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| COIN PRESSE | RÉSUMÉ | HISTOIRE DE LA BIOLOGIE | SUMMARY | JOURNALIST'S CORNER |
Before 2002, only
those publications that were quoted more than 30 times at the
ISI or at Google Scholar are shown
The 63 publications quoted more than 50 times
are indicated in larger case, and in green
Publications still quoted after 20 years are emphasized
Complete
publications
Publications in philosophy
and history of sciences
| 1967-1975 | 1992 | 1997 | 2002 | 2007 | 2012 |
| 1976-1979 | 1993 | 1998 | 2003 | 2008 | |
| 1980-1985 | 1994 | 1999 | 2004 | 2009 | |
| 1986-1990 | 1995 | 2000 | 2005 | 2010 | |
| 1991 | 1996 | 2001 | 2006 | 2011 |
M Cohn, A Danchin & M
Grunberg-Manago
Proton magnetic
relaxation studies of manganous complexes of transfer RNA and related
compounds
J Mol Biol (1969) 39: 199-217
A Danchin & M Guéron
Cooperative
binding of manganese (II) to transfer RNA
Eur J Biochem (1970) 16: 532-53
A Danchin
tRNA
structure and binding sites for cations
Biopolymers (1972) 11: 1317-1333
JP Changeux, P Courrège & A
Danchin
A
theory of the epigenesis of neuronal networks by selective stabilisation
of synapses
Proc Natl Acad Sci USA (1973) 70: 2974-2978
A Danchin
Does formylation
of initiator tRNA act as a regulatory signal in E coli ?
FEBS Letters (1973) 34: 327-332
MM Werber, A Oplatka & A
Danchin
Affinity labelling
of rabbity muscle myosin with a cobalt(III) adenosine triphosphate
complex
Biochemistry (1974) 13: 2683-2688
1976-1979
M Uzan &
A Danchin
A rapid test for the relA mutation
in E coli
Biochem Biophys Res Comm (1976) 69: 751-758
HU Petersen, A Danchin & M Grunberg-Manago
Toward
an understanding of the formylation of iniatiator tRNA methionine
in prokaryotic protein synthesis I In vitro studies of the 30S and
70S ribosomal tRNA complex
Biochemistry (1976) 15: 1362-1369
HU Petersen, A Danchin & M
Grunberg-Manago
Toward an understanding
of the formylation of initiator tRNA methionine in prokaryotic protein
synthesis II A two-state model for the 70S ribosome
Biochemistry (1976) 15: 1357-1362
JP Changeux & A Danchin
Selective
statilisation of developing synapses as a mechanism for the specification
of neuronal networks
Nature (1976) 264: 705-712
M Uzan &
A Danchin
Correlation
between the serine sensibility and derepressibility of the ilv genes
in Ecoli relA mutants
Molec Gen Genet (1978) 165: 21-30
A Ullmann, E Joseph & A Danchin
Cyclic
AMP as a modulator of polarity in polycistronic transcriptional units
Proc Natl Acad Sci USA (1979) 76: 3194-3198
1980-1985
C Guidi-Rontani,
A Danchin & A Ullmann
Catabolite
repression in Escherichia coli mutants lacking cyclic AMP
receptor protein
Proc Natl Acad Sci USA (1980) 77: 5799-5801
A Roy & A Danchin
Restriction
map of the cya region of Escherichia coli K 12 chromosome
Biochimie (1981) 63: 719-722
C Guidi-Rontani, A Danchin & A
Ullmann
Isolation and
characterization of a mutant affected in the regulation of adenylate
cyclase of Escherichia coli
J Bacteriol (1981) 148: 753-761
A Roy & A Danchin
The cya locus
of Escherichia coli K 12: organization and gene products
Molec Gen Genet (1982) 188: 465-471
A Roy, C Haziza & A Danchin
Regulation
of adenylate cyclase synthesis in Escherichia coli: nucleotide
sequence of the control region
EMBO J (1983) 2: 791-797
A Roy, A Danchin, E Joseph & A Ullmann
Two
functional domains in adenylate cyclase of Escherichia coli
J Mol Biol (1983) 165: 197-202
F Traincard, T Ternynck, A Danchin & S Avrameas
Une
technique immunoenzymatique pour la mise en évidence de l'hybridation
moléculaire entre acides nucléiques
Ann Immunol (Pasteur) (1983) 134D: 399-405
A Ullmann
& A Danchin
Role of cyclic AMP in bacteria
Adv Cyc Nucl Res (1983) 15: 1-53
H Aiba, K Mori, M Tanaka, T Ooi, A Roy & A
Danchin
The
complete nucleotide sequence of the adenylate cyclase gene of Escherichia
coli
Nucl Acid Res (1984) 12: 9427-9440
C Jacq, J Banroques, AM Becam, PP Slonimski, N Guiso & A
Danchin
Antibodies
against a fused "LacZ-yeast mitochondrial intron" gene
product allow identification of the mRNA-maturase encoded by the
fourth intron of the yeast cob-box gene
EMBO J (1984) 3: 1567-1572
L Hedegaard & A Danchin
The cya gene region of Erwinia
chrysanthemi B374: organisation and gene products
Mol Gen Genet (1985) 201: 38-42
1986-1990
O Gascuel &
A Danchin
Protein export in
prokaryotes and eukaryotes: indications for a difference in the mechanism
of exportation
J Mol Evol (1986) 24: 130-14
I St Girons, AM Gilles, D Margarita, S Michelson,
M Monnot, S Fermandjian, A Danchin & O Barzu
Structural
and catalytic characteristics of E coli adenylate kinase
J Biol Chem (1987) 262: 622-629
P Glaser, D Ladant, O
Sezer, F Pichot, A Ullmann & A Danchin
The calmodulin-sensitive adenylate cyclase
of Bordetella pertussis: cloning and expression in Escherichia
Mol Microbiol (1988) 2: 19-30
The adenylate cyclase toxin of the prokaryote Bordetella
pertussis is stimulated by the eukaryotic regulatory protein, calmodulin.
A general strategy, using the adenylate-cyclase-calmodulin interaction
as a tool, has permitted cloning and expression of the toxin in Escherichia
coli in the absence of any B. pertussis trans-activating factor. We show
that the protein is synthesized in a large precursor form composed of 1706
amino acids. The calmodulin-stimulated catalytic activity resides in the
amino-terminal 450 amino acids of the adenylate cyclase. The enzyme expressed
in E. coli is recognized in Western blots by antibodies directed against
purified B. pertussis adenylate cyclase, and its activity is inhibited
by these antibodies
H De Reuse & A Danchin
The ptsH, ptsI and crr genes
of the Escherichia coli PEP dependent phosphotransferase system
(PTS): a complex operon with several modes of transcription
J Bacteriol (1988) 170: 3827-3837
M Mock, E Labruyère, P Glaser, A Danchin & A
Ullmann
Cloning and expression of the calmodulin-sensitive Bacillus
anthracis adenylate cyclase in Escherichia coli
Gene (1988) 64: 277-284
P Glaser, H Sakamoto, J Bellalou,
A Ullmann & A Danchin
Secretion of cyclolysin, the calmodulin-sensitive
adenylate cyclase-haemolysin bifunctional protein of B. pertussis
EMBO J (1988) 7: 3997-4004
V Escuyer, E Duflot, O Sezer, A Danchin & M
Mock
Structural homology between virulence associated
bacterial adenylate cyclases
Gene (1988) 71: 293-298
P Glaser, A Elmaoglou-Lazaridou,
E Krin, D Ladant, O Barzu & A Danchin
Identification
of residues essential for catalysis and binding of calmodulin in B.
pertussis adenylate cyclase by site-directed mutagenesis
EMBO J (1989) 8: 967-972
P Bertin, P Lejeune, C Laurent-Winter & A Danchin
Mutations in bglY, the structural gene
for the DNA-binding protein H1, affect expression of several Escherichia
coli genes
Biochimie (1990) 72:889-891
C Médigue, JP Bouché,
A Hénaut & A Danchin
Mapping of sequenced genes (700 kbp) on the restriction
map of the Escherichia coli chromosome
Mol Microbiol (1990) 4: 169-187
This paper describes software (written in Pascal and
running on Macintosh computers) allowing localization of unknown DNA fragments
from the Escherichia coli chromosome on the restriction map established
by Kohara et al. (1987). The program identifies the segment's map position
using a restriction pattern analysis obtained with all, or some, of the
eight enzymes used by Kohara et al. (1987). Therefore, the sequenced genes
available in the EMBL library may be localized on the E.
coli chromosome
restriction map. This allowed correction of the map (mainly by introducing
missing sites in the published maps) at the corresponding positions. Analysis
of the data indicates that there is only a very low level of polymorphism,
at the nucleotide level, between the E. coli K12 strains used by the various
laboratories involved in DNA sequencing. The program is versatile enough
to be used with other genomes
S Lévy, GQ Zeng & A Danchin
Cyclic
AMP synthesis in Escherichia coli strains bearing known deletions
in the pts phosphotransferase operon
Gene (1990) 86: 27-33
P Lejeune & A Danchin
Mutations
in the bglY gene increase the frequency of spontaneous deletions
in E coli K-12
Proc Natl Acad Sci (1990) 87: 360-363
V De Crécy-Lagard, P Glaser, P Lejeune,
O Sismeiro, CE Barber, MJ Daniels & A Danchin
A Xanthomonas
campestris pv campestris protein similar to catabolite activationfactor
is involved in the regulation of phytopathogenicity
J Bacteriol (1990) 172: 5877-5883
H de Reuse & A
Danchin
Positive
regulation of the pts operon of E coli genetic evidence
for a signal transduction mechanism
J Bacteriol (1991) 173: 727-733
H Munier, A-M Gilles, P Glaser, E Krin, A Danchin,
R Sarfati & O Barzu
Isolation
and characterization of catalytic and calmodulin-binding domains of Bordetella
pertussis adenylate cyclase
Eur J Biochem (1991) 196: 469-474
C Médigue, T Rouxel, P Vigier, A Hénaut & A
Danchin
Evidence
for horizontal gene transfer in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856
M Santana, F Kunst, MF Hullo, G Rapoport, A Danchin & P
Glaser
Molecular
cloning, sequencing and physiological characterization of the qox operon
from Bacillus subtilis encoding the aa3-600 quinol oxidase
J Biol Chem (1992) 267: 10225-10231
A Danchin
Phylogeny
of adenylyl cyclases
Adv Cyc Nuc Prot Phos Res (1993) 27: 109-162
C Médigue, A Viari, A Hénaut & A
Danchin
Colibri: a functional data base for the Escherichia
coli genome
Microbiol Rev (1993) 57: 623-654
P Glaser, F Kunst, M Arnaud, M-P Coudart, W Gonzales,
M-F Hullo, M Ionescu, B Lubochinsky, L Marcelino, I Moszer, E Presecan,
M Santana, E Schneider, J Schweizer, A Vertes, G Rapoport & A Danchin
Bacillus subtilis genome project: cloning and
sequencing of the 97 Kb region from 325o to 333o
Mol Microbiol (1993) 10: 371-384
O Barzu & A Danchin
Adenylyl cyclases: a heterogeneous class
of ATP-utilizing enzymes
Prog Nucleic Acid Res Mol Biol (1994) 49: 241-283
P Bertin, E Terao, EH Lee, P Lejeune, C Colson,
A Danchin & E Collatz
The H-NS protein is involved in the biogenesis of
flagella in Escherichia coli
J Bacteriol (1994) 176: 5537-5540
M Santana, S Ionescu, A Vertes, R Longin, F Kunst,
A Danchin & P Glaser
Bacillus
subtilis Fo F1 ATPase: DNA sequence of the atp operon and
characterization of atp mutants
J Bacteriol (1994) 176: 6802-6811
P Glaser, A Danchin,
F Kunst, P Zuber & M Nakano
Identification
and isolation of a gene required for nitrate assimilation and anaerobic
growth of Bacillus subtilis
J Bacteriol (1995) 177: 1112-1115
I Moszer, P Glaser & A Danchin
SubtiList:
a relational database for the Bacillus subtilis genome
Microbiology (1995) 141: 261-268
L Serina, C Blondin, E Krin, O Sismeiro, A Danchin,
H Sakamoto, AM Gilles & O Barzu
Escherichia
coli UMP-kinase, a member of the aspartokinase family, is a hexamer
regulated by guanine nucleotides and UTP
Biochemistry (1995) 34: 5066-5074
M Borodovsky, J McIninch, EV Koonin, KE Rudd,
C Médigue & A Danchin
Detection
of new genes in the bacterial genome using Markov models for three gene
classes
Nucleic Acids Res (1995) 23: 3554-3562
H Cruz-Ramos, L Boursier, I Moszer, F Kunst, A
Danchin & P Glaser
Anaerobic
transcription activation in Bacillus subtilis: identification
of distinct FNR-dependent and independant regulatory mechanisms
EMBO J (1995) 14: 5984-5994
1996-2000
N Bucurenci, H Sakamoto,
P Briozzo, N Palibroda, L Serina, R S Sarfati, G Labesse, G Briand, A
Danchin, O Barzu & AM Gilles
CMP-Kinase from Escherichia coli is structurally
related to other nucleoside monophosphate kinases
J Biol Chem (1996) 271: 2856-2862
A Hénaut, T Rouxel, A Gleizes, I Moszer & A
Danchin
Uneven
distribution of GATC motifs in the Escherichia coli chromosome,
its plasmids and its phages
J Mol Biol (1996) 257: 574-585
A Hénaut
& A Danchin
Analysis and Predictions from Escherichia coli sequences
or E coliin silico, in: Escherichia
coli and Salmonella, Cellular and Molecular Biology, vol
1, chap 114, pp 2047-2065
Editor in Chief: Frederick C Neidhardt
MM Nakano, P Zuber, P Glaser, A Danchin & FM
Hulett
Two-component
regulatory proteins ResD-ResE are required for transcriptional activation
of fnr upon oxygen limitation in Bacillus subtilis
J Bacteriol (1996) 178: 3796-3802
C Laurent-Winter,
S Ngo, A Danchin & P Bertin
Role
of Escherichia coli histone-like nucleoid structuring protein
in bacterial metabolism and stress response: identification of targets
by two-dimensional electrophoresis
Eur J Biochem (1997) 244: 767-773
F Kunst, N Ogasawara, I Moszer, [...] H Yoshikawa & A
Danchin
The
complete genome sequence of the Gram-positive bacterium Bacillus subtilis
Nature (1997) 390: 249-256
O Sismeiro, P Trotot,
F Biville, C Vivarès & A Danchin
Aeromonas
hydrophila Adenylyl cyclase 2: a new class of adenylyl cyclases with
thermophilic properties and sequence similarities to proteins from hyperthermophilic
Archaebacteria
J Bacteriol (1998) 180: 3339-3344
A Sekowska,
P Bertin
& A Danchin
Characterization
of polyamines synthesis pathway in Bacillus subtilis 168
Mol Microbiol (1998) 29: 851-858
F Delbac, P Peyret, G Metenier, D David, A Danchin & C
P Vivarès
On
proteins of the microsporidian invasive apparatus: complete sequence
of a polar tube protein of Encephalitozoon cuniculi
Mol Microbiol (1998) 29: 825-834
P Nitschké, P Guerdoux-Jamet, H Chiapello,
G Faroux, C Hénaut, A Hénaut & A Danchin
Indigo:
a World-Wide-Web review of genomes and gene functions
FEMS Microbiology Reviews (1998) 22: 207-227 [PDF]
EP Rocha, A Danchin & A
Viari
Universal
replication biases in bacteria
Mol Microbiol (1999) 32: 11-16 [PDF]
E Presecan-Siedel, A Galinier, R Longin, J Deutscher,
A Danchin, P Glaser & I Martin-Verstraete
Catabolite
regulation of the pta gene as part of carbon flow pathways in Bacillus
subtilis
J Bacteriol (1999) 181: 6889-6897
I Moszer, E P Rocha & A Danchin
Codon
usage and lateral gene transfer in Bacillus subtilis
Current Opinion in Microbiology (1999) 2: 524-528
NN Baranova, A Danchin & AA Neyfakh
Mta,
a global MerR-type regulator of the Bacillus subtilis multidrug-efflux
transporters
Molecular Microbiology (1999) 31: 1549-1559
EP Rocha, A Danchin & A Viari
Analysis of long repeats in bacterial genomes
reveals alternative evolutionary mechanisms in Bacillus subtilis and
other competent prokaryotes
Molecular Biology & Evolution
(1999) 16: 1219-1230
EPC Rocha, A Danchin,
A Viari
Translation in Bacillus subtilis: roles and trends of initiation and termination,
insights from a genome analysis
Nucleic Acids Res (1999) 27: 3567-3576 
C Médigue,
F Rechenmann, A Danchin & A Viari
Imagene: an integrated computer environment for
sequence annotation and analysis
Bioinformatics (1999) 15: 2-15
O Soutourina, A Kolb, E Krin, C Laurent-Winter,
S Rimsky, A Danchin & P Bertin
Multiple
control of flagellum biosynthesis in Escherichia coli: Role of
H-NS protein and the cyclic AMP-catabolite activator protein complex
in transcription of the flhDC master operon
Journal of Bacteriology (1999) 181: 7500-7508
P Bertin, N Benhabiles, E Krin, C Laurent-Winter,
C Tendeng, E Turlin, A Thomas, A Danchin & R Brasseur
The
structural and functional organization of H-NS-like proteins is evolutionarily
conserved in gram-negative bacteria
Molecular Microbiology (1999) 31: 319-329
* A Sekowska, HF Kung & A Danchin
Sulfur
metabolism in Escherichia coli and related bacteria, facts and fiction
J Mol Microbiol Biotechnol (2000) 2 : 145-177 [PDF]
* A Sekowska, A Danchin & JL Risler
Phylogeny
of related functions: the case of polyamine biosynthetic enzymes
Microbiology (2000) 146: 1815-1828
Creation of the Unit Genetics of Bacterial Genomes
2001
F Hommais,
E Krin, C Laurent-Winter, O Soutourina, A Malpertuy, J-P Le Caer, A Danchin
& P Bertin
Large-scale
monitoring of pleiotropic regulation of gene expression by the prokaryotic
nucleoid-associated protein, H-NS
Mol Microbiol (2001) 40: 20-36
P Bertin , F Hommais, E Krin, O Soutourina, C Tendeng,
S Derzelle & A Danchin
H-NS
and H-NS-like proteins in Gram-negative bacteria and their multiple role
in the regulation of bacterial metabolism
Biochimie (2001) 83: 235-241
*A Sekowska, S Robin, J-J Daudin, A Hénaut & A
Danchin
Extracting
biological information from DNA arrays: an unexpected link between arginine
and methionine metabolism in Bacillus subtilis
GenomeBiology (2001) 2: 191-1912
*EPC Rocha, A Danchin & A Viari
Evolutionary
role of restriction/modification systems as revealed by comparative genome
analysis
Genome Research (2001) 10: 946-958
*A Sekowska, L Mulard, S Krogh, J Tse & A Danchin
MtnK,
methylthioribose kinase, is a starvation-induced protein in Bacillus
subtilis
BMC Microbiology (2001) 1: 15
MF Hullo, I Moszer, A Danchin & I Martin-Verstraete
CotA
of Bacillus subtilis is a copper-dependent laccase
J Bacteriol (2001) 183: 5426-5430
*EPC Rocha & A Danchin
Ongoing
evolution of strand composition in bacterial genomes
Mol Biol Evol (2001) 18: 1789-1799
*C Médigue, B CY Wong, M C M Lin, S Bocs & A
Danchin
The secE gene
of Helicobacter pylori
Journal of Bacteriology (2002) 184: 2837-2840
E Krin, O Sismeiro, A Danchin & P Bertin
The
regulation of Enzyme IIA(Glc) expression controls adenylate cyclase activity
in Escherichia coli
Microbiology (2002) 148: 1553-1559
OA Soutourina, E Krin, C Laurent-Winter, F Hommais,
A Danchin & P Bertin
Regulation
of bacterial motility in response to low pH in Escherichia coli:
the role of H-NS protein
Microbiology (2002) 148: 1543-1551
F Hommais, C Laurent-Winter, V Labas, E Krin, C
Tendeng, OA Soutourina,A Danchin & P Bertin
Effect
of mild acid pH on the functioning of bacterial membranes in Vibrio
cholerae
Proteomics (2002) 2: 571-579
S Brunak, A Danchin, M Hattori, H Nakamura, K Shinozaki,
T Matise, & D Preuss
Nucleotide
sequence database policies
Science (2002) 15: 298
*S Auger, A Danchin & I Martin-Verstraete
Global
expression profile of Bacillus subtilis grown in the presence of
sulfate or methionine
J Bacteriol (2002) 184: 5179-5186
I Guillouard, S Auger, MF Hullo, F Chetouani, A
Danchin & I Martin-Verstraete
Identification
of Bacillus subtilis CysL, a regulator of the cysJI operon,
which encodes sulfite reductase
J Bacteriol (2002) 184: 4681-4689
S Derzelle, E Duchaud, F Kunst, A Danchin
& P Bertin
Identification,
characterization, and regulation of a cluster of genes involved in carbapenem
biosynthesis in Photorhabdus luminescens
Appl Environ Microbiol (2002) 68: 3780-3789
*EPC Rocha & A Danchin
Base
composition bias might result from competition for metabolic resources
Trends in Genetics (2002) 18: 291-294 [PDF]
*A Sekowska & A Danchin
The methionine salvage pathway in Bacillus subtilis
BMC Microbiol (2002) 2: 8
*C Médigue, B C Y Wong, M C M Lin, S Bocs & A
Danchin
The secE gene
of Helicobacter pylori
J Bacteriol (2002) 184: 2837-2840
*S Bocs, A Danchin & C Médigue
Re-annotation
of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated
genes
BMC Bioinformatics (2002) 3: 5
*A Danchin
Not
every truth is good The dangers of publishing knowledge about
EMBO Rep (2002) 31: 102-104
*S Auger, WH Yuen, A Danchin & I Martin-Verstraete
The metIC methionine
biosynthesis operon is controlled by transcription antitermination in Bacillus
subtilis
Microbiology (2002) 148: 507-518
*I Moszer, LM Jones, S
Moreira, C Fabry &
A Danchin
SubtiList:
the reference database for the Bacillus subtilis genome
Nucleic Acids Research (2002) 30: 62-65
*SX Ren, G Fu, XG Jiang, R Zeng, YG Miao, H Xu, YX
Zhang, H Xiong, G Lu, LF Lu, HQ Jiang, J Jia, YF Tu, JX Jiang, WY Gu, YQ
Zhang, Z Cai, HH Sheng, HF Yin, Y Zhang, GF Zhu, M Wan, HL Huang, Z Qian,
SY Wang, W Ma, ZJ Yao, Y Shen, BQ Qiang, QC Xia, XK Guo, A Danchin, I Saint
Girons, RL Somerville, YM Wen, MH Shi, Z Chen, JG Xu &
GP Zhao
Unique
physiological and pathogenic features of Leptospira interrogans revealed
by whole-genome sequencing
Nature (2003) 422: 888-893 [PDF] Associated
to the LeptoList database
*A Danchin
Infection
of society
EMBO Rep (2003) 4: 333-335 [PDF]
*KY Yuen, G Pascal, SS Wong, P Glaser, PC Woo, F Kunst,
JJ Cai, EY Cheung, C Médigue & A Danchin
Exploring
the Penicillium marneffei genome
Arch Microbiol (2003) 179: 339-353
*C Tendeng, E Krin, OA Soutourina, A Marin, A Danchin & PN
Bertin
A
novel H-NS-like protein from an antarctic psychrophilic bacterium reveals
a crucial role for the N-terminal domain in thermal stability
J Biol Chem (2003) 278: 18754-18760
*K Kobayashi, SD Ehrlich, [...], A Danchin,
[...], H Yoshikawa,
U Zuber & N Ogasawara
Essential Bacillus
subtilis genes
Proceedings of the National Academy of Sciences, USA, (2003) 100:
4678-4683 [PDF]
* EPC Rocha & A Danchin
Essentiality,
not expressiveness, drives gene-strand bias
Nature Genet (2003) 34: 377-378 [PDF]
*YQ Zhang, [...] A
Danchin & YM Wen
Genome-based
analysis of virulence genes in a non-biofilm-forming Staphylococcus
epidermidis strain (ATCC 12228)
Mol Microbiol (2003) 49: 1577-1593 [PDF]
Associated to the SepiList
database
*EPC Rocha, J Fralick, G Vediyappa, A Danchin & V
Norris
A
strand-specific model for chromosome segregation in bacteria
Mol Microbiol (2003) 49: 895-903 [PDF]
TW Ng, G Turinici & A Danchin
A
Double Epidemic Model for the SARS Propagation
BMC Infect Dis (2003) 3: 19
E Duchaud, [...], A Danchin & F
Kunst
The
genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
Nature Biotechnol (2003) 21: 1307-1313 [PDF]
*EPC Rocha & A Danchin
Gene
essentiality determines chromosome organisation in bacteria
Nucleic Acids Res (2003) 31: 6570-6577 [PDF]
C Tendeng, OA Soutourina, A Danchin & PN Bertin
MvaT
proteins in Pseudomonas spp: a novel class of H-NS-like proteins
Microbiology (2003) 149: 3047-3050 [PDF]
2004 (star: publications in collaboration with the HKU-Pasteur Centre in Hong Kong)
*Y Yap, X Zhang & A Danchin*EPC Rocha & A Danchin
An
analysis of determinants of amino-acids substitution rates in bacterial proteins
Mol Biol Evol (2004) 21: 108-116 [PDF]
F Hommais, E Krin, JY Coppée, C Lacroix, E Yeramian,
A Danchin & P Bertin
GadE
(YhiE): a novel activator involved in the response to acid environment in Escherichia
coli
Microbiology (2004) 150: 61-72 [PDF]
S Derzelle, E Turlin, E Duchau, S Page, F Kunst, A
Givaudan & A Danchin
The
PhoP-PhoQ two-component regulatory system of Photorhabdus luminescens is
essential for virulence in insects
J Bacteriol (2004) 186: 1270-1279 [PDF]
S Derzelle, S Ngo, E Turlin, E Duchaud, A Namane, F
Kunst, A Danchin, P Bertin & JF Charles
AstR-AstS,
a new two-component signal transduction system, mediates swarming,
adaptation to stationary phase and phenotypic variation in Photorhabdus
luminescens
Microbiology (2004) 150: 897-910 [PDF]
MF Hullo, S Auger, E Dassa, A Danchin
& I Martin-Verstraete
The metNPQ operon
of Bacillus subtilis encodes an ABC permease transporting methionine
sulfoxide, D- and L-methionine
Res Microbiol (2004) 155: 80-86 [PDF]
* A Sekowska, V Dénervaud, H Ashida, K Michoud,
D Haas, A Yokota & A Danchin
Bacterial
variations on the methionine salvage pathway
BMC Microbiol (2004) 4: 9
* Y Wang, EPC Rocha, FCC Leung & A Danchin
Cytosine
methylation is not the major factor inducing CpG dinucleotide deficiency
in bacterial genomes
J Mol Evol (2004) 58: 692-700
P Burguière, S Auger, MF Hullo, A Danchin & I
Martin-Verstraete
Three
different systems participate in L-cystine uptake in Bacillus subtilis
J Bacteriol (2004) 186: 4875-4884
* YL Yap, XW Zhang, MT Ling, XH Wang, YC Wong & A Danchin
Classification
between tumor and normal tissues based on the pair-wise gene expression ratio
BMC Cancer (2004) 4: 72
* XW Zhang, YL Yap & A Danchin
Testing
hypothesis of a recombinant origin of the SARS-associated coronavirus
Arch Virol (2004) 150: 1-20
2005 (star: publications in collaboration with the HKU-Pasteur Centre)
H Ashida, A Danchin & A YokotaHD
Song, [...] A Danchin, N Niccolai, YX Li, CI Wu & GP Zhao
Cross-host
evolution of severe acute respiratory syndrome coronavirus in palm civet
and human
Proc Natl Acad Sci USA (2005) 102: 2430-2435
*G Fang, C Ho, YW Qiu, V Cubas, Z Yu, C Cabau, F Cheung,
I Moszer & A Danchin
Specialized
microbial databases for inductive exploration of microbial genome sequences
BMC Genomics (2005) 6: 14
S Auger, MP Gomez, A Danchin & I Martin-Verstraete
The
PatB protein of Bacillus subtilis is a C-S-lyase
Biochimie (2005) 87: 231-238
E Turlin, O Sismeiro, JP Le Caer, V Labas, A Danchin & F
Biville
3-phenylpropionate
catabolism and the Escherichia coli oxidative stress response
Res Microbiol (2005) 156: 312-321
* G Pascal, C Médigue & A Danchin
Universal
biases in protein composition of model prokaryotes
Proteins (2005) 60: 27-35
* YL Yap, DC Lam, L Girard, XW Zhang, D Hernandez,
R Gras, E Wang, SW Chiu, LP Chung, WK Lam, DK Smith, JD Minna, A Danchin & MP
Wong
Conserved
transcription factor binding sites of cancer markers derived from primary
lung adenocarcinoma microarrays
Nucleic Acids Res (2005) 14: 409-421
G Fang, EPC Rocha & A Danchin
How
essential are non-essential genes?
Mol Biol Evol (2005) 22: 2147-2156
V Barbe, A Bernsel, [...], G von Heijne, A Danchin
Coping
with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas
haloplanktis TAC125
Genome Res (2005) 15: 1325-1335 
2006 (star: publications in collaboration with the HKU-Pasteur Centre in Hong Kong)
M
Bailly-Bechet, A Danchin, M Iqbal, M Marsili, M Vergassola
Codon
usage domains over bacterial chromosomes
PLoS Computational Biology (2006) 2: e37 
C
Carapito, D Muller, E Turlin, S Koechler, A Danchin, A Van Dorsselaer,
E Leize-Wagner, PN Bertin, MC Lett
Identification
of genes and proteins involved in the pleiotropic response to arsenic stress
in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium
with an unsequenced genome
Biochimie (2006) 8: 595-606
A Danchin
Beneficial biological warfare
EMBO Rep (2006) 7:767
S
Even, P Burguière, S Auger, O Soutourina, A Danchin, I Martin-Verstraete
Global control of cysteine metabolism by CymR
in Bacillus subtilis
J Bacteriol (2006) 188: 2184-2197 
U Mechold,
V Ogryzko, S Ngo, A Danchin
Oligoribonuclease is a common downstream target
of lithium-induced pAp accumulation in Escherichia coli and
human cells
Nucleic Acids Res (2006) 34: 2364-2373 
G
Pascal, C Médigue, A Danchin
Persistent biases in the amino-acid composition
of prokaryotic proteins
Bioessays (2006) 28: 726-738
Z
Qin, J Zhang, B Xu, L Chen, Y Wu, X Yang, X Shen, S Molin, A Danchin,
H Jiang, D Qu
Structure-based discovery of inhibitors of the
YycG histidine kinase: New chemical leads to combat Staphylococcus
epidermidis infections
BMC Microbiology (2006) 6: 96 
E
Turlin, G Pascal, JC Rousselle, P Lenormand, S Ngo, A Danchin, S Derzelle
Proteome analysis of the phenotypic variation
process in Photorhabdus luminescens
Proteomics (2006) 6: 2705-2725
S Chalabaev,
E Turlin, JF Charles, A Namane, S Pagès, A Givaudan, E Brito-Fravallo,
A Danchin, Biville F
The HcaR regulatory protein of Photorhabdus
luminescens affects the production of proteins involved in oxidative
stress and toxemia
Proteomics (2007) 7: 4499-4510
A
Danchin
Archives or palimpsests? Bacterial genomes unveil
a scenario for the origin of life
Biological Theory (2007) 2: 52-61
A Danchin, G Fang, S Noria
The extant core bacterial proteome
is an archive of the origin of life
Proteomics (2007) 7: 875-889
MF
Hullo, S Auger, O Soutourina, O, Barzu, M Yvon, A Danchin, I Martin-Verstraete
The conversion of methionine to cysteine in Bacillus
subtilis and its regulation
J Bacteriol (2007) 189: 187-197
U
Mechold, G Fang, S Ngo, V Ogryzko, A Danchin
YtqI from Bacillus subtilis has both
oligoribonuclease and pAp-phosphatase activity
Nucleic Acids Res (2007) 35: 4552-4561
D
Muller, C Medigue, [...] A Danchin, PN Bertin
A tale of two oxidation states: bacterial colonization
of arsenic-rich environments.
PLoS Genetics (2007) 3: e53
TW
Ng, G Turinici, WK Ching, SK Chung, A Danchin
A parasite vector-host epidemic model for TSE
propagation
Medical Science Monitor (2007) 13: 59-66
Y
Wu, K Yu, B Xu, L Chen, X Chen, J Mao, A Danchin, X Shen, D Qu, H Jiang
Potent and selective inhibitors of Staphylococcus
epidermidis tryptophanyl-tRNA synthetase
J Antimicrobial Chemotherapy (2007) 60: 502-509
H Ashida, Y Saito, T Nakano, N
Tandeau de Marsac, A Sekowska, A Danchin, A Yokota
RuBisCO-like proteins as the enolase enzyme in
the methionine salvage pathway: functional and evolutionary relationships
between RuBisCO-like proteins and photosynthetic RuBisCO
J Exp Bot (2008) Apr 9; [Epub ahead of print]
S Chalabaev, E Turlin, S Bay, C
Ganneau, E Brito-Fravallo, J-F Charles, A Danchin, F Biville
Cinnamic acid, an autoinducer of its own biosynthesis,
is processed via Hca enzymes in Photorhabdus luminescens
Appl Environ Microbiol (2008) 74:1717-1725
G Fang, EP Rocha, A Danchin
Persistence drives gene clustering in bacterial
genomes
BMC Genomics (2008) 9: 4
E Krin, S Derzelle, K Bedard, M Adib-Conquy, E Turlin,
P Lenormand, M-F Hullo, I Bonne, N Chakroun, C Lacroix, A Danchin
Regulatory role of UvrY in adaptation of Photorhabdus
luminescens growth inside the insect
Environmental Microbiology (2008) 10: 1118–1134
M Riley, JT Staley, A Danchin, TZ Wang, TS Brettin,
LJ Hauser, ML Land, LS Thompson
Genomics of an extreme psychrophile, Psychromonas
ingrahamii
BMC Genomics 9: 210
V Barbe, S Cruveiller, F Kunst,
P Lenoble, G Meurice, A Sekowska, D Vallenet, TZ Wang, I Moszer, C Médigue,
A Danchin
From a consortium sequence to a unified sequence: The Bacillus
subtilis 168 reference genome a decade later
Microbiology (2009) 155: 1758-1775
|
|
In
memoriam Frank Kunst, let us remember that, when the article reporting
the first complete sequencing of
the genome appeared in 1997, Chet
Raymo, for the Boston Globe wrote (january 5th, 1998): |
A Danchin
Natural selection and immortality
Biogerontology (2009) 10: 503-516
A Danchin
Bacteria as computers making computers
FEMS Microbiol Rev (2009) 33: 3-26
A Danchin
A phylogenetic view of bacterial ribonucleases
Prog Nucleic Acid Res Mol Biol (2009) 85: 1-41
A Danchin
Nature, artifice and emerging diseases
EMBO Reports (2009) 10: 418-419
A Danchin
Cells need safety valves
Bioessays (2009) 31: 769-773
In Escherichia coli, the role of lacA, the third gene of the lactose operon, has remained an enigma. I suggest that its role is the consequence of the need for cells to have safety valves that protect them from the osmotic effect created by their permeases. Safety valves allow them to cope with the buildup of osmotic pressure under accidental transient conditions. Multidrug resistance (MDR) efflux, thus named because of our anthropocentrism, is ubiquitous. Yet, the formation of simple leaks would result in futile influx/efflux cycles. Versatile modification enzymes with low sensitivity solve the problem if the modified metabolite is the one exported by MDR permeases. This may account for the pervasive presence of acetyltransferases, such as LacA, associated to acetyl-metabolite exporters. This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells
A Danchin
Sélection naturelle et immortalité
in: Les mondes darwiniens (T
Heams, P Huneman, G Lecointre, M Silberstein, eds), Syllepse (2009) pp 445-470
Tous les organismes – bactéries incluses – vieillissent et meurent. En raison de l’incroyable diversité de ce processus (les plantes vieillissent lentement, par exemple), c’est un lieu commun des études sur le vieillissement que de considérer qu’il s’agit d’un paradoxe, qui requiert par conséquent une explication en profondeur. Cette observation a suscité une profusion d’études fascinantes (et de discussions enflammées) destinées à mettre au jour la variété des causes et des mécanismes impliqués dans le vieillissement. Dans ce contexte, l’« immortalité » est considérée comme la norme. Pourquoi et comment vieillissons-nous ? Ce n’est pas cette question que je traiterai ici, je vais prendre le chemin exactement opposé. Considérant que le vieillissement est une conséquence directe de la physique – et c’est en effet l’une des conclusions majeures à laquelle parviennent ceux qui analysent le vieillissement en profondeur quand il repensent les théories de l’« avalanche d’erreurs» d’Orgel ou le « cliquet de Muller –, j’observe au contraire que c’est l’immortalité (que nous observons dans le cancer) qui soulève un paradoxe...
唐善﹒安東
向合成细胞迈进：细胞与计算机的复制过程中的遗传问题
微生物与感染 Journal
of Microbes and Infection (2009) 4: 12
A. Danchin
Information of the chassis and information of the program in synthetic
cells
Syst Synth Biol (2009) 3(1-4):125-134
A Danchin, A Sekowska
Physico-chemical prerequisites for
the construction of a synthetic cell
in: Synthetic Chemistry, May 26th - 30th, 2008, in Bozen, Italy
Beilstein Institut for the Advancement of Chemical Sciences (2009) 1-13
M Fang, WM Zeisberg, C Condon,
V Ogryzko, A Danchin, U Mechold
Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus
subtilis
Nucleic Acids Res (2009) 37: 5114-5125
Y Jin, RM Watt, A Danchin, JD Huang
Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia
coli
BMC Genomics (2009) 10: 165
Y Saito, H Ashida, T Sakiyama, N Tandeau de Marsac,
A Danchin, A Sekowska, A Yokota
Structural and functional similarities between a RuBisCO-like
protein from Bacillus subtilis and photosynthetic RuBisCO
J Biol Chem (2009) 284:13256-13264 
E Parrilli, M Giuliani, C Pezzella, A Danchin,
G Marino, ML Tutino
PhPssA is required for alpha-amylase secretion
in Antarctic Pseudoalteromonas haloplanktis
Microbiology (2009) Sep 24. [Epub ahead of print]
A Sekowska, JB Masson, A Celani, A Danchin, M Vergassola
Repulsion and metabolic switches in the collective
behavior of bacterial colonies
Biophys J (2009) 97: 688-698
O Soutourina, O Poupel, JY Coppée, A Danchin, T
Msadek, I Martin-Verstraete
CymR, the master regulator of cysteine metabolism
in Staphylococcus aureus, controls host sulfur source utilization and
plays a role in biofilm formation
Mol Microbiol (2009) 73: 194-211
J Thornton and the BioSapiens Network
Annotations for all by all - the BioSapiens network
Genome Biology (2009) 10: 2
M Touchon, [...], A Danchin, [...], C Médigue, EPC Rocha,
E Denamur
Organised genome dynamics in the Escherichia coli species results
in highly diverse adaptive paths
PLoS Genetics (2009) 5: e1000344
A Danchin
Perfect time or perfect crime?
EMBO Reports (2010) 11: 74
Opening: Imagine the situation: “[O]ne
day, you notice an old country woman crossing a downtown street, just about to
put one foot down on the rails of the streetcar line. […] Suppose, now, that
at the very moment she puts her foot on the rail a streetcar comes rushing down
the tracks toward her. If the old woman does not notice the car and continues
across the tracks nothing will happen. But if someone should happen to shout
‘Look out, old woman!’ what would be her natural reaction? […] she would suddenly
become flustered and would pause to decide whether to go on or step back […]
the mere words ‘Look out, old woman!’ would be as dangerous a weapon as any knife
or firearm. […] the man who sounds the warning actually becomes a murderer!" (Ranpo,
1956). In this sense, the Asilomar conference on genetic engineering in 1974
was the perfect crime in using cautionary exclamations asa weapon that had far-reaching
consequences for the emerging field of molecular biology: a moratorium stopped
research in some places while others proceeded and took the lead. The same fate
may lie in store for synthetic biology (SB). The usual crooners have understood
the importance of resorting to appeals to ethics and playing on people’s fears
to make themselves known and have begun a discussion of the purported dangers
of creating organisms a la carte. Such clamouring for attention may
yet end up being a shot to our own feet. Moreover, does minimization of a bacterial
genome really pose ethical questions? Should we worry, and if so why? After all,
what is the purpose of SB? We need to explore the knowledge that we are required
to master to (re)construct life in order to gain a better idea of the economic
and ethical questions that we have to ask before we start asking them.
A Danchin
Motivated research
EMBO Reports (2010) 11: 488
Opening: Three years ago, a senior
politician attended his country’s Annual Congress for the Advancement of Science
to give the introductory lecture. He asked the attending scientists to make
science and research more attractive to young students and the general public,
and asked his countrymen to support scientists to address the urgent challenges
of global climate change, energy needs and dwindling water resources. It was
neither a European nor a US politician, but the Indian Prime Minister Manmohan
Singh who made this speech about the relationship between research and its
practical applications. This is such an important topic that one might think
it deserves appropriate attention in Europe, yet we fail to address it properly.
Instead, we just discuss how science should serve society or contribute to
the ‘knowledge-based economy’, or how ‘basic’ or ‘fundamental’ research is
opposed to ‘applied’ or ‘industrial’ research and how funding for ‘big science’
comes at the expense of ‘little academic’ research.
A Danchin
A path from predation to mutualism
Molecular Microbiology (2010) 77: 1346-1350
A Danchin
Science and
arsenic fool's gold: a toxic broth
Journal of Cosmology (2010) 13 : 3617-3620
Abstract: Making stable informational
polymers in water at 300K limits chemical variations within extremely
narrow borders. This is why the basic atoms of life — those that are
found in meteoritic molecules — are hydrogen, carbon, nitrogen and oxygen.
In these same conditions, management of energy to support life used the
unique property of phosphorus to make energy-rich metastable phosphoester
or polyphosphate bonds. Analysis of the genome of arsenic-loving bacteria
suggests that arsenic can nevertheless be accumulated in bacteria via
formation of innocuous derivatives that may decorate inert (mostly non
informational) biopolymers. However, arsenic cannot replace phosphorus
in this core function of life. This has been previously firmly established
by numerous biochemical experiments. Likewise, recent claims by Wolfe-Simon
et al. (2010) that this replacement could happen, have not been experimentally
verified, and are based on experiments lacking proper controls; the purpose
of which was to substantiate these beliefs. However, the authors are
not sole to be blamed, but the journals that try to maintain their high
impact factors at all cost, publishing articles that should never have
reached the public
A Danchin, G Fang
Babies are born very young. The synthesis of change
Journal of Cosmology (2010) 7: May
2010 Artificial Life
A Danchin, A Sekowska
The role of information in evolutionary genomics of bacteria
In: Evolutionary genomics and systems biology (G Caetano-Anollés,
Editor), Wiley & sons, Hoboken, NJ (2010) pp 81-94
E Krin, A Danchin, O Soutourina
RcsB plays a central role in H-NS-dependent regulation of motility and
acid stress resistance in Escherichia coli
Res Microbiol (2010) 161: 363-371
E Krin, A Danchin, O Soutourina
Decrypting the H-NS-dependent regulatory cascade of acid stress resistance
in Escherichia coli
BMC Microbiology (2010) 10: 273
E Parrilli, M Giuliani, C Pezzella, A Danchin, G
Marino, ML Tutino
PhPssA is required for alpha-amylase secretion in Antarctic Pseudoalteromonas
haloplanktis
Microbiology (2010) 156: 211-219
F Piette, S D’Amico, C Struvay, G Mazzucchelli,
J Renaut, ML Tutino, A Danchin, P Leprince, G Feller
Proteomics of life at low temperatures: trigger factor is the primary
chaperone in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125
Molecular Microbiology (2010) 76: 120-132
G Postic, A Danchin, U Mechold
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma
pneumoniae
Symplectic Biology (2010) 1: c390t9c12uxx.1
M Vayssier-Taussat, D Le Rhun, HK Deng, F Biville,
S Cescau, A Danchin, G Marignac, E Lenaour, HJ Boulouis, M Mavris, L
Arnaud, H Yang, J Wang, M Quebatte, P Engel, H Saenz, C Dehio
The Trw type IV secretion system of Bartonella mediates host-specific adhesion
to erythrocytes
PLoS Pathogens (2010) 6: e1000946
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