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Publications cited at the ISI |
Publication
list |
Peer-reviewed publications are indicated in red
Publications in the domain of Philosophy, History of Sciences and Ethics
This sign indicates that the corresponding work has been performed
with or at the HKU-Pasteur
Research Centre
M Bailly-Bechet, A Danchin, M Iqbal, M
Marsili, M Vergassola
Codon usage domains over bacterial chromosomes
PLoS Computational Biology (2006) 2: e37 
( 20 K) |
An issue left unexplained in this paper is the striking quantitative difference between E. coli and B. subtilis. This is clearly visible in Fig. 6, where it is shown the probability that two genes at distance l belong to the same cluster of codon usage. Clusters are characterized by a similar codon bias and were identified using a novel information-based clustering method. While both curves decay on distances sizably longer than what could be accounted by operons, B. subtilis curve manifestly features much longer correlations. It is hard to develop a biologically well-founded explanation for such a striking difference between the two organisms. |
(28 K) |
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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 
E Couturier, EPC Rocha
Replication-associated gene dosage effects
shape the genomes of fast-growing bacteria but only for transcription and
translation genes
Mol Microbiol. (2006) 59:1 506-1518
A
Danchin
Chroniques 2006 dans La Recherche
Les deux bouts de la lorgnette 397: 97
Le goût de la fraude 399: 113
Du bon usage de la guerre biologique 402: 97
A Danchin
Beneficial biological warfare
EMBO Rep (2006) 7:767
A Danchin
Le Syndrome Chinois
(commentaire sur le livre de KT Greenfeld)
La Recherche (2006) 401:89
| A Danchin Genomics in the fight against mycobacterial diseases In: Development of New Antituberculosis Drugs (Editor WW Yew), Nova Science Publishers, Hauppauge NY, USA, (2006) pp 17-28 |
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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
G Fischer, EPC Rocha, F Brunet, M Vergassola, B Dujon
Highly variable rates of genome rearrangements between hemiascomycetous
yeast lineages
PLoS Genet (2006) 2: e32
SL Iverson-Cabral, SG Astete, CR Cohen, EPC Rocha,
PA Totten
Intrastrain heterogeneity
of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo
and suggests that variation is generated via recombination with repetitive
chromosomal sequences
Infect Immun (2006) 74: 3715-3726
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 
R Papa, S Glagla, A Danchin, T Schweder, G Marino, A Duilio
Proteomic identification of a two-component regulatory system
in Pseudoalteromonas haloplanktis TAC125
Extremophiles (2006) 10: 483-490
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 
EPC
Rocha
Inference and analysis of the relative stability of
bacterial chromosomes
Mol Biol Evol. (2006) 23: 513-522
EPC
Rocha, JM Smith, LD Hurst, MT Holden, JE Cooper, NH Smith, EJ Feil
Comparisons
of dN/dS are time dependent for closely related bacterial genomes
J
Theor Biol. 2006 239: 226-235
EPC
Rocha
The quest for the universals of protein evolution
Trends
Genet (2006) Jun 27; [Epub ahead of print]
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
W Wei, ZW Cao, YL
Zhu, XJ Wang, GH Ding, H Xu, PL Jia, D Qu, A Danchin, YX Li
Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic
profiles of Staphylococcus epidermidis RP62A and ATCC12228
BMC Genomics (2006) 7: 112
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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
From the origin of life to Synthetic Biology
BIOforum Europe (2007) 6: 30-31; Highlights
Issue (2008)
12: 4-6
A
Danchin
De la biologie symplectique à la biologie synthétique
In: L'Homme Artificiel (sous la direction de JP Changeux),
Odile Jacob, Paris (2007) pp 61-86
A
Danchin
Chroniques 2007 dans La Recherche
Masse et connaissance 404: 95
La recherche "motivée" 406: 97
Papillons cosmiques 408: 95
Le malade peut attendre 411: 97
A
Danchin
Sapremo
costruire un batterio artificiale?
Prometeo (2007) 25 (100): 14-29
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
Y Makita, MJL de Hoon, A Danchin
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation
sites in prokaryotes
BMC Bioinformatics (2007) 8: 47
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, S Koechler,V
Barbe, M Barakat, E Talla, V Bonnefoy, E Krin, F Arsene-Ploetze, C Carapito,
M Chandler, B Cournoyer, S Cruveiller, C Dossat, S Duval, M Heymann, E Leize,
A Lieutaud, D Lievremont, Y Makita, S Mangenot, W Nitschke, P Ortet, N Perdrial,
B Schoepp, P Siguier, DD Simeonova, Z Rouy, B Segurens, E Turlin, D Vallenet,
A Van Dorsselaer, S Weiss, J Weissenbach, MC Lett, 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
| G Turinici, A Danchin SARS: an alarm clock In: Encyclopedia of infectious diseases. Modern methodologies (M Tibayrenc, Editor), Wiley, NY (2007) pp 151-162 |
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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
| Revenir
au début |
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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) 59: 1543-1554
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
A
Danchin
Chroniques 2008 dans La Recherche
Est-il permis de penser l'avenir ?, 415:
113
Voir et regarder, entendre et écouter 418: 97
A
Danchin
Saurons-nous construire une bactérie synthétique ?
Médecine/Sciences 24: 533-540
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
A Ménard, A Danchin, S Dupouy, F Mégraud, P Lehours
A variable gene in a conserved region of the Helicobacter
pylori genome: Isotopic
gene replacement or rapid evolution?
DNA Res (2008) 15: 163-168
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
| Dernière
mise à jour 7 juillet 2008 |
Follow up |
Last
update july 7th, 2008 |
 Publications of the Unit Regulation of Gene Expression |
