1967-1971 IBPC-1981 REG-1986 REG-1991 REG-1996 GGB-2001 GGB-2006 AMA-2011 AMA-2016 Cochin-2021
1972-1974 IBPC-1982 REG-1987 REG-1992 REG-1997 GGB-2002 GGB-2007 AMA-2012 ICAN-2017 
1975-1978 BRC-1983 REG-1988 REG-1993 REG-1998 GGB-2003 GGB-2008 AMA-2013 ICAN-2018
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

Authors of peer-reviewed publications are indicated in red

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

Symplectic Biology

Lectures and seminars

hkuprc This indicates that the corresponding work has been performed with or at the HKU-Pasteur Research Centre, Hong Kong

A Danchin
A brief history of genome research and bioinformatics in France
Bioinformatics (2000) 16: 65-75 pubmed

fr A Danchin
L'identité génétique
Quatrième conférence de l'Université de tous les savoirs, cycle: Qu'est-ce que la vie? video
coordonné par Yves Michaud, Odile Jacob (2000) 1: 59-68

fr A Danchin
Etapes et devenir de la révolution génomique
Regards mai 2000

The natural war [book review: The Biology of Doom by Ed Regis]
EMBO Reports (2000) 1: 216 EMBO
A Danchin
Zi ran yu ren wei (en Chinois) (UKUS Nature and Artifice)

Ke xue yu ren wen, Transcultural Dialogue (2000), Yue Daiyun, 樂 黛雲 (乐 黛云) ed., Beijing University Press 5: 1-9

A Danchin
chine Sheng wu ji shu jie he dian; meng huw xian shi?
In: Yin te wang chuang xin ji tou zi - lai zi hua er jie he gui gu de bao gao
published by the Chinese Association for Science and Business (UKUS The biotech connection: dream or reality?) (2000) 166-179
A Danchin, A Sekowska
Expression profiling in reference bacteria: dreams and reality
Genome Biol (2000) 1: REVIEWS1024 pubmed genomebiology

A Danchin, P Guerdoux-Jamet, I Moszer, P Nitschké
Mapping the bacterial cell architecture into the chromosome
Philos Trans R Soc Lond B Biol Sci (2000) 355: 179-190  pdf

V Norris, J Fralick, A Danchin
A SeqA hyperstructure and its interactions direct the replication and sequestration of DNA
Mol Microbiol (2000) 37: 696-702 pubmed

EPC Rocha, A Danchin, A Viari
The DB case: pattern matching evidence is not significant
Mol Microbiol (2000) 37: 216-218  pdf

EPC Rocha, A Sekowska, A Danchin
Sulphur islands in the Escherichia coli genome: markers of the cell's architecture?
FEBS Lett (2000) 476: 8-11  pdf

EPC Rocha, P Guerdoux-Jamet, I Moszer, A Viari, A Danchin
Implication of gene distribution in the bacterial chromosome for the bacterial cell factory
J Biotechnol (2000) 78: 209-219  pdf

A Sekowska, A Danchin, JL Risler
Phylogeny of related functions: the case of polyamine biosynthetic enzymes
Microbiology (2000) 146: 1815-1828  pdf

A Sekowska, JY Coppée, JP Le Caer, I Martin-Verstraete, A Danchin
S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts
Mol Microbiol (2000) 36: 1135-1147  pdf

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

C Tendeng, C Badaut, E Krin, P Gounon, S Ngo, A Danchin, S Rimsky, P Bertin
Isolation and characterization of vicH, encoding a new pleiotropic regulator in Vibrio cholerae
J Bacteriol (2000) 182: 2026-2032  J_Bact


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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 pubmed

JY Coppée, S Auger, E Turlin, A Sekowska, JP Le Caer, V Labas, V Vagner, A Danchin, I Martin-Verstraete
Sulfur-limitation-regulated proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study
Microbiology (2001) 147: 1631-1640  pdf

fr A Danchin
 Nature et artifice [Nature and Artifice]
Alliage (2001) 45-46: 125-133  alliage

it-flag A Danchin
II modi di produzione del sapere: esiste une specificità occidentale?
In " Tecnocrazia "
Keiron (2001) 9: 52-62 logofarm

A Danchin
Bacillus subtilis
In: “Encyclopedia of Genetics”, Academic Press, New York (2001): 135-144

A Danchin
Bacillus subtilis
Biotechnology Volume 5b: Genome Projects of Model Organisms (HJ Rehm, G Reed, A Puehler, C Sensen, editors), Wiley-VCH (2001) 12-16

A Danchin, KY Yuen
Bacterial genomics in the study of virulence
Academic Press (2001): 341-353

F Hommais, E Krin, C Laurent-Winter, O Soutourina, A Malpertuy, JP 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  pdf

MF Hullo, I Moszer, A Danchin, I Martin-Verstraete
CotA of Bacillus subtilis is a copper-dependent laccase
J Bacteriol (2001) 183: 5426-5430  J_Bact

MF Hullo, A Sekowska, E Presecan-Siedel, JY Coppée, I Martin-Verstraete, P Glaser & A Danchin
Screening for growth and lacZ reporter gene induction with metal ions and chelators, amino-acid analogs, antibiotics, inhibitors of oxidative phosphorylation and miscellaneous stress factors
In: " Functional Analysis of Bacterial Genes, A Practical Manual " (W Schumann, SD Ehrlich, N Ogasawara eds), J Wiley & Sons, Ltd (2001) 9B: 87-93

E Krin, F Hommais, O Soutourina, S Ngo, A Danchin, P Bertin
Description and application of a rapid method for genomic DNA direct sequencing
FEMS Microbiol Lett (2001) 199: 229-233  pdf

I Moszer & A Danchin
List of Bacillus subtilis unknown genes of known function
In: " Functional Analysis of Bacterial Genes, A Practical Manual " (W Schumann, S D Ehrlich, N Ogasawara eds), J Wiley & Sons, Ltd (2001) 30: 293-326

EPC Rocha, A Danchin
Ongoing evolution of strand composition in bacterial genomes
Mol Biol Evol (2001) 18: 1789-1799  pdf

EPC Rocha, A Danchin, A Viari
Evolutionary role of restriction/modification systems as revealed by comparative genome analysis
Genome Res (2001) 11: 946-958  pdf

EPC Rocha, I Moszer, M Klaerr-Blanchard, A Sekowska, C Médigue, A Viari & A Danchin
In silico Genome Analysis
In: " Functional Analysis of Bacterial Genes, A Practical Manual " (W Schumann, S D Ehrlich, N Ogasawara eds), J Wiley & Sons, Ltd (2001) 2: 5-19

A Sekowska, L Mulard, S Krogh, JK Tse, A Danchin
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis
BMC Microbiol (2001) 1: 15  BMC
A Sekowska, S Robin, JJ Daudin, A Hénaut, A Danchin
Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis
Genome Biol (2001) 2: 0019  genomebiology

OA Soutourina, EA Semenova, VV Parfenova, A Danchin, PN Bertin
Control of bacterial motility by environmental factors in polarly flagellated and peritrichous bacteria isolated from Lake Baikal
Appl Environ Microbiol (2001) 67: 3852-3859 pubmed

E Turlin, M Perrotte-Piquemal, A Danchin, F Biville
Regulation of the early steps of 3-phenylpropionate catabolism in Escherichia coli
J Mol Microbiol Biotechnol (2001) 3: 127-133 pubmed

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S Auger, WH Yuen, A Danchin, I Martin-Verstraete
The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination
Microbiology (2002) 148: 507-518  pdf

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 pubmed J_Bact
S Bocs, A Danchin, C Médigue
Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes
BMC Bioinformatics (2002) 3:BMC
S Brunak, A Danchin, M Hattori, H Nakamura, K Shinozaki, T Matise & D Preuss
Nucleotide sequence database policies
Science (2002) 298: 1333 pdf
A Danchin
Not every truth is good. The dangers of publishing knowledge about potential bioweapons
EMBO Rep (2002) 3: 102-104 pdf
fr A Danchin
Quelques problèmes éthiques posés par la biologie 
Alliage (2002) 52alliage

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  F1000_6.0 AEM
S Noria, A Danchin
Just so genome stories: what does my neighbor tell me
Proceedings of the Uehara Memorial Foundation Symposium: Genome Science: towards a new paradigm? H Yoshikawa, N Ogasawara, N Satoh, eds. Elsevier Science BV(2002) International congress series 1246: 3-13 pdf

fr-flagCette conférence explore de façon inductive les voisinages de gènes variés chez les bactéries modèles. L'illustration principale montre un couplage fort entre la synthèse de l'ADN et la dégradation des ARN par le dégradosome. La cause principale de ce couplage est la façon dont est construit le métabolisme des pyrimidines: le CDP nécessaire à la synthèse du dCDP manque au cours de la synthèse de novo. Au contraire ce métabolisme crée de l'UDP qui serait un précurseur dangereux du dUDP. L'uridylate kinase doit donc être compartimentée, ce qui est observé en effet. Mais le gène correspondant (pyrH) est associé au gène codant le facteur du recyclage du ribosome. L'étude prédit donc que la fonction de ce facteur est régulée par la présence d'UTP dans la cellule, et sa carence au moment de la synthèse des tiges et boucles terminant la transcription des opérons


UKThis conference explores inductively the neighborhoods of several genes in model bacteria. The main illustration shows a strong coupling between DNA synthesis and RNA degradation by the degradosome. The main cause of this coupling is the way pyrimidine metabolism is set up in most cells: the CDP required for dCDP synthesis is absent from the de novo synthesis pathway. In contrast, this pathway creates UDP, which would be a dangerous precursor of dUDP. Uridylate kinase must therefore be compartmentalized, which is indeed observed. But the corresponding gene (pyrH) is cotranscribed with the gene coding for the ribosome recycling factor. The study predicts that the function of this facort is regulated by the presence of UTP in the cell, and that local starvation in UTP due to the synthesis of transcription termination stem and loops at the end of operons is involved in ribosome recycling

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  J_Bact

F Hommais, C Laurent-Winter, V Labas, E Krin, C Tendeng, O Soutourina, A Danchin, P Bertin
Effect of mild acid pH on the functioning of bacterial membranes in Vibrio cholerae
Proteomics (2002) 2: 571-579 pubmed

E Krin, O Sismeiro, A Danchin, PN Bertin
The regulation of Enzyme IIA(Glc) expression controls adenylate cyclase activity in Escherichia coli
Microbiology (2002) 148: 1553-1559  pdf

C Médigue, BC Wong, MC Lin, S Bocs, A Danchin
The secE gene of Helicobacter pylori
J Bacteriol (2002) 184: 2837-2840  J_Bact
I Moszer, LM Jones, S Moreira, C Fabry, A Danchin
SubtiList: the reference database for the Bacillus subtilis genome
Nucleic Acids Res (2002) 30: 62-65  pAp

EPC Rocha, A Danchin
Base composition bias might result from competition for metabolic resources
Trends Genet (2002) 18: 291-294  pdf

fr-flagLe contenu en GC des génomes varie chez les bactéries de 25 à 75%. Nous montrons dans ce travail que le génome des bactéries qui dépendent d'un hôte pour survivre (pathogènes obligatoires ou symbiontes) tendent à devenir riches en AT. Mieux, l'analyse des bactériophages, des plasmides et des séquences d'insertion, qui peuvent être considérés comme des pathogènes intracellulaires, nous a montré qu'ils sont aussi bien plus riches en AT que leurs hôtes. Nous interprétons ce fait par le coût énergétique et la difficulté d'obtention de C et G par rapport à T/U et A, en raison de la construction des voies métaboliques. Ces conclusions s'appliquent aux virus eucaryotes comme ceux de la grippe ou du Sida  

UKThe GC content of bacterial genomes varies from 25 to 75%, but the reason for this variation is unclear. Here, we show that genomes of bacteria that rely on their host for survival (obligatory pathogens or symbionts) tend to be AT rich. Furthermore, we have analysed bacterial phages, plasmids and insertion sequences, which might also be regarded as 'intracellular pathogens', and show that they too are significantly richer in AT than their hosts. We suggest that the higher energy cost and limited availability of C and G over T/U and A could be a basis for the understanding of these differences. The same constraints apply to eukaryotic viruses such as influenza or HIV

A Sekowska, A Danchin
The methionine salvage pathway in Bacillus subtilis
BMC Microbiol (2002) 2:BMC  F1000_6.0

en-flagMany metabolites are "orphans", in that their becoming has almost never been studied in details. This is the case of methyl-thioadenosine, produced during polyamines synthesis (and production of ethylene in plants). This work in B. subtilis is the first one to use a genetic systematic approach to identify the genes involved in thiomethyl- salvage, in an economical way, without oxidation. It shows that a gene with considerable resemblance to ribulose bisphophate carboxylase oxygenase (RuBisCO, the most abundant enzyme on Earth) is involved in the cycle, and it identifies all the genes that are necessary for the "methionine salvage pathway".   fr-flagBeaucoup de métabolites sont "orphelins" en ce que leur devenir n'a pratiquement pas été étudié. C'est le cas du méthyl-thioadénosine, produit au cours de la synthèse des polyamines (et de l'éthylène chez les plantes). Ce travail chez B. subtilis est le premier a utiliser une approche génétique pour tenter d'identifier les gènes impliqués dans le cycle qui permet la récupération du groupement thiométhyl d'une façon économique, sans oxydation. Il montre en particulier qu'un gène très semblable à la ribulose bisphophate carboxylase oxygénase (RuBisCO, l'enzyme la plus abondante de la planète) est impliquée dans le cycle, et il identifie tous les gènes nécessaire au recyclage.

OA Soutourina, E Krin, C Laurent-Winter, F Hommais, A Danchin, PN Bertin
Regulation of bacterial motility in response to low pH in Escherichia coli: the role of H-NS protein
Microbiology (2002) 148: 1543-1551  pdf

X Xia, T Wei, Z Xie, A Danchin
Genomic changes in nucleotide and dinucleotide frequencies in Pasteurella multocida cultured under high temperature
Genetics (2002) 161: 1385-1394  pdf


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A Danchin
The Delphic Boat. What genomes tell us, Harvard University Press (2003)
[comment in EMBO Reports, comment in Nature Genetics, comment in Nature pdf, comment in the American Journal of Human Biology pdf, in Human Biology, comment in Magyar: A genetikai identitás (a memóriától a manipulációig) hu-flag, see also other references and comments at our "Philosophy" publications page]

en-flagLiving organisms are those material systems that tamed processes allowing them to survive in an unpredictable world. To do so they organised a way to probe and explore their environment, while keeping a memory of what it is. This memory was progressively built up by combining modules that can be used and reused in completelly different contexts. Hence, complex systems can be built up in a combinatorial approach, in a highly discontinuous way resulting from reassignment of functions for pre-selected modules. The specific case of the transparency of the lens (or of the bodyText of some animals) is used to show how systems composed of multiple elements can progressively be used to make new functions emerge.


fr-flagLes organismes vivants sont les systèmes matériels qui ont domestiqué des processus capables de leur permettre de survivre dans un environnement imprévisible. A cette fin, ils ont organisé une façon de percevoir et d'explorer leur environnement, tout en gardant la mémoire de ce qu'il est. Cette mémoire a été constituée peu à peu par la combinaison de modules qui peuvent être utilisés et réutilisés dans des contextes différents. En conséquence des systèmes complexes s'élaborent par une combinatoire, d'une façon très discontinue, du fait qu'elle résulte de la réattribution des fonctions de modules pré-existants. Le cas de la transparence du cristallin (ou du corps de certains animaux) est choisi pour montrer comment des systèmes formés d'éléments multiples peuvent voir émerger de nouvelles fonctions.

F Biville, T Oshima, H Mori, Y Kawagoe, O Bouvet, MN Rager, M Perrotte-Piquemal, A Danchin
Escherichia coli response to exogenous pyrophosphate and analogs
J Mol Microbiol Biotechnol (2003) 5: 37-45 pubmed

A Danchin
Genomes and evolution
Curr Issues Mol Biol (2003) 5: 37-42  pdf

en-flagAs described in this article, a surprising lack of curiosity of scientists prevented them to investigate the role of each of the four genes of the lactose operon. While lacI codes for the repressor, lacZ for β-galactosidase and lacY for lactose permease, the role of lacA, galactoside transacetylase, remained just anecdotal, including its remarkable poor KM. However, a simple reasoning shows that because lactose permease is so efficient any accidental induction of the operon, when bacteria are placed in a lactose-rich medium would result in building up an osmotic pressure that would make the cell explode. One needs therefore a safety valve that would begin to excrete lactose when its intracellular concentration is too high. And, to avoid building up a futile cycle with lactose getting simultaneously in and out, one needs that a labelled form of lactose is excreted. Hence acetylation, with its inefficient KM. It is more than likely that transacetylases and efflux systems are mainly playing this role of a safety valve for the many products that may be transported into cells.


fr-flagUn bizarre manque de curiosité a empêché l'étude approfondie des quatre gènes de l'opéron lactose. Alors que lacI code le represseur, lacZ la β-galactosidase et lacY la lactose perméase, le rôle de lacA, la galactoside transacétylase, est resté anecdotique, y compris son remarquable haut KM. Pourtant, un raisonnement simple montre que parce que la perméase est très active, le moindre accident d'induction dans un milieu riche en lactose va conduire à la construction d'une pression osmotique explosive. Il faut donc imaginer une soupape qui permette d'excréter le lactose dès que sa concentration devient trop élevée. Et, pour éviter le cycle futile d'une entrée-sortie du lactose, il faut que la molécule excrétée soit étiquetée. D'où l'acétylation, avec son KM inefficace. Et il est plus que probable que les nombreuses transacétylases et les systèmes d'efflux joue le rôle de soupape de sûreté pour bien des produits transportés dans la cellule.

fr A Danchin
Une nouvelle grippe pourrait faire des ravages dans le monde entier
La Recherche (2003) 365: 45

E Duchaud, C Rusniok, L Frangeul, C Buchrieser, A Givaudan, S Taourit, S Bocs, C Boursaux-Eude, M Chandler, JF Charles, E Dassa, R Derose, S Derzelle, G Freyssinet, S Gaudriault, C Médigue, A Lanois, K Powell, P Siguier, R Vincent, V Wingate, M Zouine, P Glaser, N Boemare, A Danchin, F Kunst
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
Nature Biotechnol (2003) 21: 1307-1313  PhotoList pdf F1000_6.0

C Gagyi, N Bucurenci, O Sirbu, G Labesse, M Ionescu, A Ofiteru, L Assairi, S Landais, A Danchin, O Barzu, AM Gilles
UMP kinase from the Gram-positive bacterium Bacillus subtilis is strongly dependent on GTP for optimal activity
Eur J Biochem (2003) 270: 3196-3204 pubmed


K Kobayashi, SD Ehrlich, A Albertini, G Amati, KK Andersen, M Arnaud, K Asai, S Ashikaga, S Aymerich, P Bessieres, F Boland, SC Brignell, S Bron, K Bunai, J Chapuis, LC Christiansen, A Danchin, M Debarbouille, E Dervyn, E Deuerling, K Devine, SK Devine, O Dreesen, J Errington, S Fillinger, SJ Foster, Y Fujita, A Galizzi, R Gardan, C Eschevins, T Fukushima, K Haga, CR Harwood, M Hecker, D Hosoya, MF Hullo, H Kakeshita, D Karamata, Y Kasahara, F Kawamura, K Koga, P Koski, R Kuwana, D Imamura, M Ishimaru, S Ishikawa, I Ishio, D Le Coq, A Masson, C Mauel, R Meima, RP Mellado, A Moir, S Moriya, E Nagakawa, H Nanamiya, S Nakai, P Nygaard, M Ogura, T Ohanan, M O'Reilly, M O'Rourke, Z Pragai, HM Pooley, G Rapoport, JP Rawlins, LA Rivas, C Rivolta, A Sadaie, Y Sadaie, M Sarvas, T Sato, HH Saxild, E Scanlan, W Schumann, JF Seegers, J Sekiguchi, A Sekowska, SJ Seror, M Simon, P Stragier, R Studer, H Takamatsu, T Tanaka, M Takeuchi, HB Thomaides, V Vagner, JM van Dijl, K Watabe, A Wipat, H Yamamoto, M Yamamoto, Y Yamamoto, K Yamane, K Yata, K Yoshida, H Yoshikawa, U Zuber, N Ogasawara
Essential Bacillus subtilis genes
Proc Natl Acad Sci U S A (2003) 100: 4678-4683  PNAS

fr-flagCet article, pour la première fois, inactive un à un tous les gènes d'une bactérie modèle. Cela a permis au consortium Japonais/Européen d'identifier 277 gènes essentiels pour la croissance en milieu riche, en laboratoire. On attendait avec intérêt qu'un travail semblable soit enfin réalisé pour l'autre modèle bactérien, Escherichia coli

UKThis article, for the first time, describes the inactivation, one by one, of all the genes of a model bacterium. This allowed the Japanese/European consortium of scientists to identify 277 genes that are essential for growth in a rich medium, under laboratory conditions. A similar work, with the other model bacterium, Escherichia coli, was urgently needed for comparison

E Krin, C Laurent-Winter, PN Bertin, A Danchin, A Kolb
Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12
J Bacteriol (2003) 185: 3139-3146  J_Bact

TW Ng, G Turinici, A Danchin
A double epidemic model for the SARS propagation
BMC Infect Dis (2003) 3: 19  BMC
The 2009 pattern of the H1N1 influenza epidemic is highly consistent with a double epidemic pattern, explaining the considerable difference in virulence in different regions.

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  LeptoList pdf

EPC Rocha, A Danchin
Gene essentiality determines chromosome organisation in bacteria
Nucleic Acids Res (2003) 31: 6570-6577 pubmed
EPC Rocha, J Fralick, G Vediyappan, A Danchin, V Norris
A strand-specific model for chromosome segregation in bacteria
Mol Microbiol (2003) 49: 895-903  pdf F1000_6.0
EPC Rocha, A Danchin
Essentiality, not expressiveness, drives gene-strand bias in bacteria
Nature Genetics (2003) 34: 377-378  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
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  JBC
V Tosato, K Gjuracic, K Vlahovicek, S Pongor, A Danchin, CV Bruschi
The DNA secondary structure of the Bacillus subtilis genome
FEMS Microbiol Lett (2003) 218: 23-30  pdf
YL Yap, XW Zhang, A Danchin
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
BMC Bioinformatics (2003) 4: 43  BMC
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  pdf
YQ Zhang, SX Ren, HL Li, YX Wang, G Fu, J Yang, ZQ Qin, YG Miao, WY Wang, RS Chen, Y Shen, Z Chen, ZH Yuan, GP Zhao, D Qu, 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  SepiList pdf


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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  J_Bact

The animal in the machine: is there a geometric program in the genetic program?
Proceedings of the Deuxièmes Entretiens de Bures (E Westhof, N Hardy, eds) World Scientific (2004) pp 375-399
A Danchin
The bag or the spindle: the cell factory at the time of system's biology
Microb Cell Fact (2004) 3: 13  mcf biosapiens
A Danchin, S Noria
Genome structures, operating systems and the image of the machine
In: Molecules in time and space. Bacterial shape, division and phylogeny (M Vicente, J Tamames, A Valencia, J Mingorance, eds) Kluver (2004) pp 195-208 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

S Derzelle, E Turlin, E Duchaud, S Pages, 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  J_Bact

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 pubmed 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

EPC Rocha, A Danchin
An analysis of determinants of amino-acids substitution rates in bacterial proteins
Mol Biol Evol (2004) 21: 108-116  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:BMC biosapiens
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
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 BMC

XW Zhang, YL Yap, A Danchin Testing hypothesis of a recombinant origin of the SARS-associated coronavirus
Arch Virol (2004) 150: 1-20  pdf


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H Ashida, A Danchin, A Yokota
Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?
Res Microbiol (2005) 156: 611-618  pdf

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 pubmed

A Danchin
Genome diversity: A grammar of microbial genomes
ComPlexUs (2004/2005) 2: 61-70 turing_machines  biosapiens

uk-flagThe metaphor of the genetic program is ubiquitously used. Does it bring about a deeper insight into what cells are? In brief, computers do not make computers, but cells make cells. Pursuing the analogy in its deepest consequences, we explore bacterial genome diversity as organized around core programs meant to couple the expression of the program with the architecture of the cell. At first sight genomes appear to evolve fast and exhibit no rule of organization. However, when the huge number of generations separating various organisms is taken into account, diversity appears only as a trivial observation. In contrast, rules of gene organization are observed, for example in the separation between Archaea and Bacteria, in the composition of the leading and lagging strand of the chromosomes, in the distribution of genes along the DNA strands, or in the formation (and conservation) of operons and pathogenicity islands. This leads to the conjecture that the core genome makes a kind of "celluloculus" which would control and organise the construction of the cell.   fr-flagOn utilise universellement la métaphore du programme génétique. Mais nous donne-t-elle une vision profonde de ce que sont les cellules ? En bref, les ordinateurs ne font pas des ordinateurs alors que les cellules font des cellules. Si l'on explore en profondeur les conséquences de l'analogie, on remarque que la diversité génomique bactérienne s'organise autour de programmes centraux qui organisent l'expression du programme en parallèle avec l'architecture cellulaire. A première vue les génomes semblent évoluer rapidement et sans règle. Pourtant, quand on remarque le nombre considérable des générations qui séparent les divers organismes, cette diversité semble bien banale. Tout au contraire, on remarque la présence de règles d'organisation, par exemple dans la séparation entre les Archaea et les Bacteria, ou dans la composition du brin direct et du brin complémentaire des chromosomes, dans la répartition des gènes dans ces brins, ou dans la formation (ou la conservation) des opérons et des îlots de pathogénicité. En bref on peut postuler l'existence d'un "celluloculus" qui organiserait le programme de construction de la cellule.
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 BMC biosapiens

A Pühler, D Jording, J Kalinowski, D Buttgereit, R Renkawitz-Pohl, L Altschmied, A Danchin, A Sekowska, H Feldmann, HP Klenk, M Kröger
Genome projects on model organisms
Handbook of Genome Research, Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical and Legal Issues, CW Sensen ed
Wiley-VCH (2005) 1: 3-43pdf

HD Song, CC Tu, GW Zhang, SY Wang, K Zheng, LC Lei, QX Chen, YW Gao, HQ Zhou, H Xiang, HJ Zheng, SW Wang Chern, F Cheng, CM Pan, H Xuan, SJ Chen, HM Luo, DH Zhou, YF Liu, JF He, PZ Qin, LH Li, YQ Ren, WJ Liang, YD Yu, L Anderson, M Wang, RH Xu, XW Wu, HY Zheng, JD Chen, GD Liang, Y Gao, M Liao, L Fang, LY Jiang, H Li, F Chen, B Di, LJ He, JY Lin, SX Tong, XG Kong, L Du, P Hao, H Tang, A Bernini, XJ Yu, O Spiga, ZM Guo, HY Pan, WZ He, JC Manuguerra, A Fontanet, 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  PNAS

fr-flagCet article analyse l'évolution, en temps réel, du virus du SRAS à la fois chez l'Homme et chez la civette. L'occasion en a été fournie par l'épisode de la maladie à Canton au cours de l'hiver 2003-2004. Le résultat le plus remarquable de cette étude est que le virus est en pleine évolution, à la fois chez l'Homme et chez la civette, ce qui démontre que son réservoir est antérieur, et reste pour l'instant inconnu. Cela pourrait être un rongeur


UKThis article analyses, in real time, the evolution of the SARS virus, in Man and in the civet cat. The opportunity to study this evolution came from the 2003-2004 episode in the Guangdong province. The most fascinating result of this study is that the virus is still evolving at a fast pace in both its hosts. This demonstrates in an unambiguous manner that its reservoir is upstream, and is still unknown. It could be a rodent

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  pdf
G Pascal, C Médigue, A Danchin
Universal biases in protein composition of model prokaryotes
Proteins (2005) 60: 27-35 pubmed biosapiens

fr-flagLe nuage des points formés des protéines d'un organisme, réparties dans un espace construit sur la composition en acides aminés sépare d'abord selon la charge électrique des acides aminés, opposée à leur caractère hydrophobe. Cela crée une classe homogène bien indentifiée, formée des protéines intégrales de la membrane interne. Un second biais est imposé par le contenu en G+C du génome, et sépare les protéines en fonction du contenu en G+C de la première position des codons correspondants aux acides aminés. Enfin un rôle remarquable des acides aminés aromatiques crée un troisième biais universel. Les protéines "orphelines" sont enrichies en ces derniers, suggérant qu'ils ont un rôle privilégié dans la création de fonctions nouvelles au cours de l'évolution. Nous postulons que la majorité d'entre elles — les gluons — sont impliquées dans la stabilisation de complexes multimériques, et participent ainsi à la définition du "soi" de l'espèce.


UKIn the cloud of points of proteins distributed along the axes of their amino acid composition, the electric charge of amino-acids measured against hydrophobicity creates a highly homogeneous cluster, made exclusively of proteins that areintegral inner membrane proteins. A second bias is imposed by the G+C content of the genome, separating protein according to the G+C content of their first codon position. A remarkable role of aromatic amino-acids creates a third universal bias. Expressed orphan proteins are enriched in these residues, suggesting that they might participate in a process of gain of function during evolution. We postulate that the majority is made of proteins — gluons — involved in stabilising complexes, thus defining the "self" of the species.

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  NAR

G Fang, EPC Rocha, A Danchin
How essential are non-essential genes?
Mol Biol Evol (2005) 22: 2147-2156   pdf biosapiensb7

fr-flagOn identifie habituellement le caractère essentiel d'un gène par les propriétés de croissance d'une bactérie en laboratoire. Cette vue est évidemment extrêmement biaisée et ne rend nullement compte de l'importance d'un gène dans la vie réelle. Nous avons exploré la nature de l'essentialité des gènes chez les Bactéries (un travail analogue sera nécessaire pour les autres règnes) en recherchant le caractère de "persistance" des gènes, c-à-d non seulement leur caractère d'orthologie dans un grand nombre de Bactéries, mais aussi le fait qu'ils conservent un certain nombre de propriétés par rapport à l'organisation du génome et un certain schéma d'évolution. Cela nous a permis de mesurer la nature réelle de l'essentialité et nous a donné quelques idées sur la capture de structures destinées à remplir une même fonction (évolution acquisitive). Resource pour l'annotation fonctionnelle des gènes (programme BioSapiens).   UKGene essentiality has usually been identified in prokaryotes by growth properties under laboratory conditions. This is obviously an extremely biased view of the importance of a gene in real life. We explored the nature of essentiality in Bacteria (a similar work has to be done in the other kingdoms of life) by looking for "persistent" genes, i;e. genes that not only are kept as orthologs in a wide variety of Bacteria, but also that keep common rules of organisation in the genome, as well as a certain pattern of evolution. This allowed us to measure the real nature of essentiality and to have some insight about the extent of acquisitive evolution whereby different structures are recruited for a given function. This work provides a phylogenetic contribution to the BioSapiens effort by creating a resource for functional gene annotation

P Burguière, J Fert, I Guillouard, S Auger S, A Danchin, I Martin-Verstraete
Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism.
J Bacteriol (2005) 187: 6019-6030  J_Bact

E Larsabal, A Danchin
Genomes are covered with ubiquitous 11bp periodic patterns, the "class A flexible patterns"
BMC Bioinformatics (2005) 6: 206  BMC

fr-flagOn sait depuis longtemps que les génomes ne sont pas une suite aléatoire de nucléotides. On y remarque en particulier une corrélation entre les nucléotides toutes les trois positions, ce qui s'explique facilement par la présence des régions codant les protéines. Mais on observe aussi une corrélation, un peu floue entre les nucléotides toutes les 10 à 12 positions. On n'avait jusqu'à présent aucune idée de leur cause. Le travail présenté montre que cette corrélation est due à des motifs discontinus, flexibles (en ce sens que les nucléotides conservés sont en des positions à peu près conservées), et probablement la marque de l'interaction avec des protéines qui se lient avec le chromosome. Ces motifs sont si densément répartis que, dans certains cas, comme celui de Helicobacter pylori, un nucléotide sur 4 dans le génome est déterminé par ces motifs


UKIt has long been known that genomes are not random nucleotide sequences. In particular they are covered by regions where nucleotides are correlated every third position. This is the consequence of the dense presence of protein coding regions in the genomes. A second correlation has also been uncovered, but it remained totally unexplained until the present work: there is a correlation on the nature of nucleotides every 10-12 nucleotide. We show that this is due to the presence of a dense network of discontinuous motifs, which are "flexible" (in that the conserved nucleotides are not exactly located at the same position in each and every motif but only approximately so). These motifs are likely to be the hallmark of protein-DNA interactions. There are so densely distributed that in some cases, such as the genome of Helicobacter pylori, one nucleotide in four is determined by a conserved flexible motif

J Thornton, A Tramontano, U Roma, A Valencia, S Brunak, S Antonarakis, P Bork, R Casadio, A Danchin, R Durbin, D Frishman, R Guigo, G von Heijne, J van Helden, T Lengauer, M Linial, R Mott, C Orengo, D Jones, L Patthy, L Rychlewski, V Schachter, D Schomburg, E Ukkonen, AL Veuthey, M Vingron, G Vriend, K Nyberg
BioSapiens: a European network for integrated genome annotation
Eur J Hum Genet (2005) 13: 994-997 biosapiens


C Médigue, E Krin, G Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G Marino, J Nilsson, E Parrilli, EPC Rocha, Z Rouy, A Sekowska, ML Tutino, D Vallenet, 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  GR biosapiens b7

CH You, HY Lu, A Sekowska, G Fang, YP Wang, AM Gilles, A Danchin
The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis
BMC Microbiology (2005) 5: 57  BMC
XW Zhang, YL Yap, D Wei, F Chen, A Danchin
Molecular diagnosis of human cancer type by gene expression profiles and independent component analysis
Eur J Hum Genet (2005) 13: 1303-1311  pdf

Publications in the Unit Regulation of Gene Expression