1. Fourmentin, Eric; Danchin, Antoine. (2010) A sequel to "Cells need safety valves" [Internet]. Version 7. Symplectic Biology.

2. Silva-Rocha, R. and de Lorenzo V (2010) Noise and robusteness in prokaryotic regulatory networks. Ann Rev Microbiol 64:257-75.

3. Kersey P., Medigue C., Ouzounis C., De Lorenzo V. (2010) Life under the microscope. Research Media Ldt.

4. Postic, Guillaume; Danchin, Antoine; Mechold, Undine. (2010) Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae [Internet]. Version 54. Symplectic Biology.

5. Danchin A. (2010) A path from predation to mutualism. Mol Microbiol. 77(6):1346-50.

6. Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E. (2010) The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res. 38(12):3857-68.

7. Gilles Vieira, Victor Sabarly, Pierre-Yves Bourguignon, Maxime Durot, François Le Fèvre,
Damien Mornico, David Vallenet, Odile Bouvet, Erick Denamur, Vincent Schachter & Claudine Médigue.
The core and pan-metabolism in the Escherichia coli species. Journal of Bacteriology.01192-10v1

8. Danchin A.(2010) Science and Arsenic Fool's Gold: A Toxic Broth. Journal of Cosmology 13, 3617-3620.

9. PM Binder, A Danchin (2011) Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life? EMBO Reports.

10. A Danchin (2011) Les gènes du démon de Maxwell: est-il possible de construire une usine cellulaire ? Maxwell's demon's genes: Can we build a cell factory? Comptes Rendus de l'Académie des Sciences, Chimie 14: 413-419.

11. Martínez-García, E., Calles, B., Arévalo-Rodríguez, M. and de Lorenzo, V. (2011) pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiology 11: 38.

12. Chavarría, M., Santiago, C., Platero, R., Krell, T., Casasnovas, J.M. and de Lorenzo, V. (2011) Fructose 1-Phosphate is the preferred effector of the metabolic regulator Cra of Pseudomonas putida. J. Biol. Chem. 286: 9351-9359.

13. de las Heras, A. and de Lorenzo, V. (2011). Cooperative amino acid changes shift the response of the s54-dependent regulator XylR from natural m-xylene towards xenobiotic 2,4-dinitrotoluene. Mol Microbiol 79: 1248-1259.

14. Milanesio, P., Arce, A., Muñoz, A., Calles, B. and de Lorenzo, V. (2011) Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. Environ Microbiol 13: 324-39.

15. Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn M C Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A P Martins dos Santos and Jing Wang (2011) Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC Systems Biology 5:83.

16. H Rohde, J Qin, Y Cui, D Li, NJ Loman, M Hentschke, W Chen, Fei Pu, Y Peng, J Li, F Xi, S Li, Y Li, Z Zhang, X Yang, M Zhao, Peng Wang, Y Guan, Z Cen, X Zhao, M Christner, R Kobbe, S Loos, J Oh, L Yang, A Danchin, GF Gao, Y Song, Y Li, H Yang, J Wang, J Xu, the E. coli O104:H4 Genome Analysis Crowd-sourcing consortium, MJ Pallen, J Wang, M Aepfelbacher, R Yang (2011) Open-source genomics of an isolate from a german family outbreak of Shiga-toxin-producing Escherichia coli O104:H4. New England Journal of Medicine

17. Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M, Petty NK, Kingsley RA, Bäumler AJ, Nuccio SP, Contreras I, Santiviago CA, Maskell D, Barrow P, Humphrey T, Nastasi A, Roberts M, Frankel G, Parkhill J, Dougan G, Thomson NR (2011) PLoS Pathog. 7(8):e1002191

18. K. Yizhak, T. Tuller, B. Papp, E. Ruppin (2011) Metabolic modeling of endosymbiont genome reduction on a temporal scale. Molecular Systems Biology 7: 479.

19. de las Heras, A., Chavarría, M. and de Lorenzo V (2011). Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation. Mol Microbiol 82: 287-299

20. Silva-Rocha, R. and de Lorenzo, V. (2011) A composite feed forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations. Mol BioSys 7: 2982-2990.

21. Valls, M., Silva-Rocha, R., Cases, I., Muñoz, A., and de Lorenzo, V. (2011) Functional analysis of the integration host factor site of the s54 Pu promoter of Pseudomonas putida by in vivo UV imprinting. Mol Microbiol 82 (3): 591–601

22. Martínez-Rodriguez, E., De Lorenzo, V. (2011) Engineering multiple genomic deletions in Gram-negative bacteria: Analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environmental Microbiology and Environmental Microbiology Reports. 13: 2702 - 16

23. Silva-Rocha, R., de Lorenzo, V. (2011). Implementing an OR-NOT (ORN) logic gate with components the SOS regulatory network of Escherichia coli. Molecular BioSystems. 7: 2389 -96

24. Silva-Rocha R, Tamames J, dos Santos VM and de Lorenzo V (2011) The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol. 13: 2389 - 4402

25. Pflüger-Grau, K, Chavarría, M. and de Lorenzo, V. (2011) The interplay of the EIIANtr component of the nitrogen-related phosphotransferase system (PTSNtr) of Pseudomonas putida with pyruvate dehydrogenase. Bioch. Biophys. Acta. 1810: 995 - 1005

26. de las Heras, A. and de Lorenzo, V. (2011). In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Analyt. Bioanalyt. Chem. 400:1093-1104

27. Papanikolaou N, Pafilis E, Nikolaou S, Ouzounis CA, Iliopoulos I, Promponas VJ. (2011) BioTextQuest: A Web-based Biomedical Text Mining Suite for Concept Discovery. Bioinformatics (doi: 10.1093/bioinformatics/btr564).

28. Aristeidis Kallimanis, Eugenia Karabika, Konstantinos Mavromatis, Alla Lapidus, Kurt M. LaButti, Konstantinos Liolios, Natalia Ivanova, Lynne Goodwin, Tanja Woyke, Athanasios D. Velentzas, Angelos Perisynakis, Christos C. Ouzounis, Nikos C. Kyrpides, Anna I. Koukkou, Constantin Drainas (2011) Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1. Standards in Genomic Sciences 5:1.

29. Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A. (2011) UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res. doi: 10.1093/nar/gkr1023

30. Rafael Alcantara; Kristian B. Axelsen; Anne Morgat; Eugeni Belda; Elisabeth Coudert; Alan Bridge; Hong Cao; Paula de Matos; Marcus Ennis; Steve Turner; Gareth Owen; Lydie Bougueleret; Ioannis Xenarios; Christoph Steinbeck (2011) Rhea - a manually curated resource of biochemical reactions. Nucleic Acids Research 2011; doi: 10.1093/nar/gkr1126

31. A Danchin, PM Binder, S Noria (2011) Antifragility and tinkering in biology (and in business): Flexibility provides an efficient epigenetic way to manage risk.Genes2: 998-1016; doi:10.3390/genes2040998.

32. G Postic, A Danchin, U Mechold (2011) Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae.RNA. doi:10.1261/rna.029132.111

33. A. Danchin (2012)Scaling up Synthetic Biology: Do not forget the chassis.FEBS Letters.doi: 10.1016/j.febslet.2011.12.024.

34. Stefan Engelen, David Vallenet, Claudine Medigue, Antoine Danchin (2012)Distinct co-evolution patterns of genes associated to bacterial DNA polymerase III DnaE and PolC.BMC Genomics 13:69