2017

  1. 1. Le Morvan M, Zinovyev A, Vert JP. NetNorM: Capturing Cancer-relevant Information in Somatic Exome Mutation Data with Gene Networks for Cancer Stratification and Prognosis. 2017. PLoS Computational Biology, in press.
  2. 2. Dorel M, Viara E, Barillot E, Zinovyev A and Kuperstein I. NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. Database (Oxford), 2017, 1-11.
  3. 3. Stoll G., Caron B., Viara E., Dugourd A., Zinovyev A., Naldi A., Kroemer G., Barillot E., Calzone L. MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinformatics 2017 btx123.
  4. 4. Cantini L., Caselle M., Forget A., Zinovyev A., Barillot E., Martignetti L. A review of computational approaches for the detection of microRNAs involved in cancer. 2017. Frontiers in Biosciences 22:1774-1791.
  5. 5. Ashoor H, Louis-Brennetot C, Janoueix-Lerosey I, Bajic VB, Boeva V. HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. Nucleic Acids Res. 2017, pii: gkw1319.
  6. 6. Naldi A., Larive R., Czerwinska U., Urbach S., Montcourrier P., Roy C., Solassol J., Freiss G., Coopman P., Radulescu O. Reconstruction and Signal Propagation Analysis of the Syk Signaling Network in Breast Cancer Cells. 2017. PLoS Computational Biology 13(3):e1005432.
  7. 7. Barillot E., Hupé P. Les Big data en oncologie : de la recherche fondamentale à des applications au bénéfice du patient. 2017. Les Annales des Mines - Réalités Industrielles 1:15-18.
  8. 8. Pérez-Rico Y.A., Boeva V., Mallory A.C., Bitetti A., Majello S., Barillot E., and Shkumatava A. Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Genome Research. 2017. Feb;27(2):259-268.
  9. 9. Kondratova M, Barillot E, Zinovyev A, Kuperstein I. Knowledge formalization and high-throughput data visualization using signaling network maps. In 'Bio-Molecular Modeling' book, Austin Publishing group, 2017 . [Book chapter]

2016

  1. 1. Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun JS, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M. Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of Dbait and PARP inhibitors. Clin Cancer Res. 2016, pii: clincanres.1193.2016. [Epub ahead of print]
  2. 2. Boeva V. Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. Front Genet. 2016. 7:24. Review.
  3. 3. Verlingue L, Dugourd A, Stoll G, Barillot E, Calzone L*, Londoño-Vallejo A.* A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion. Aging Cell. 2016 Sep 9. doi: 10.1111/acel.12504.
  4. 4. Gorban AN, Mirkes EM, Zinovyev A. Piece-wise quadratic approximations of arbitrary error functions for fast and robust machine learning. Neural Netw. 2016, 84:28-38.
  5. 5. Popova T, Manié E, Boeva V, Battistella A, Goundiam O, Smith NK, Mueller CR, Raynal V, Mariani O, Sastre-Garau X, Stern MH. Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications. Cancer Res. 2016. 76(7):1882-91.
  6. 6. Rougny A, Froidevaux C, Calzone L, Paulevé L. Qualitative dynamics semantics for SBGN process description. BMC Syst Biol. 2016. 10(1):42.
  7. 7. Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A. ROMA: Representation and Quantification of Module Activity from Target Expression Data. Front Genet. 2016. 7:18.
  8. 8. Kovar H., et al (46 authors). The second European interdisciplinary Ewing sarcoma research summit - A joint effort to deconstructing the multiple layers of a complex disease. Oncotarget 7(8):8613-24.
  9. 9. Iakovishina D, Janoueix-Lerosey I, Barillot E, Regnier M, Boeva V. SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. Bioinformatics. 2016. 32(7):984-92.
  10. 10. Brinda K, Boeva V, Kucherov G. RNF: a general framework to evaluate NGS read mappers. Bioinformatics. 2016. 32(1):136-9.
  11. 11. Jacob B., Haddock-Angelli T., Gershater M., de Mora K., Lizarazo M., Hollenhorst J., Rettberg R. and iGEM Interlab Study Contributors. Reproducibility of fluorescent expression from engineered biological constructs in E. coli. PloS ONE 11, no. 3 (2016): e0150182.
  12. 12. Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VS, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications. 2016; 7:12460.
  13. 13. The Computational Pan-Genomics Consortium (Includes V. Boeva). Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics. 2016. pii: bbw089.
  14. 14. Deveau P, Barillot E, Boeva V, Zinovyev A, Bonnet E. Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell packages. 2016. The R Journal 8:2, p.293-306.

2015

  1. 1. Moarii M, Boeva V, Vert JP, Reyal F. Changes in correlation between promoter methylation and gene expression in cancer. BMC Genomics. 2015. 16(1):873.
  2. 2. Cohen PAD, Martignetti L, Robine S., Barillot E., Zinovyev A., Calzone L. Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. 2015. PLoS Computational Biology 11(11):e1004571.
  3. 3. Kuperstein I, Robine S, Zinovyev A. Network biology elucidates metastatic colon cancer mechanisms. 2015. Cell Cycle 14(14):2189-90.
  4. 4. Dorel M, Barillot E, Zinovyev A, Kuperstein I. Network-based approaches for drug response prediction and targeted therapy development in cancer. 2015. Biochem Biophys Res Commun. 464(2):386-91.
  5. 5. Grünewald TG, Bernard V, Gilardi-Hebenstreit P, Raynal V, Surdez D, Aynaud MM, Mirabeau O, Cidre-Aranaz F, Tirode F, Zaidi S, Perot G, Jonker AH, Lucchesi C, Le Deley MC, Oberlin O, Marec-Bérard P, Véron AS, Reynaud S, Lapouble E, Boeva V, Frio TR, Alonso J, Bhatia S, Pierron G, Cancel-Tassin G, Cussenot O, Cox DG, Morton LM, Machiela MJ, Chanock SJ, Charnay P, Delattre O. Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite. Nat Genet. 2015 Sep;47(9):1073-1078.
  6. 6. Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. 2015. Oncogenesis 4:e160.
  7. 7. Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L. A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis. 2015. Cancer Res. 75(19):4042-52.
  8. 8. Zinovyev A. Overcoming Complexity of Biological Systems: from Data Analysis to Mathematical Modeling. Mathematical Modeling of Natural Phenomena 10(3), 186-205.
  9. 9. Naldi A, Monteiro PT, Müssel C; Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C. Cooperative development of logical modelling standards and tools with CoLoMoTo. 2015. Bioinformatics 1;31(7):1154-9.
  10. 10. Czerwinska U, Calzone L, Barillot E, Zinovyev A. DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. 2015. BMC Syst Biol. 14;9:46.
  11. 11. Nicolas Servant, Nelle Varoquaux, Bryan R Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome biology 16: 12.
  12. 12. Martignetti L, Tesson B, Almeida A, Zinovyev A, Tucker GC, Dubois T, Barillot E. Detection of miRNA regulatory effect on triple negative breast cancer transcriptome. 2015. BMC Genomics 16:S4.
  13. 13. Nicolas Servant, Julien Roméjon, Pierre Gestraud, Philippe La Rosa, Georges Lucotte, Séverine Lair, Virginie Bernard, Bruno Zeitouni, Fanny Coffin, Gérôme Jules-Clément, Florent Yvon, Alban Lermine, Patrick Poullet, Stéphane Liva, Stuart Pook, Tatiana Popova, Camille Barette, Francois Prud'homme, Jean-Gabriel Dick, Maud Kamal, Christophe Le Tourneau, Emmanuel Barillot, Philippe Hupé (2014) Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial. Frontiers in genetics 5: 05.
  14. 14. Calzone L, Barillot E, Zinovyev A. Predicting genetic interactions from Boolean models of biological networks. Integr Biol (Camb) 2015 May 11.
  15. 15. Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A. NaviCell Web Service for network-based data visualization. 2015. Nucleic Acids Res. 43(W1):W560-5.
  16. 16. Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E. The shortest path is not the one you know: application of biological network resources in precision oncology research. 2015. Mutagenesis 30(2):191-204.
  17. 17. Bonnet E., Calzone L. and Michoel T. Integrative multi-omics module network inference with Lemon-Tree. 2014. PLoS Computational Biology. PLoS Comput Biol. 2015. 11(2): e1003983.
  18. Conference paper: Gorban A.N. and Zinovyev A. Fast and user-friendly non-linear principal manifold learning by method of elastic maps. Proceedings of IEEE DSAA-2015 conference, 06-09/10/2015, Paris, France.
  19. Conference paper: Gorban A.N., Mirkes E.M., Zinovyev A. Robust principal graphs for data approximation. Proceedings of European Conference on Data Analysis-2015, 2-4/9/2015, Colchester, UK.

2014

  1. 1. Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Rio Frio T, Hupé P, Barillot E, Laes JF. Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. 2014. Bioinformatics pii: btu436.
  2. 2. Hocking TD, Boeva V, Rigaill G, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Richer W, Bourdeaut F, Suguro M, Seto M, Bach F, Vert JP. SegAnnDB: interactive Web-based genomic segmentation. 2014. Bioinformatics 30(11):1539-46.
  3. 3. da Rocha ST, Boeva V, Escamilla-Del-Arenal M, Ancelin K, Granier C, Matias NR, Sanulli S, Chow J, Schulz E, Picard C, Kaneko S, Helin K, Reinberg D, Stewart AF, Wutz A, Margueron R, Heard E. Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome. 2014. Mol Cell. 53(2):301-16.
  4. 4. Biton A., Bernard-Pierrot I., Lou Y., Krucker C., Chapeaublanc E., Rubio Perez C., Lopez Bigas N., Kamoun A., Neuzillet Y., Gestraud P., Grieco G., Rebouissou S., de Reyniès A., Benhamou S., Lebret T., Southgate J., Barillot E., Allory Y., Zinovyev A., Radvanyi F. Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. Cell Reports. 2014. 9(4):1235-45.
  5. 5. Chanrion M, Kuperstein I, Barriè re C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Biè che I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Né P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A, Robine S. Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. 2014. Nat Commun. 5:5005.
  6. 6. [Biological network modelling and precision medicine in oncology]. Calzone L, Kuperstein I, Cohen D, Grieco L, Bonnet E, Servant N, Hupé P, Zinovyev A, Barillot E. 2014. Bull Cancer. Suppl 1:S18-21. Review. French.
  7. 7. Waltemath D., Bergmann F.T., Chaouiya C., Czauderna T., Gleeson P., Goble C., Golebiewski M., Hucka M., Juty N., Krebs O., Le Novère N., Mi H., Moraru I.I., Myers C.J., Nickerson D., Olivier B.G., Rodriguez N., Schreiber F., Smith L., Zhang F., Bonnet E. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). 2014. Standards in Genomic Sciences 9: 3.

2013

  1. 1. Kuperstein I, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. 2013. BMC Syst Biol 7(1):100.
  2. 2. Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A, Delattre O. Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis. 2013. Nucleic Acids Res., 41(19):8853-71.
  3. 3. Vera-Licona P, Bonnet E, Barillot E, Zinovyev A. OCSANA: Optimal Combinations of Interventions from Network Analysis. 2013. Bioinformatics 15:29: 1571-1573.
  4. 4. Zinovyev A, Kuperstein I, Barillot E, Heyer W-D. Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps. 2013. PLoS Comput Biol 9(4): e1003016.
  5. 5. Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. 2013. BMC Syst Biol. 7(1):18.
  6. 6. Kutumova E, Zinovyev A, Sharipov R, Kolpakov F. Model composition through model reduction: a combined model of CD95 and NF-kappaB signaling pathways. 2013. BMC Syst Biol. 7(1):13.
  7. 7. Zinovyev A., Kairov U., Karpenyuk T., Ramanculov E. Blind Source Separation Methods For Deconvolution Of Complex Signals In Cancer Biology. 2013. Biochemical and Biophysical Research Communications 430(3), 1182-1187.
  8. 8. Zinovyev A. and Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:1471-1482.
  9. 9. Hocking T.D. , Schleiermacher G. , Janoueix-Lerosey I. , Boeva V. , Cappo J. , Delattre O., Bach F. and Vert J.-P. Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinformatics. 2013. 14(1):164.
  10. 10. Cazes A., Louis-Brennetot C., Mazot P., Dingli F., Lombard B., Boeva V., Daveau R., Cappo J., Combaret V., Schleiermacher G., Jouannet S., Ferrand S., Pierron G., Barillot E., Loew D., Vigny M., Delattre O.,Janoueix-Lerosey I. Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma. Cancer Res. 2013. 73(1):195-204.
  11. 11. Boeva V., Jouannet S., Daveau R., Combaret V., Pierre-Eugène C., Cazes A., Louis-Brennetot C., Schleiermacher G., Ferrand S.,Pierron G. , Lermine A., Rio Frio T., Raynal V., Vassal G., Barillot E., Delattre O. and Janoueix-Lerosey I. Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis. PLoS ONE, 2013, 8(8): e72182.
  12. 12. Ashoor H., Hérault A., Kamoun A., Radvanyi F., Bajic V.B., Barillot E. and Boeva V. HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. Bioinformatics. 2013 Oct 3.
  13. 13. Comet JP, Noual M, Richard A, Aracena J, Calzone L, Demongeot J, Kaufman M, Naldi A, Snoussi el H, Thieffry D. On circuit functionality in boolean networks. Bull Math Biol. 2013 75(6):906-19.
  14. 14. Grieco, L., Calzone, L., Bernard-Pierrot, I., Radvanyi, F., Kahn-Perlès, B., Thieffry, D. Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS Comput Biol. 2013 Oct;9(10):e1003286. Erratum in: PLoS Comput Biol. 2013 Nov;9(11).
  15. Chapter: Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. Practical Use of BiNoM: A Biological Network Manager Software. Methods Mol Biol. 2013;1021:127-46.
  16. Chapter: Cohen D, Kuperstein I, Barillot E, Zinovyev A, Calzone L. From a biological hypothesis to the construction of a mathematical model. Methods Mol Biol. 2013;1021:107-25.
  17. Chapter: Zinovyev A, Morozova N, Gorban A, Harel-Belan A. Mathematical modeling of microRNA-mediated mechanisms of translation repression. In MiRNA Cancer Regulation: Advanced Concepts, Bioinformatics and Systems Biology Tools (ed. Schmitz U, Wolkenhauer O, Vera J), Springer, 2013. pp. 189-224.
  18. Chapter: Popova T., Boeva V., Mani E., Rozenholc Y., Barillot E., Stern M.-H. Analysis of somatic alterations in cancer genome: from SNP arrays to Next Generation Sequencing. iConcept Press, 2013.

2012

  1. Book: Barillot E., Calzone L., Hupe P., Vert J.-P., Zinovyev A. Computational Systems Biology of Cancer . Chapman & Hall, CRC Mathematical & Computational Biology, 2012, 452 p.
  2. 1. Kutumova E.O., Zinovyev A., Sharipov R.N., Kolpakov F.A. [Application of model reduction methods for constructing a composite model of apoptosis signaling]. 2012. Math. Biol. i Bioinformatika 7(2):572-588 (In Russian).
  3. 2. Boeva V., Lermine A., Barette C., Guillouf C., Barillot E. Nebula - a web-server for advanced ChIP-seq data analysis. 2012. Bioinformatics 28(19):2517-9.
  4. 3. Ridinger-Saison M., Boeva V, Rimmelé P., Kulakovskiy I., Gallais I., Levavasseur B., Paccard C., Legoix-Né P., Morlé F., Nicolas A., Hupé P., Barillot E., Moreau-Gachelin F., Guillouf C. Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia. 2012. Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/22790984
  5. 4. Stoll G., Viara E., Barillot E. and Calzone L. Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm. 2012. BMC Systems Biology 6:116
  6. 5. Radulescu O, Gorban AN, Zinovyev A and Noel V. Reduction of dynamical biochemical reactions networks in computational biology. 2012. Frontiers in Genetics 3: 00131.
  7. 6. Pauwels E, Surdez D, Stoll G, Lescure A, Del Nery E, Delattre O, Stoven V. A Probabilistic Model for Cell Population Phenotyping Using HCS Data. 2012. PLoS One 7(8):e42715. (Link)
  8. 7. Haury AC, Mordelet F, Vera-Licona P, Vert JP. TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. 2012. BMC Syst Biol. 6:145. (Link)
  9. 8. Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. 2012. Nat Methods. 9(8):796-804
  10. 9. Kairov U., Karpenyuk T., Ramanculov E., Zinovyev A. Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures. 2012. Bioinformation 18(6):773-776.
  11. 10. Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A. Antagonism Pattern Detection between MicroRNA and Target Expression in Ewing's Sarcoma. 2012. PLoS One 7(7):e41770
  12. 11. Radulescu O, Gorban AN, Zinovyev A and Noel V. Reduction of dynamical biochemical reactions networks in computational biology. 2012. Frontiers in Genetics 3: 00131.
  13. 12. Morozova N., Zinovyev A., Nonne N., Pritchard L.-L., Gorban A.N., Harel-Bellan A. Kinetic signatures of microRNA modes of action. 2012. RNA 18(9): 032284.
  14. 13. Pinna G., Zinovyev A., Araujo N., Morozova N. and Harel-Bellan A. Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells. 2012. Mathematical Modelling of Natural Phenomena 7(01):337-368
  15. 14. Boeva V., Popova T., Bleakley K., Chiche P., Cappo J., Schleiermacher G., Janoueix-Lerosey I., Delattre O., and Barillot E. Control-FREEC: a tool for assessing copy number and allelic content using next generation sequencing data. 2012. Bioinformatics 28:3, 423-425.
  16. 15. Martignetti L., Zinovyev A., Barillot E. Identification of shortened 3' untranslated regions from expression arrays. 2012. Journal of Bioinformatics and Computational Biology 10:1241001.
  17. 16. Zinovyev A., Fourquet S., Tournier L., Calzone L. and Barillot E. Cell death and life in cancer: mathematical modeling of cell fate decisions. 2012. Adv Exp Med Biol 736:261-74.

2011

    1. 1. Brancotte B., Biton A., Bernard-Pierrot I., Radvanyi F., Reyal F., Cohen-Boulakia S. Gene List significance at-a-glance with GeneValorization. Bioinformatics 27:8:1187-9 (2011)
    2. Encyclopedia article: Calzone L. Cell cycle transition, detailed regulation of the restriction point. Encyclopedia of Systems Biology. Springer Major Reference Works in http://refworks.springer.com/Systems_Biology
    3. 2. Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E. Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics. 2011 Jan 15;27(2):268-9. Epub 2010 Nov 15.
    4. 3. Dimitrova E., Garcia-Puente L.D., Hinkelmann F., Jarrah A.S., Laubenbacher R., Stigler B., Stillman M. and Vera-Licona P. Parameter estimation for Boolean models of biological networks. 2011. Journal of Theoretical Computer Science 412(26).

    2010

      1. 1. Stoll G., Bischofberger M., Rougemont J., Naef F. Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico. 2010. Biosystems 102(1), 3-10. (PDF)
      2. 2. Orlando D., Al, Fink T. Detecting separate time scales in genetic expression data. 2010. BMC Genomics 11, 381.
      3. 3. Ahnert S, Al, Fink T. Self-assembly, modularity and physical complexity. 2010. Physical Review E 82, 026117.
      4. 4. Lepelletier Y, Zollinger R, Ghirelli C, Raynaud F, Hadj-Slimane R, Cappuccio A, Hermine O, Liu YJ, Soumelis V. Toll-like receptor control of glucocorticoid-induced apoptosis in human plasmacytoid predendritic cells (pDCs). 2010. Blood 4;116(18):3389-97. (PDF)
      5. 5. Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ. Deep and wide digging for binding motifs in ChIP-Seq data. 2010. Bioinformatics 15;26(20):2622-3.
      6. 6. Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-ne P, Nicolas A, Delattre O, Barillot E. SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. 2010. Bioinformatics 1;26(15):1895-6. (Link)
      7. 7. Baker SG, Cappuccio A, Potter JD. Research on early-stage carcinogenesis: are we approaching paradigm instability? 2010. J Clin Oncol 10;28(20):3215-8. (PDF)
      8. 8. Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. 2010. Nucleic Acids Res. 38(11):e126. (Link)
      9. 9. Baumuratova T, Surdez D, Delyon B, Stoll G, Delattre O, Radulescu O, Siegel A. Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. 2010. BMC Syst Biol 2;4(1):146. (Link)
      10. 10. Guziolowski C, Blachon S, Baumuratova T, Stoll G, Radulescu O, Siegel A. Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. 2010. IEEE/ACM Trans Comput Biol Bioinform Aug 19. [Epub ahead of print]. (PDF)
      11. 11. Dimitrova E., Vera-Licona P., McGee J., Laubenbacher R.. Discretization of Time Series Data. 2010. Journal of Computational Biology 17(6): 853-868.
      12. 12. Gorban A.N., Zinovyev A. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. 2010. Int J Neural Syst 20(3):219-32 (PDF)
      13. 13. Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A. 2010. Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol 5;6(3):e1000702. (Link)
      14. 14. Zinovyev A, Morozova N, Nonne N, Barillot E, Harel-Bellan A, Gorban AN. Dynamical modeling of microRNA action on the protein translation process. 2010. BMC Systems Biology 4:13. (Link)
      15. 15. Gorban AN, Radulescu O, Zinovyev AY. Asymptotology of chemical reaction networks. 2010. Chemical Engineering Science 65, 2310-2324. (PDF)

      2009

        1. 1. Baker S.G., Soto A.M., Sonnenschein C., Cappuccio A., Potter J.D., Kramer B.S. Plausibility of stromal initiation of epithelial cancers without a mutation in the epithelium: a computer simulation of morphostats. 2009. BMC Cancer 23(9):89 (Link)
        2. 2. Le Novere N. et al. The Systems Biology Graphical Notation. 2009. Nat Biotechnol 27(8):735-41. (Link)
        3. 3. Barillot E., Calzone L., Zinovyev A. Biologie des Systemes du Cancer. Med Sci (Paris). 2009. 25(6-7):601-7.
        4. 4. Novikov E., Barillot E. Model selection in the reconstruction of regulatory networks from time-series data. 2009. BMC Res Notes 2:68.
        5. 5. Guillon N, Tirode F, Boeva V, Zinovyev A, Barillot E, Delattre O. The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. 2009. PLoS ONE 4(3):e4932. (Link)
        6. 6. Aebersold, R. et al., Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research. 2009. Molecular Oncology 3(1): 9-17. (PDF)

        2008

          1. Book: Gorban A, Kegl B, Wunch D, Zinovyev A. (eds.) Principal Manifolds for Data Visualisation and Dimension Reduction. 2008. Lecture Notes in Computational Science and Engeneering 58, p.340.
          2. 1. Radulescu O., Gorban A., Zinovyev A., Lilienbaum A. Robust simplifications of multiscale biochemical networks. 2008. BMC Systems Biology 2:86 (Link)
          3. 2. Ahnert S.E. and Fink T.M.A. Clustering signature classifies directed networks. 2008. Physical Review E 78, 036112 (PDF)
          4. 3. Dequeant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquie O. Comparison of pattern detection methods in microarray time series of the segmentation clock. 2008. PLoS ONE 3(8):e2856. (Link)
          5. 4. Ahnert S.E., Garlaschelli D., Fink T.M.A. and Caldarelli G. Applying weighted network measures to microarray distance matrices. J. Phys. A: Math. Theor. 41 (2008) 224011 (PDF)
          6. 5. Rapaport F., Barillot E., Vert J.-P. Classification of arrayCGH data using fused SVM. 2008. Bioinformatics 24(13), i375-82. (PDF)
          7. 6. Novikov E, Barillot E. Regulatory network reconstruction using an integral additive model with flexible kernel functions. 2008. BMC Syst Biol. 2:8. (PDF)
          8. 7. Ahnert S.E, Fink T.M.A and Zinovyev A. 2008. How much non-coding DNA do eukaryotes require? Journal of Theoretical Biology, doi:10.1016/j.jtbi.2008.02.005 (PDF)
          9. 8. Calzone L., Gelay A., Zinovyev A., Radvanyi F., Barillot E. A comprehensive modular map of molecular interactions in RB/E2F pathway. 2008. Molecular Systems Biology 4:174 doi:10.1038/msb.2008.7 (Link) (in Top Downloads of Molecular Systems Biology!)
          10. 9. Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for using and analyzing biological networks. 2008. Bioinformatics 24(6):876-877 (PDF)
          11. 10. Rapaport F, Barillot E, Vert JP. Bioinformatics. Classification of arrayCGH data using fused SVM. 2008 Jul 1;24(13):i375-82.

          2007

            1. 1. Elati, M., Neuvial, P., Bolotin-Fukuhara, M., Barillot, E., Radvanyi, F., Rouveirol, C. LICORN: learning cooperative regulation networks from gene expression data. 2007. Bioinformatics 23:18, p.2407-2414 (PDF)
            2. 2. Fink, T. M., Willbrand, K., Brown, F.C.S. 1-D random landscapes and non-random data series. 2007. EPL, 79, 38006 (PDF)
            3. 3. Ahnert, S. E., Garlaschelli, D., Fink, T. M., Caldarelli, G. Ensemble approach to the analysis of weighted networks. 2007. Phys Rev E 76, 016101 (PDF)
            4. 4. Calzone L., Thieffry D., Tyson J., Novak B. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos. 2007. Molecular Systems Biology 3 Article number: 131(Link)
            5. 5. Rapaport F., Zinovyev A., Dutreix M., Barillot E., Vert J.-P. Classification of microarray data using gene networks. 2007. BMC Bioinformatics 8:35. (Link)

Highlights