2019-PRESENT:
BIBLIOGRAPHY, ABSTRACTS, COMMENTS| PHILOSOPHIE | HISTORY OF BIOLOGY | PHILOSOPHY |
| 2019-PRESENT:
BIBLIOGRAPHY, ABSTRACTS, COMMENTS |
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Liste des publications
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Selected publications |
Publication list
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Peer-reviewed publications are indicated in red
Publications in the domain of Philosophy, History of Sciences and Ethics
Publications listed at Google Scholar
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Amann RI, Baichoo S, Blencowe BJ, Bork P,
Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG,
Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM,
Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK,
Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides
NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN,
Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra
R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R,
Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock
GM, White O, Whitman WB, Xenarios I Consent insufficient for data release—Response. Science (2019) 364: 446 doi: 10.1126/science.aax7509 |
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Iliopoulos I, Ananiadou S, Danchin A,
Ioannidis JP, Katsikis PD, Ouzounis CA, Promponas VJ Hypothesis, analysis and synthesis, it's all Greek to me eLife (2019) 8: e43514 doi: 10.7554/eLife.43514 10.1111/1751-7915.13324 |
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Iliopoulos I, Ananiadou S, Danchin A, Ioannidis JP, Katsikis PD,
Ouzounis CA, Promponas VJ Preprint with more details Hypothesis, analysis and synthesis, it's all Greek to me BioRxiv 561175 doi: 10.1101/561175. |
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A Sekowska, H Ashida, A Danchin Revisiting the methionine salvage pathway and its paralogues Microb Biotechnol. (2019) 12: 77-97 doi: 10.1111/1751-7915.13324 |
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A Danchin Conceptual sequel to biological expeditions at the time of global changes Environ Microbiol Rep. (2019) 11: 38-40 doi:10.1111/1758-2229.12722 |
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Frendorf PO, Lauritsen I, Sekowska A,
Danchin A, Nørholm MHH Mutations in the global transcription factor CRP/CAP: insights from experimental evolution and deep sequencing. Comput Struct Biotechnol J. (2019) 17: 730-736 doi: 10.1016/j.csbj.2019.05.009. |
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Amann RI, Baichoo S, Blencowe BJ, Bork P,
Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG,
Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM,
Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK,
Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides
NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN,
Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra
R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R,
Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock
GM, White O, Whitman WB, Xenarios I Toward unrestricted use of public genomic data. Science (2019) 363: 350-352 doi: 10.1126/science.aaw1280 |
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G Boël, O Danot, V de Lorenzo, A Danchin Omnipresent Maxwell’s demons orchestrate information management in living cells Microb Biotechnol. (2019) 12: 210-242 doi: 10.1111/1751-7915.13378 |
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Z Li, Q Pan, Y Xiao, X Fang X, R Shi, C Fu,
A Danchin, C You Deciphering global gene expression and regulation strategy in Escherichia coli during carbon limitation Microb Biotechnol. (2019) 12: 360-376 doi:10.1111/1751-7915.13343 |
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Timmis K, Cavicchioli R, Garcia JL, Nogales
B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK,
Handelsman J, de Lorenzo V, Pruzzo C, Timmis J, Martín JLR,
Verstraete W, Jetten M, Danchin A, Huang W, Gilbert J, Lal R,
Santos H, Lee SY, Sessitsch A, Bonfante P, Gram L, Lin RTP, Ron E,
Karahan ZC, van der Meer JR, Artunkal S, Jahn D, Harper L The urgent need for microbiology literacy in society Environ Microbiol. (2019) 21: 1513-1528 doi: 10.1111/1462-2920.14611 |
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Danchin A, Nikel PI Why nature chose potassium J Mol Evol. (2019) 87: 271-288 doi: 10.1007/s00239-019-09915-2 |
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Brown, Peter, Tan, Aik-Choon, El-Esawi,
Mohamed A. et al. RELISH Consortium Large expert-curated database for benchmarking document similarity detection in biomedical literature search Database (2019) baz085 doi: 10.1093/database/baz085 |
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V Courtier-Orgogozo, A Danchin, P-H Gouyon, C Boëte Preprint Evaluating the probability of CRISPR-based gene drive contaminating another species BioRxiv 776609 doi: 10.1101/776609. |
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| P Lubrano, A Danchin, CG
Acevedo-Rocha From minimal to minimized genomes: Functional design of microbial cell factories pp. 177-210 In: Minimal Cells: Design, Construction, Biotechnological Applications (2019) edited by Alvaro R. Lara, G.Gosset Springer ISBN: 978-3-030-31897-0 |
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A Danchin
Origin
of the first cells: the engineer’s point of view
Encyclopédie de l'environnement. UGA Éditions, Grenoble
2020 Chromosome length and allometry / SARS-CoV-2
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Lian CA, Yan GY, Huang JM, Danchin A, Wang Y
and LS He Genomic characterization of a novel gut symbiont from the hadal snailfish Front Microbiol (2020) 10: 2978 doi: 10.3389/fmicb.2019.02978 |
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Danchin A, Ng TWP, Turinici, G A new transmission route for the propagation of the SARS-CoV-2 coronavirus Biology (Basel) (2020) doi: 10.1111/1462-2920.15487. |
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Danchin A, Sekowska A, You CY One-carbon metabolism, folate, zinc and translation Microbial Biotechnology (2020) 13: 899-925 doi: 10.1111/1751-7915.13550 |
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Danchin A Zinc, an unexpected integrator of metabolism? Microbial Biotechnology (2020) 13: 895-898 doi: 10.1111/1751-7915.13549 |
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Prifti E, Chevaleyre Y, Hanczar B, Belda E,
Danchin A, Clément K, Zucker JD Interpretable and accurate prediction models for metagenomics data Gigascience (2020) 9: pii: giaa010 doi: 10.1093/gigascience/giaa010 |
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Danchin A Isobiology: A variational principle for exploring synthetic life Chembiochem (2020) 21: 1781-1792 doi: 10.1002/cbic.202000060 |
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Danchin A, Marlière P Cytosine drives evolution of SARS-CoV-2 Environ Microbiol (2020) 22: 1977-1985 doi: 10.1111/1462-2920.15025 |
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Armengaud J, Delaunay-Moisan A, Thuret JY,
van Anken E, Acosta-Alvear D, Aragón T, Arias C, Blondel M,
Braakman I, Collet JF, Courcol R, Danchin A, Deleuze JF, Lavigne
JP, Lucas S, Michiels T, Moore ERB, Nixon-Abell J, Rossello-Mora
R, Shi Z, Siccardi AG, Sitia R, Tillett D, Timmis KN, Toledano MB,
van der Sluijs P, Vicenzi E The importance of naturally attenuated SARS-CoV-2 in the fight against Covid-19. Environ Microbiol (2020) 22: 1997-2000 doi: 10.1111/1462-2920.15039 |
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Danchin A, Timmis K SARS-CoV-2 variants: relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment? Environ Microbiol (2020) 22: 2001-2006 doi: 10.1111/1462-2920.15053 |
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McGenity TJ, Gessesse A, Hallsworth JE,
Garcia Cela E, Verheecke-Vaessen C, Wang F, Chavarría M, Haggblom
MM, Molin S, Danchin A, Smid EJ, Lood C, Cockell CS, Whitby C, Liu
SJ, Keller NP, Stein LY, Bordenstein SR, Lal R, Nunes OC, Gram L,
Singh BK, Webster NS, Morris C, Sivinski S, Bindschedler S, Junier
P, Antunes A, Baxter BK, Scavone P, Timmis K Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes Microbial Biotechnology (2020) 13: 844-887 doi: 10.1111/1751-7915.13576 |
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn
RD, Danchin A, He LS Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli BMC Genomics (2020) 21: 408 doi: 10.1186/s12864-020-06807-4 |
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Courtier-Orgogozo V, Danchin A, Gouyon PH,
Boëte C Evaluating the probability of CRISPR-based gene drive contaminating another species Evol Appl (2020) 13: 1888-1905 doi: 10.1111/eva.12939 |
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Cluzel N, Lambert A, Maday Y, Turinici G,
Danchin A Biochemical and statistical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare CR Biol (2020) 343: 177-209 doi: 10.5802/crbiol.16 |
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Danchin A Le feu sacré de la vie Pour la Science (2020) 109: 58-63 |
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Ou Z, Ouzounis C, Wang D, Sun W, Li J, Chen
W, Marlière P, Danchin A A path toward SARS-CoV-2 attenuation: Metabolic pressure on CTP synthesis rules the virus evolution Genome Biol Evol (2020) 12: 2467-2485 doi: 10.1093/gbe/evaa229 |
2021 CTP synthetase solves the non-homothetic growth paradox
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Luo R, Delaunay-Moisan A, Timmis K, Danchin
A SARS-CoV-2 biology and variants: anticipation of viral evolution and what needs to be done Environ Microbiol (2021) 23: 2339-2363 doi: 10.1111/1462-2920.15487 |
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Pan Q, Li Z, Ju X, Hou C, Xiao Y, Shi R, Fu
C, Danchin A, You C Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations Microb Biotechnol (2021) 14: 1084-1106 doi: 10.1111/1751-7915.13776 |
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Danchin A, Turinici G Immunity after COVID-19: Protection or sensitization? Math Biosci (2021) 331: 108499 doi: 10.1016/j.mbs.2020.108499 |
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Richard P, Kozlowski L, Guillorit H, Garnier
P, McKnight NC, Danchin A, Manière X Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration PLoS ONE (2021) 16: e0253216 doi: 10.1371/journal.pone.0253216 |
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Lauritsen I, Frendorf PO, Capucci S, Heyde
SAH, Blomquist SD, Wendel S, Fischer EC, Sekowska A, Danchin A,
Nørholm MHH Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors. Nat Commun (2021) 12: 5880 doi: 10.1038/s41467-021-26098-x |
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Danchin A Biological innovation in the functional landscape of a model regulator, or the lactose operon repressor CR Biol (2021) 344: 111-126 doi: 10.5802/crbiol.52 |
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Karapiperis C, Kouklis P, Papastratos S,
Chasapi A, Danchin A, Angelis L, Ouzounis CA A strong seasonality pattern for Covid-19 incidence rates modulated by UV radiation levels Viruses (2021) 13:574 doi: 10.3390/v13040574 |
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Danchin A Three overlooked key functional classes for building up minimal synthetic cells Synthetic Biology (Oxford) (2021) 6: ysab010 doi: 10.1093/synbio/ysab010 |
2022 Time for Synthetic Biology: Maxwell demons and CTP synthesis
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Danchin A In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology Microb Biotechnol (2022) 15: 42-64 doi: 10.1111/1751-7915.13937 |
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Danchin A, AA Fenton From analog to digital computing: Is Homo sapiens’ brain on its way to become a Turing Machine? Front Ecol Evol (2022) 10: 796413 doi: 10.3389/fevo.2022.796413 |
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Wang Y, Li WL, Baker BJ, Zhou YL, He LS,
Danchin A, Li QM, Gao ZM Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines Environ Microbiol Rep (2022) 14: 308-319 doi: 10.1111/1758-2229.13052 |
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Hu YF, Hu JC, Gong HR, Danchin A, Sun R, Chu
H, Hung IF, Yuen KY, To KK, Zhang BZ, Yau T, Huang JD Computation of antigenicity predicts SARS-CoV-2 vaccine breakthrough variants Front Immunol (2022) 13: 861050 doi: 10.3389/fimmu.2022.861050 |
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Hazra S, Bhandari DM, Krishnamoorthy K,
Sekowska A, Danchin A, Begley TP Cysteine dealkylation in Bacillus subtilis by a novel flavin-dependent monooxygenase Biochemistry (2022) 61: 952-955 doi: 10.1021/acs.biochem.2c00020 |
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Danchin A, Pagani-Azizi O, Turinici G,
Yahiaoui G COVID-19 Adaptive Humoral Immunity Models: Weakly Neutralizing Versus Antibody-Disease Enhancement Scenarios Acta Biotheoretica (2022) 70: 23 doi: 10.1007/s10441-022-09447-1 |
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de Crécy-Lagard V, Amorin de Hegedus R,
Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ,
Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin
A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg
I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G,
Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin
MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale
DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P,
Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L,
Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D,
Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J A roadmap for the functional annotation of protein families: a community perspective Database (2022) 2022: baac062 doi: 10.1093/database/baac062 |
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Pollo-Oliveira L, Davis NK, Hossain I, Ho P,
Yuan Y, Salguero García P, Pereira C, Byrne SR, Leng J, Sze M,
Blaby-Haas CE, Sekowska A, Montoya A, Begley T, Danchin A,
Aalberts DP, Angerhofer A, Hunt J, Conesa A, Dedon PC, de
Crécy-Lagard V The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12 Metallomics (2022) 14: mfac065 doi: 10.1093/mtomcs/mfac065 |
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Danchin A Pasteur and "motivated" research C R Biol (2022) 345: 109-119 doi: 10.5802/crbiol.89 |
2023 Synthetic Biology / Antivirals
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Danchin A, Huang JD SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience Environ Microbiol (2023) 25: 64-68 doi: 10.1111/1462-2920.16140 |
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Timmis K, Berry D, Bonfante P, Coleman M,
Cunliffe M, Danchin A, Galperin M, Huang W, Lopez P, Stewart F,
Wood T Juan Luis Ramos: an exceptional editor of Environmental Microbiology Environ Microbiol (2023) 25: 595-596 doi: 10.1111/1462-2920.16315 |
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Bremer E, Calteau A, Danchin A, Harwood C,
Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga
A, Zuniga C A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century Microb biotechnol (2023) 16: 1203-1231 doi: 10.1111/1751-7915.14257 |
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Danchin A Science, method and critical thinking Microb biotechnol (2023) 16: 1888-1894 doi: 10.1111/1751-7915.14315 |
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Wirth NT, Rohr K, Danchin A, Nikel PI Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440 mBio (2023) : e0108123 doi: 10.1128/mbio.01081-23 |
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Danchin A La guerre biologique au temps de la biologie synthétique Raison présente (2023) 225: 47-56 doi: 10.3917/rpre.225.0047 |
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Danchin A Faire évoluer les virus vers des formes plus pathogènes, est-ce vraiment raisonnable ? Raison présente (2023) 228: 35-43 doi: 10.3917/rpre.228.0035 |
2024 Synthetic Biology / Artificial Intelligence
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Danchin A Exploring overlooked growth-promoting mechanisms by plant-associated bacteria Sustainable Microbiology (2024) 1: qvae011 doi: 10.1093/sumbio/qvae011 |
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Danchin A Artificial intelligence-based prediction of pathogen emergence and evolution in the world of synthetic biology Microb biotechnol (2024) 17: e70014 doi: 10.1111/1751-7915.70014 |
| Dernière mise à jour 5 Octobre 2024 |
Last update October 5, 2024 |