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Conceptual sequel to biological expeditions at the time of global changes.

Danchin A.

Environ Microbiol Rep. 2018 Dec 4. doi: 10.1111/1758-2229.12722. [Epub ahead of print] No abstract available.


[Revisiting the origins of life: from atoms to molecules, reproduction, then replication].

Danchin A.

Med Sci (Paris). 2018 Oct;34(10):857-864. doi: 10.1051/medsci/2018212. Epub 2018 Nov 19. French. No abstract available.


Revisiting the methionine salvage pathway and its paralogues.

Sekowska A, Ashida H, Danchin A.

Microb Biotechnol. 2018 Oct 10. doi: 10.1111/1751-7915.13324. [Epub ahead of print]


No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects.

Danchin A, Ouzounis C, Tokuyasu T, Zucker JD.

Microb Biotechnol. 2018 Jul;11(4):588-605. doi: 10.1111/1751-7915.13284. Epub 2018 May 28.


Bacteria in the ageing gut: did the taming of fire promote a long human lifespan?

Danchin A.

Environ Microbiol. 2018 May 4. doi: 10.1111/1462-2920.14255. [Epub ahead of print]


Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma.

Wang Y, Zhu FC, He LS, Danchin A.

Nucleic Acids Res. 2018 Mar 16;46(5):2197-2203. doi: 10.1093/nar/gky045.


Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement.

Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EPC, Sekowska A, Vallenet D.

Microb Biotechnol. 2018 Jan;11(1):3-17. doi: 10.1111/1751-7915.13043.


The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian.

He LS, Zhang PW, Huang JM, Zhu FC, Danchin A, Wang Y.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01965-17. doi: 10.1128/AEM.01965-17. Print 2018 Jan 1.


Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.

Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V.

Nat Chem Biol. 2017 Sep 19;13(10):1137. doi: 10.1038/nchembio1017-1137c. No abstract available.


The contribution of microbial biotechnology to economic growth and employment creation.

Timmis K, de Lorenzo V, Verstraete W, Ramos JL, Danchin A, Brüssow H, Singh BK, Timmis JK.

Microb Biotechnol. 2017 Sep;10(5):1137-1144. doi: 10.1111/1751-7915.12845. Epub 2017 Sep 4.


The contribution of microbial biotechnology to sustainable development goals.

Timmis K, de Vos WM, Ramos JL, Vlaeminck SE, Prieto A, Danchin A, Verstraete W, de Lorenzo V, Lee SY, Brüssow H, Timmis JK, Singh BK.

Microb Biotechnol. 2017 Sep;10(5):984-987. doi: 10.1111/1751-7915.12818. Epub 2017 Aug 25.


From chemical metabolism to life: the origin of the genetic coding process.

Danchin A.

Beilstein J Org Chem. 2017 Jun 12;13:1119-1135. doi: 10.3762/bjoc.13.111. eCollection 2017. Review.


Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota.

Danchin A, Braham S.

Microb Biotechnol. 2017 Jul;10(4):688-701. doi: 10.1111/1751-7915.12722. Epub 2017 Jun 14.


Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.

Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V.

Nat Chem Biol. 2017 Aug;13(8):858-866. doi: 10.1038/nchembio.2397. Epub 2017 Jun 5. Erratum in: Nat Chem Biol. 2017 Sep 19;13(10 ):1137.


Generation of mutation hotspots in ageing bacterial colonies.

Sekowska A, Wendel S, Fischer EC, Nørholm MHH, Danchin A.

Sci Rep. 2016 Dec 5;6(1):2. doi: 10.1038/s41598-016-0005-4.


Coping with inevitable accidents in metabolism.

Danchin A.

Microb Biotechnol. 2017 Jan;10(1):57-72. doi: 10.1111/1751-7915.12461. Epub 2016 Dec 29. Review.


Microbial Biotechnology-2020.

Timmis K, Ramos JL, de Vos W, Vlaeminck S, Prieto A, Danchin A, Verstraete W, de Lorenzo V.

Microb Biotechnol. 2016 Sep;9(5):529. doi: 10.1111/1751-7915.12403. Epub 2016 Aug 11. No abstract available.


Unknown unknowns: essential genes in quest for function.

Danchin A, Fang G.

Microb Biotechnol. 2016 Sep;9(5):530-40. doi: 10.1111/1751-7915.12384. Epub 2016 Jul 20. Review.


Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod bathynomus sp.

Wang Y, Huang JM, Wang SL, Gao ZM, Zhang AQ, Danchin A, He LS.

Environ Microbiol. 2016 Sep;18(8):2646-59. doi: 10.1111/1462-2920.13411. Epub 2016 Aug 5.


Nature or manufacture: What should we fear most?

Danchin A.

C R Biol. 2016 Jul-Aug;339(7-8):329-35. doi: 10.1016/j.crvi.2016.05.001. Epub 2016 May 31. Review.


From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions.

Nikel PI, Chavarría M, Danchin A, de Lorenzo V.

Curr Opin Chem Biol. 2016 Oct;34:20-29. doi: 10.1016/j.cbpa.2016.05.011. Epub 2016 May 27. Review.


Reminder to deposit DNA sequences.

Blaxter M, Danchin A, Savakis B, Fukami-Kobayashi K, Kurokawa K, Sugano S, Roberts RJ, Salzberg SL, Wu CI.

Science. 2016 May 13;352(6287):780. doi: 10.1126/science.aaf7672. Epub 2016 May 11. No abstract available.


From function to structure take the archaeal TRAM.

Danchin A.

Environ Microbiol. 2016 Sep;18(9):2776-8. doi: 10.1111/1462-2920.13300. Epub 2016 Apr 28. No abstract available.


The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.

Belda E, van Heck RG, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins Dos Santos VA, de Lorenzo V, Danchin A, Médigue C.

Environ Microbiol. 2016 Oct;18(10):3403-3424. doi: 10.1111/1462-2920.13230. Epub 2016 Apr 28.


Confidence, tolerance, and allowance in biological engineering: the nuts and bolts of living things.

Porcar M, Danchin A, de Lorenzo V.

Bioessays. 2015 Jan;37(1):95-102. doi: 10.1002/bies.201400091. Epub 2014 Oct 27. Review.


Chemical reactivity drives spatiotemporal organisation of bacterial metabolism.

de Lorenzo V, Sekowska A, Danchin A.

FEMS Microbiol Rev. 2015 Jan;39(1):96-119. doi: 10.1111/1574-6976.12089. Epub 2014 Dec 4. Review.


Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP.

PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.


The logic of metabolism and its fuzzy consequences.

Danchin A, Sekowska A.

Environ Microbiol. 2014 Jan;16(1):19-28. doi: 10.1111/1462-2920.12270. Epub 2013 Oct 6. Review.


Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis.

Chan CM, Danchin A, Marlière P, Sekowska A.

Environ Microbiol. 2014 Jan;16(1):101-17. doi: 10.1111/1462-2920.12210. Epub 2013 Aug 15.


An updated metabolic view of the Bacillus subtilis 168 genome.

Belda E, Sekowska A, Le Fèvre F, Morgat A, Mornico D, Ouzounis C, Vallenet D, Médigue C, Danchin A.

Microbiology. 2013 Apr;159(Pt 4):757-70. doi: 10.1099/mic.0.064691-0. Epub 2013 Feb 21.


From essential to persistent genes: a functional approach to constructing synthetic life.

Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A.

Trends Genet. 2013 May;29(5):273-9. doi: 10.1016/j.tig.2012.11.001. Epub 2012 Dec 6.


Linking selenium biogeochemistry to the sulfur-dependent biological detoxification of arsenic.

Couture RM, Sekowska A, Fang G, Danchin A.

Environ Microbiol. 2012 Jul;14(7):1612-23. doi: 10.1111/j.1462-2920.2012.02758.x. Epub 2012 Apr 20. Review.


Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC.

Engelen S, Vallenet D, Médigue C, Danchin A.

BMC Genomics. 2012 Feb 14;13:69. doi: 10.1186/1471-2164-13-69.


Identification of a novel nanoRNase in Bartonella.

Liu MF, Cescau S, Mechold U, Wang J, Cohen D, Danchin A, Boulouis HJ, Biville F.

Microbiology. 2012 Apr;158(Pt 4):886-95. doi: 10.1099/mic.0.054619-0. Epub 2012 Jan 19.


3'-5' phosphoadenosine phosphate is an inhibitor of PARP-1 and a potential mediator of the lithium-dependent inhibition of PARP-1 in vivo.

Toledano E, Ogryzko V, Danchin A, Ladant D, Mechold U.

Biochem J. 2012 Apr 15;443(2):485-90. doi: 10.1042/BJ20111057.


Scaling up synthetic biology: Do not forget the chassis.

Danchin A.

FEBS Lett. 2012 Jul 16;586(15):2129-37. doi: 10.1016/j.febslet.2011.12.024. Epub 2012 Jan 2. Review.


Synthetic biology's flywheel.

Danchin A.

EMBO Rep. 2012 Feb 1;13(2):92. doi: 10.1038/embor.2011.253. No abstract available.


Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

Wang Y, Yang JK, Lee OO, Li TG, Al-Suwailem A, Danchin A, Qian PY.

PLoS One. 2011;6(12):e29149. doi: 10.1371/journal.pone.0029149. Epub 2011 Dec 21.


Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae.

Postic G, Danchin A, Mechold U.

RNA. 2012 Jan;18(1):155-65. doi: 10.1261/rna.029132.111. Epub 2011 Nov 23.


The ten grand challenges of synthetic life.

Porcar M, Danchin A, de Lorenzo V, Dos Santos VA, Krasnogor N, Rasmussen S, Moya A.

Syst Synth Biol. 2011 Jun;5(1-2):1-9. doi: 10.1007/s11693-011-9084-5. Epub 2011 Aug 5.


Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.

Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R; E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium.

N Engl J Med. 2011 Aug 25;365(8):718-24. doi: 10.1056/NEJMoa1107643. Epub 2011 Jul 27.


Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life?

Binder PM, Danchin A.

EMBO Rep. 2011 Jun;12(6):495-9. doi: 10.1038/embor.2011.83. Epub 2011 May 6. No abstract available.


Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea.

Wang Y, Yang J, Lee OO, Dash S, Lau SC, Al-Suwailem A, Wong TY, Danchin A, Qian PY.

ISME J. 2011 Oct;5(10):1652-9. doi: 10.1038/ismej.2011.42. Epub 2011 Apr 28.


Life in the cold: a proteomic study of cold-repressed proteins in the antarctic bacterium pseudoalteromonas haloplanktis TAC125.

Piette F, D'Amico S, Mazzucchelli G, Danchin A, Leprince P, Feller G.

Appl Environ Microbiol. 2011 Jun;77(11):3881-3. doi: 10.1128/AEM.02757-10. Epub 2011 Apr 8.


Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk.

Danchin A, Binder PM, Noria S.

Genes (Basel). 2011 Nov 29;2(4):998-1016. doi: 10.3390/genes2040998.


Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125.

Wilmes B, Kock H, Glagla S, Albrecht D, Voigt B, Markert S, Gardebrecht A, Bode R, Danchin A, Feller G, Hecker M, Schweder T.

Appl Environ Microbiol. 2011 Feb;77(4):1276-83. doi: 10.1128/AEM.01750-10. Epub 2010 Dec 23.


Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli.

Krin E, Danchin A, Soutourina O.

BMC Microbiol. 2010 Oct 29;10:273. doi: 10.1186/1471-2180-10-273.


A path from predation to mutualism.

Danchin A.

Mol Microbiol. 2010 Sep;77(6):1346-50.


Motivated research.

Danchin A.

EMBO Rep. 2010 Jul;11(7):488. doi: 10.1038/embor.2010.85. No abstract available.


The Trw type IV secretion system of Bartonella mediates host-specific adhesion to erythrocytes.

Vayssier-Taussat M, Le Rhun D, Deng HK, Biville F, Cescau S, Danchin A, Marignac G, Lenaour E, Boulouis HJ, Mavris M, Arnaud L, Yang H, Wang J, Quebatte M, Engel P, Saenz H, Dehio C.

PLoS Pathog. 2010 Jun 10;6(6):e1000946. doi: 10.1371/journal.ppat.1000946.

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