; Evgeny M. Mirkes; Victor B. Kazantsev; Alexander N. Gorban (Commun. Nonlinear Sci. Numer. Simul., 2024)

scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics. - Gustavo Magaña López; Laurence Calzone; Andrei Yu. Zinovyev; Loïc Paulevé (PLoS Comput. Biol., 2024)