PLAN DU SITE PHILOSOPHIE HISTORY OF BIOLOGY PHILOSOPHY SITE MAP



1967-1971 IBPC-1981 REG-1986 REG-1991 REG-1996 GGB-2001 GGB-2006 AMA-2011 AMA-2016 HKU-2021
1972-1974 IBPC-1982 REG-1987 REG-1992 REG-1997 GGB-2002 GGB-2007 AMA-2012 ICAN-2017 HKU-2022
1975-1978 BRC-1983 REG-1988 REG-1993 REG-1998 GGB-2003 GGB-2008 AMA-2013 ICAN-2018 HKU-2023
IBPC-1979 BRC-1984 REG-1989 REG-1994 REG-1999 GGB-2004 AMA-2009 AMA-2014 Cochin-2019
IBPC-1980 BRC-1985 REG-1990 REG-1995 GGB-2000 GGB-2005 AMA-2010 AMA-2015 Cochin-2020

Publications in the domain of Philosophy, History of Sciences and Ethics

Symplectic Biology

Lectures and seminars

Publications listed at PubMed

Publications listed at Google Scholar

 

 


 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

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

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.

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

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

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.

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

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

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

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

Danchin A, Nikel PI
Why nature chose potassium
J Mol Evol. (2019) 87: 271-288 doi: 10.1007/s00239-019-09915-2

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

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.

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		 evolution

A Danchin
Origin of the first cells: the engineer’s point of view
Encyclopédie de l'environnement. UGA Éditions, Grenoble


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

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.

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

Danchin A
Zinc, an unexpected integrator of metabolism?
Microbial Biotechnology (2020) 13: 895-898 doi: 10.1111/1751-7915.13549

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

Danchin A
Isobiology: A variational principle for exploring synthetic life
Chembiochem (2020) 21: 1781-1792  doi: 10.1002/cbic.202000060

Danchin A, Marlière P
Cytosine drives evolution of SARS-CoV-2
Environ Microbiol (2020) 22: 1977-1985 doi: 10.1111/1462-2920.15025

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

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

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

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

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

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

Danchin A
Le feu sacré de la vie
Pour la Science (2020) 109: 58-63

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


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

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

Danchin A, Turinici G
Immunity after COVID-19: Protection or sensitization?
Math Biosci (2021) 331: 108499 doi: 10.1016/j.mbs.2020.108499

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

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

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

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

Danchin A
Three overlooked key functional classes for building up minimal synthetic cells
Synthetic Biology (Oxford) (2021) 6: ysab010 doi: 10.1093/synbio/ysab010


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

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

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

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

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

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

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

Danchin A
Pasteur and "motivated" research
C R Biol (2022) 345: 109-119 doi: 10.5802/crbiol.89


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

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

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

Danchin A
Science, method and critical thinking
Microb biotechnol (2023) : doi: 10.1111/1751-7915.14315

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

Danchin A
La guerre biologique au temps de la biologie synthétique
Raison présente (2023) 225: 47-56 doi: 10.3917/rpre.225.0047

Danchin A
Faire évoluer les virus vers des formes plus pathogènes, est-ce vraiment raisonnable ?
Raison présente (2023) 227: xx-xx doi: 10.xxx