A. Zinovyev

发表

ROMA: Representation and Quantification of Module Activity from Target Expression Data

E. Barillot, E. Bonnet, L. Calzone, 2016, Front. Genet..

Beyond The Concept of Manifolds: Principal Trees, Metro Maps, and Elastic Cubic Complexes

Alexander N Gorban, A. Zinovyev, N. Sumner, 2007, 0801.0176.

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

E. Barillot, E. Bonnet, L. Calzone, 2015, Oncogenesis.

Network-based approaches for drug response prediction and targeted therapy development in cancer.

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2015, Biochemical and biophysical research communications.

Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling

Andrei Zinovyev, A. Zinovyev, 2015 .

A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis.

É. Remy, F. Radvanyi, L. Calzone, 2015, Cancer research.

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes.

P. Gestraud, E. Barillot, N. López-Bigas, 2014, Cell reports.

Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer: New Insights from Matrix Factorization

E. Barillot, V. Pancaldi, A. Valencia, 2019, bioRxiv.

Molecular Inverse Comorbidity between Alzheimer’s disease and Lung Cancer: new insights from Matrix Factorization

E. Barillot, V. Pancaldi, A. Valencia, 2019, bioRxiv.

Systems Biology Analysis for Ewing Sarcoma.

A. Zinovyev, M. Petrizzelli, J. Merlevede, 2020, Methods in molecular biology.

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

Giosuè Lo Bosco, Martin J. Aryee, Jason D. Buenrostro, 2018, bioRxiv.

The shortest path is not the one you know: application of biological network resources in precision oncology research.

E. Barillot, D. Thieffry, A. Zinovyev, 2015, Mutagenesis.

A comprehensive modular map of molecular interactions in RB/E2F pathway

E. Barillot, F. Radvanyi, L. Calzone, 2008, Molecular systems biology.

Principal Graphs and Manifolds

Andrei Zinovyev, Alexander N. Gorban, A. Gorban, 2010 .

BiNoM : a Cytoscape plugin for using and analyzing biological networks

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2007 .

Determining the optimal number of independent components for reproducible transcriptomic data analysis

E. Barillot, A. Zinovyev, L. Cantini, 2017, bioRxiv.

Determining the optimal number of independent components for reproducible transcriptomic data analysis

Andrei Zinovyev, Emmanuel Barillot, Urszula Czerwinska, 2017, BMC Genomics.

Invariant grids for reaction kinetics

Alexander N Gorban, A. N. Gorban, I. V. Karlin, 2003 .

Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer.

Inna Kuperstein, Andrei Zinovyev, Anne Vincent-Salomon, 2018, Cancer cell.

Antagonism Pattern Detection between MicroRNA and Target Expression in Ewing’s Sarcoma

Andrei Zinovyev, Emmanuel Barillot, Loredana Martignetti, 2012, PloS one.

Interpreting pathways to discover cancer driver genes with Moonlight

Matthew H Bailey, Gabriel J. Odom, Gianluca Bontempi, 2020, Nature Communications.

How much non-coding DNA do eukaryotes require?

Andrei Zinovyev, Sebastian E Ahnert, Thomas M A Fink, 2006, Journal of theoretical biology.

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Aurélien Naldi, Denis Thieffry, Andrei Zinovyev, 2018, Front. Physiol..

Codon bias signatures, organization of microorganisms in codon space, and lifestyle.

A Carbone, F. Képès, A. Carbone, 2005, Molecular biology and evolution.

Classification of gene signatures for their information value and functional redundancy

E. Barillot, N. Blüthgen, L. Calzone, 2017, bioRxiv.

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

R. Fleming, I. Thiele, Reinhard Schneider, 2018, bioRxiv.

Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures

Andrei Zinovyev, Erlan Ramanculov, Ulykbek Kairov, 2012, Bioinformation.

Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2016, Clinical Cancer Research.

Hierarchies and modules in complex biological systems

Alexander N Gorban, A. Zinovyev, O. Radulescu, 2006 .

Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response

E. Barillot, L. Calzone, A. Zinovyev, 2020, Cancers.

A review of computational approaches detecting microRNAs involved in cancer

E. Barillot, L. Martignetti, A. Zinovyev, 2022 .

PCA deciphers genome

Alexander N Gorban, A. Zinovyev, 2005 .

Understanding Different Types of Cell Death Using Systems Biology

L. Calzone, B. Zhivotovsky, A. Zinovyev, 2012 .

Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer

E. Barillot, L. Martignetti, A. Zinovyev, 2018, bioRxiv.

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer

E. Barillot, L. Martignetti, A. Zinovyev, 2018, bioRxiv.

Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer.

K. Tarte, A. Vincent-Salomon, A. Zinovyev, 2020, Cancer discovery.

Kinetic signatures of microRNA modes of action Material Supplemental

Alexander N Gorban, A. Harel-Bellan, A. Zinovyev, 2012 .

Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells

A. Harel-Bellan, A. Zinovyev, N. Morozova, 2012 .

Basic, simple and extendable kinetic model of protein synthesis.

A. Gorban, A. Harel-Bellan, A. Zinovyev, 2012, Mathematical biosciences and engineering : MBE.

Creation and analysis of biochemical constraint-based models : the COBRA Toolbox v 3 . 0 26 th February 2018

Francisco J. Planes, Ronan M. T. Fleming, Maike K. Aurich, 2018 .

Computational challenges of cell cycle analysis using single cell transcriptomics

A. Zinovyev, A. Chervov, 2022, 2208.05229.

Domain Adaptation Principal Component Analysis: base linear method for learning with out-of-distribution data

Alexander N. Gorban, A. Zinovyev, E. Mirkes, 2022, ArXiv.

Constructive methods of invariant manifolds for kinetic problems

Alexander N Gorban, A. Gorban, A. Zinovyev, 2003, cond-mat/0311017.

Invariant grids for reaction kinetics

Alexander N Gorban, A. Zinovyev, I. Karlin, 2003, cond-mat/0307076.

[Biological network modelling and precision medicine in oncology].

E. Barillot, E. Bonnet, L. Calzone, 2014, Bulletin du Cancer.

Elastic Principal Graphs and Manifolds and their Practical Applications

Alexander N Gorban, A. Zinovyev, 2004, Computing.

Coloring Panchromatic Nighttime Satellite Images: Comparing the Performance of Several Machine Learning Methods

Alexander N Gorban, A. Brook, A. Zinovyev, 2020, IEEE Transactions on Geoscience and Remote Sensing.

Dealing with complexity of biological systems: from data to models

A. Zinovyev, 2014, 1404.1626.

MODEL REDUCTION AND MODEL COMPARISON FOR NF κ B SIGNALING

A. Zinovyev, O. Radulescu, A. Lilienbaum, 2007 .

transmorph: a unifying computational framework for single-cell data integration

A. Zinovyev, O. Delattre, Loic Chadoutaud, 2022, bioRxiv.

Simulating cancer: computational models in oncology

L. Galluzzi, A. Zinovyev, H. Lee, 2013 .

Early pre-neural serotonin modulates balance of late monoamines and behavioral patterns in fish model system

J. Kehr, E. Arenas, A. Zinovyev, 2022, bioRxiv.

Multiscale model of the different modes of cancer cell invasion

E. Barillot, L. Calzone, A. Zinovyev, 2022, bioRxiv.

Domain Adaptation Principal Component Analysis: Base Linear Method for Learning with Out-of-Distribution Data

Alexander N. Gorban, E. M. Mirkes, A. Zinovyev, 2022, Entropy.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Anne Richelle, Iñigo Apaolaza, Lin Wang, 2019, Nature Protocols.

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

Andrei Zinovyev, Emmanuel Barillot, Alexander Gorban, 2019, International journal of molecular sciences.

Minimum Spanning vs. Principal Trees for Structured Approximations of Multi-Dimensional Datasets

Andrei Zinovyev, Jonathan Bac, Alexander Chervov, 2020, Entropy.

Applications of single-cell and bulk RNA sequencing in onco-immunology.

Daniel Gautheret, Andrei Zinovyev, Maria Kuksin, 2021, European journal of cancer.

Codon adaptation index as a measure of dominating codon bias

Alessandra Carbone, François Képès, Andrei Yu. Zinovyev, 2003, Bioinform..

Blind source separation methods for deconvolution of complex signals in cancer biology

Andrei Yu. Zinovyev, Erlan Ramanculov, Ulykbek Kairov, 2013, Biochemical and biophysical research communications.

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Emmanuel Barillot, Laura Cantini, Ulykbek Kairov, 2019, Bioinform..

Classification of microarray data using gene networks

Emmanuel Barillot, Jean-Philippe Vert, Andrei Yu. Zinovyev, 2007, BMC Bioinformatics.

The multilayer community structure of medulloblastoma

D. Cirillo, A. Valencia, A. Zinovyev, 2021, iScience.

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis

Jean-Philippe Vert, Andrei Yu. Zinovyev, Marine Le Morvan, 2017, PLoS Comput. Biol..

Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches

Alexander N Gorban, E. Barillot, L. Calzone, 2021, bioRxiv.

Mathematical modeling of microRNA-mediated mechanisms of translation repression.

Andrei Zinovyev, Nadya Morozova, Alexander N Gorban, 2012, Advances in experimental medicine and biology.

Kinetic signatures of microRNA modes of action.

Andrei Zinovyev, Annick Harel-Bellan, Nadya Morozova, 2012, RNA.

Dynamical modeling of microRNA action on the protein translation process

Emmanuel Barillot, Annick Harel-Bellan, Nadya Morozova, 2009, BMC Systems Biology.

scEvoNet: a gradient boosting-based method for prediction of cell state evolution

A. Zinovyev, A. Monsoro-Burq, Aleksandr Kotov, 2022, bioRxiv.

Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data

A. Zinovyev, V. Soumelis, A. Chervov, 2021, bioRxiv.

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

Shuigeng Zhou, Jihong Guan, Andrei Zinovyev, 2019, Nature Communications.

Reduction of dynamical biochemical reactions networks in computational biology

Alexander N Gorban, A. N. Gorban, O. Radulescu, 2012, Front. Gene..

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Andrei Zinovyev, Emmanuel Barillot, Luca Pinello, 2018, Entropy.

Detection of miRNA regulatory effect on triple negative breast cancer transcriptome

E. Barillot, L. Martignetti, A. Zinovyev, 2015, BMC Genomics.

Unsupervised weights selection for optimal transport based dataset integration

A. Zinovyev, Aziz Fouché, 2021, bioRxiv.

Self-Organizing Approach for Automated Gene Identification

Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova, 2003, Open Syst. Inf. Dyn..

Classification of gene signatures for their information value and functional redundancy

Nils Blüthgen, Andrei Zinovyev, Emmanuel Barillot, 2017, npj Systems Biology and Applications.

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients

Francisco Azuaje, Andrei Zinovyev, Petr V. Nazarov, 2019, BMC Medical Genomics.

Independent component analysis provides clinically relevant insights into the biology of melanoma patients

Francisco Azuaje, Andrei Zinovyev, Arnaud Muller, 2018, bioRxiv.

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

Denis Thieffry, Emmanuel Barillot, Laurence Calzone, 2010, PLoS Comput. Biol..

Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)

Olaf Wolkenhauer, Blaz Zupan, Ravi Iyengar, 2009, Molecular oncology.

A review of computational approaches detecting microRNAs involved in cancer.

Andrei Zinovyev, Emmanuel Barillot, Loredana Martignetti, 2017, Frontiers in bioscience.

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks

E. Barillot, A. Zinovyev, G. Stoll, 2009, AIAI Workshops.

Signalling maps in cancer research: construction and data analysis

Inna Kuperstein, Emmanuel Barillot, Andrei Yu. Zinovyev, 2018, Database J. Biol. Databases Curation.

Knowledge Formalization and High-Throughput Data Visualization Using Signaling Network Maps

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2016, bioRxiv.

From a biological hypothesis to the construction of a mathematical model.

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2013, Methods in molecular biology.

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.

Andrei Zinovyev, Emmanuel Barillot, Jean-Philippe Vert, 2020, Cell reports.

ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma

I. Amit, Eyal David, D. Surdez, 2019, Cell reports.

Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis

Andrei Zinovyev, Emmanuel Barillot, Gautier Stoll, 2013, Nucleic acids research.

Stabilized Independent Component Analysis outperforms other methods in finding reproducible signals in tumoral transcriptomes

Andrei Zinovyev, Emmanuel Barillot, Laura Cantini, 2018, bioRxiv.

WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

E. Barillot, L. Calzone, A. Zinovyev, 2021, Frontiers in Molecular Biosciences.

Exact solving and sensitivity analysis of stochastic continuous time Boolean models

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2020, BMC Bioinformatics.

Exact calculation of stationary solution and parameter sensitivity analysis of stochastic continuous time Boolean models

E. Barillot, L. Calzone, A. Zinovyev, 2019 .

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases

Andrei Zinovyev, Emmanuel Barillot, Arnau Montagud, 2019, Briefings Bioinform..

MaBoSS 2.0: an environment for stochastic Boolean modeling

Aurélien Naldi, Emmanuel Barillot, Laurence Calzone, 2017, Bioinform..

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

Emmanuel Barillot, Loredana Martignetti, Laurence Calzone, 2015, PLoS Comput. Biol..

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

Emmanuel Barillot, Jean-Philippe Vert, Andrei Yu. Zinovyev, 2010, Bioinform..

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Piotr Gawron, Inna Kuperstein, Ronan M. T. Fleming, 2018, bioRxiv.

Cell death and life in cancer: mathematical modeling of cell fate decisions.

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2013, Advances in experimental medicine and biology.

Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution

E Barillot, Jean-Philippe Vert, E. Barillot, 2019, bioRxiv.

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

Inna Kuperstein, Ronan M. T. Fleming, Emmanuel Barillot, 2019, BMC Bioinformatics.

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

Inna Kuperstein, Emmanuel Barillot, Mathurin Dorel, 2016, bioRxiv.

NaviCell Web Service for network-based data visualization

Inna Kuperstein, Emmanuel Barillot, Eric Bonnet, 2015, Nucleic Acids Res..

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

Emmanuel Barillot, Laurence Calzone, Eric Viara, 2008, Bioinform..

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages

Andrei Zinovyev, Emmanuel Barillot, Eric Bonnet, 2016, The R Journal.

Application of Atlas of Cancer Signalling Network in pre-clinical studies

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2017, bioRxiv.

Unsupervised computational deconvolution of mixed signals in tumor microenvironment using blind source deconvolution approach

Andrei Zinovyev, Emmanuel Barillot, Urszula Czerwinska, 2018, Annual International Conference on Research in Computational Molecular Biology.

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

Emmanuel Barillot, Arnau Montagud, Laurence Calzone, 2018, bioRxiv.

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018, bioRxiv.

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

Inna Kuperstein, Emmanuel Barillot, Loredana Martignetti, 2014, Nature Communications.

Lizard Brain: Tackling Locally Low-Dimensional Yet Globally Complex Organization of Multi-Dimensional Datasets

Andrei Zinovyev, Jonathan Bac, A. Zinovyev, 2020, Frontiers in Neurorobotics.

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Feng He, Piotr Gawron, Stephan Gebel, 2018, npj Systems Biology and Applications.

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2020, Cancers.

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

C. Auffray, E. Barillot, Feng Q. He, 2018, npj Systems Biology and Applications.

Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps

Inna Kuperstein, Emmanuel Barillot, Andrei Yu. Zinovyev, 2013, PLoS Comput. Biol..

The Mystery of Two Straight Lines in Bacterial Genome Statistics

Alexander N Gorban, A N Gorban, A Y Zinovyev, 2004, Bulletin of mathematical biology.

Community-driven roadmap for integrated disease maps

Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, 2018, Briefings Bioinform..

Identification of Shortened 3′ untranslated Regions from Expression Arrays

Emmanuel Barillot, Loredana Martignetti, Andrei Yu. Zinovyev, 2012, J. Bioinform. Comput. Biol..

Robust simplifications of multiscale biochemical networks

Alexander N. Gorban, Andrei Yu. Zinovyev, Ovidiu Radulescu, 2008, BMC Systems Biology.

Evidence for a parallel regulatory system in eukaryotes based on non-coding RNA

S. Ahnert, T. Fink, A. Zinovyev, 2006 .

Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data

E. M. Mirkes, S. E. Golovenkin, E. Barillot, 2020, GigaScience.

Categorization and Estimation of Relative Connectivity of Genes from Meta-OFTEN Network

Andrei Zinovyev, Ulykbek Kairov, Tatyana Karpenyuk, 2012 .

A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures

Inna Kuperstein, Andrei Zinovyev, Emmanuel Barillot, 2019, Nature Communications.

Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways

Elena Kutumova, Andrei Zinovyev, Fedor Kolpakov, 2013, BMC Systems Biology.

Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation

Andrei Zinovyev, Ivan Tyukin, Alexander N. Gorban, 2021, Entropy.

Principal Manifolds for Data Visualization and Dimension Reduction

Andrei Zinovyev, Donald C. Wunsch, Alexander N. Gorban, 2007 .

Seven clusters in genomic triplet distributions

Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova, 2003, Silico Biol..

Robust and scalable learning of data manifolds with complex topologies via ElPiGraph pdf

Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, 2018, ArXiv.

Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis

A. Zinovyev, U. Kairov, A. Molkenov, 2021, Frontiers in Genetics.

Moonlight: a tool for biological interpretation and driver genes discovery

Gianluca Bontempi, H. Noushmehr, E. Papaleo, 2018, bioRxiv.

Principal Manifolds and Graphs in Practice: from Molecular Biology to Dynamical Systems

Alexander N. Gorban, Andrei Yu. Zinovyev, Alexander N Gorban, 2010, Int. J. Neural Syst..

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Alexander N Gorban, A. N. Gorban, A. Y. Zinovyev, 2007, 0801.0168.

Visualization of Any Data with Elastic Map Method

Andrei Zinovyev, Donald C. Wunsch, Alexander N. Gorban, 2001 .

Atlas of Cancer Signaling Network: A Resource of Multi-Scale Biological Maps to Study Disease Mechanisms

E. Barillot, A. Zinovyev, I. Kuperstein, 2021 .

Estimating the effective dimension of large biological datasets using Fisher separability analysis

Andrei Yu. Zinovyev, Luca Albergante, Jonathan Bac, 2019, 2019 International Joint Conference on Neural Networks (IJCNN).

Predicting genetic interactions from Boolean models of biological networks

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2015, bioRxiv.

Predicting genetic interactions from Boolean models of biological networks.

Emmanuel Barillot, Laurence Calzone, Andrei Zinovyev, 2015, Integrative biology : quantitative biosciences from nano to macro.

DeDaL: Cytoscape 3.0 app for producing and morphing data-driven and structure-driven network layouts

Emmanuel Barillot, Laurence Calzone, Andrei Yu. Zinovyev, 2015, bioRxiv.

Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision

Laurence Calzone, Loïc Paulevé, Vincent Noel, 2020, CMSB.

Geometrical Complexity of Data Approximators

Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, 2013, IWANN.

Representation and quantification Of Module Activity from omics data with rROMA

L. Calzone, L. Martignetti, A. Zinovyev, 2022, bioRxiv.

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Andrei Zinovyev, Ugur Dogrusoz, Emmanuel Barillot, 2020, Bioinform..

Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees

Alexander Chervov, Andrei Yu. Zinovyev, A. Zinovyev, 2021, 2021 International Joint Conference on Neural Networks (IJCNN).

Coloring panchromatic nighttime satellite images: Elastic maps vs. kernel smoothing and multivariate regression approach

N. Rybnikova, B. A. Portnov, E. M. Mirkes, 2020 .

Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks

José Lages, Andrei Zinovyev, Dima L Shepelyansky, 2017, bioRxiv.

PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling

Andrei Zinovyev, Emmanuel Barillot, Arnau Montagud, 2018, bioRxiv.

Interpreting pathways to discover cancer driver genes with Moonlight

Gabriel J. Odom, Gianluca Bontempi, H. Noushmehr, 2020, Nature Communications.

The second European interdisciplinary Ewing sarcoma research summit – A joint effort to deconstructing the multiple layers of a complex disease

Nathan C. Sheffield, P. Meltzer, P. Sorensen, 2016, Oncotarget.

Adaptation through the lense of single-cell multi-omics data: Comment on "Dynamic and thermodynamic models of adaptation" by A.N. Gorban et al.

A. Zinovyev, 2021, Physics of life reviews.

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks

Emmanuel Barillot, Carito Guziolowski, Andrei Yu. Zinovyev, 2009, AIAI Workshops.

Proteogenomic Characterization of Bladder Cancer Reveals Sensitivity to Apoptosis Induced by Tumor Necrosis Factor-related Apoptosis-inducing Ligand in FGFR3-mutated Tumors.

Y. Allory, F. Radvanyi, I. Bernard-Pierrot, 2023, European urology.

Computational Systems Biology of Cancer

Andrei Zinovyev, Emmanuel Barillot, Jean-Philippe Vert, 2020 .

Determining the optimal number of independent components for reproducible transcriptomic data analysis

E. Barillot, A. Zinovyev, L. Cantini, 2017, bioRxiv.

Four basic symmetry types in the universal 7-clusterstructure of 143 complete bacterial genomic sequences

Alexander N Gorban, A. N. Gorban, A. Zinovyev, 2004, q-bio/0410033.

Asymptotology of chemical reaction networks

Alexander N Gorban, A. N. Gorban, O. Radulescu, 2009, 0903.5072.

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

Emmanuel Barillot, Eric Bonnet, Laurence Calzone, 2013, BMC Systems Biology.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Inna Kuperstein, Emmanuel Barillot, Laurence Calzone, 2013, BMC Systems Biology.

OP-CBIO190984 2620..2622

E. Barillot, U. Dogrusoz, A. Mazein, 2020 .

Practical use of BiNoM: a biological network manager software.

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2013, Methods in molecular biology.

Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences

Alexander N. Gorban, Andrei Yu. Zinovyev, Tatyana G. Popova, 2005, Silico Biol..

Pruning, pooling and limiting steps in metabolic networks

Alexander N Gorban, A. Zinovyev, O. Radulescu, 2010 .

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell R packages

Andrei Zinovyev, Emmanuel Barillot, Eric Bonnet, 2016, bioRxiv.

Network biology elucidates metastatic colon cancer mechanisms

Inna Kuperstein, Andrei Zinovyev, A. Zinovyev, 2015, Cell cycle.

Author ' s personal copy Asymptotology of chemical reaction networks

Alexander N Gorban, A. Zinovyev, O. Radulescu, 2010 .

Ac ce pt ed m an us cr ip t Asymptotology of Chemical Reaction Networks

Alexander N Gorban, A. Zinovyev, O. Radulescu, 2009 .

Principal Graphs and Manifolds pdf

Alexander N. Gorban, Andrei Yu. Zinovyev, Alexander N Gorban, 2008, ArXiv.

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.

E. Barillot, U. Dogrusoz, A. Mazein, 2020, Bioinformatics.

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals

Emmanuel Barillot, Andrei Yu. Zinovyev, Urszula Czerwinska, 2018, LVA/ICA.

Omics data integration in computational biology viewed through the prism of machine learning paradigms

A. Zinovyev, Aziz Fouché, 2023, Frontiers Bioinform..

Transmorph: a unifying computational framework for modular single-cell RNA-seq data integration

A. Zinovyev, O. Delattre, Loic Chadoutaud, 2023, NAR genomics and bioinformatics.

Detection of miRNA regulatory effect on triple negative breast cancer transcriptome

Andrei Zinovyev, Emmanuel Barillot, Loredana Martignetti, 2015, BMC Genomics.

Local intrinsic dimensionality estimators based on concentration of measure

A. Zinovyev, Jonathan Bac, 2020, 2020 International Joint Conference on Neural Networks (IJCNN).

Bioinformatics and Computational Systems Biology of Cancer

E. Barillot, A. Zinovyev, Team Leader, 2018 .

Bioinformatics Applications Note Genome Analysis Control-free Calling of Copy Number Alterations in Deep-sequencing Data Using Gc-content Normalization

Jean-Philippe Vert, K. Bleakley, E. Barillot, 2022 .

Representation and quantification of module activity from omics data with rROMA

L. Martignetti, A. Zinovyev, I. Sermet-Gaudelus, 2023, bioRxiv.

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes.

P. Gestraud, E. Barillot, N. López-Bigas, 2014, Cell reports.

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

Jean-Philippe Vert, K. Bleakley, E. Barillot, 2010, Bioinform..

Classification of microarray data using gene networks

Jean-Philippe Vert, E. Barillot, A. Zinovyev, 2007, BMC Bioinformatics.

Network biology elucidates metastatic colon cancer mechanisms

A. Zinovyev, I. Kuperstein, S. Robine, 2015, Cell cycle.

Handbook of Research on Machine Learning Applications and Trends : Algorithms , Methods , and Techniques

Emilio Soria Olivas, José Rafael Magdalena Benedito, José David Martín Guerrero, 2009 .

scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics

A. Zinovyev, Loïc Paulevé, Laurence Calzone, 2023, bioRxiv.

Supplementary File 2 : Simulations of cell fate model Supplementary for PhysiBoSS : a multi-scale agent based modelling framework integrating physical dimension and cell signalling

E. Barillot, R. Heiland, A. Zinovyev, 2018 .

Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning

Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, 2016, Neural Networks.

Exploring the impact of social stress on the adaptive dynamics of COVID-19: Typing the behavior of naïve populations faced with epidemics

A. Zinovyev, E. Mirkes, I. Kastalskiy, 2023, Communications in Nonlinear Science and Numerical Simulation.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Sarah M. Keating, Maike K. Aurich, H. S. Hinton, 2019, Nature Protocols.

OCSANA: optimal combinations of interventions from network analysis

E. Barillot, E. Bonnet, A. Zinovyev, 2013, Bioinform..

Robust simplifications of multiscale biochemical networks

A. Zinovyev, Ovidiu Radulescu, Alexander N. Gorban, 2008, BMC Systems Biology.

Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors

Y. Pommier, E. Barillot, A. Zinovyev, 2016, Clinical Cancer Research.

Logical versus kinetic modeling of biological networks: applications in cancer research

Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone, 2018, Current Opinion in Chemical Engineering.

Data analysis with arbitrary error measures approximated by piece-wise quadratic PQSQ functions

Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, 2018, 2018 International Joint Conference on Neural Networks (IJCNN).

Piece-wise quadratic lego set for constructing arbitrary error potentials and their fast optimization pdf

Alexander N. Gorban, Eugenij Moiseevich Mirkes, Andrei Yu. Zinovyev, 2016, ArXiv.