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Andrei Yu. Zinovyev
- > Home > Persons > Andrei Yu. Zinovyev
Publications
- 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) - 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) - [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) - [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) - 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) - 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 - [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) - 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) - 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) - 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) - [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) - [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) - 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) - 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) - [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) - 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) - 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)
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