Génétique des Génomes Bactériens
Genetics of Bacterial Genomes
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Our microbial genome projects
Nos projets génomes

Copyright/Disclaimer/Mentions légales

   

 

Foreword / Avertissement

 

O Gascuel, A Danchin
Protein export in prokaryotes and eukaryotes: indications of a difference in the mechanism of exportation
J Mol Evol (1986) 24: 130-142

     

A Danchin
Complete genome sequencing: future and prospects
Commission of the European Communities Directorate general Science, Research and Development; Biotechnology Action Programme 1988-1989 (1988) Chapter I: pp 1-24

A Danchin, C Médigue, O Gascuel, H Soldano, A Hénaut
From data banks to data bases

[keywords: Data bank, Data base, Library; B. subtilis, E. coli, Nucleotide and protein sequences, Updating, Learning techniques, In silico.

This paper summarizes a conference given at the beginning of the summer of 1990 on the biology of Bacillus subtilis and its genome program

Abstract: The information collected in national and international libraries on nucleotide and protein sequences cannot be directly treated for proper handling by existing software. Therefore we evaluated the feasibility of constructing a data base for Escherichia coli using the data present in the banks. The knowhow thus acquired was applied to Bacillus subtilis. Specific examples of the general procedure are given.]

Res Microbiol (1991) 142: 913-916

 

The expression "in silico" has been used in White Papers written to support the creation of bacterial genome programs. The sentence where "in silico" appeared first publicly is the following:

"Experimentation in silico

Using the data available in libraries [...]
Two sets of experiments were performed on computers (experiments in silico) using the consistency of the data extracted. [...]"

    1985 - 1997, 2007-2009

    The Bacillus subtilis genome programme

P Glaser, F Kunst, M Debarbouille, A Vertes, A Danchin, R Dedonder
A gene encoding a tyrosine tRNA synthetase is located near sacS in Bacillus subtilis
DNA Seq (1991) 1: 251-261

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

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
[this article is found in PubMed with a truncated list of authors]

     

M Santana, MS Ionescu, A Vertes, R Longin, F Kunst, A Danchin, P Glaser
Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants
J Bacteriol (1994) 176: 6802-6811

F Kunst, A Vassarotti, A Danchin
Organization of the European Bacillus subtilis genome sequencing project
Microbiology (1995) 141 ( Pt 2): 249-255

C Médigue, I Moszer, A Viari, A Danchin
Analysis of a Bacillus subtilis genome fragment using a co-operative computer system prototype
Gene (1995) 165: GC37-51

C Médigue, T Vermat, G Bisson, A Viari, A Danchin
Cooperative computer system for genome sequence analysis
Proc Int Conf Intell Syst Mol Biol (1995) 3: 249-258

I Moszer, P Glaser, A Danchin
SubtiList: a relational database for the Bacillus subtilis genome
Microbiology (1995) 141 ( Pt 2): 261-268

I Moszer, F Kunst, A Danchin
The European Bacillus subtilis genome sequencing project: current status and accessibility of the data from a new World Wide Web site
Microbiology (1996) 142: 2987-2991

F Kunst, N Ogasawara, I Moszer, AM Albertini, G Alloni, V Azevedo, MG Bertero, P Bessières, A Bolotin, S Borchert, R Borriss, L Boursier, A Brans, M Braun, SC Brignell, S Bron, S Brouillet, CV Bruschi, B Caldwell, V Capuano, NM Carter, SK Choi, JJ Codani, IF Connerton, NJ Cummings, RA Daniel, F Denizot, KM Devine, A Düsterhöft, SD Ehrlich, PT Emmerson, KD Entian, J Errington, C Fabret, E Ferrari, D Foulger, C Fritz, M Fujita, Y Fujita, S Fuma, A Galizzi, N Galleron, SY Ghim, P Glaser, A Goffeau, EJ Golightly, G Grandi, G Guiseppi, BJ Guy, K Haga, J Haiech, CR Harwood, A Hénaut, H Hilbert, S Holsappel, S Hosono, MF Hullo, M Itaya, L Jones, B Joris, D Karamata, Y Kasahara, M Klaerr-Blanchard, C Klein, Y Kobayashi, P Koetter, G Koningstein, S Krogh, M Kumano, K Kurita, A Lapidus, S Lardinois, J Lauber, V Lazarevic, SM Lee, A Levine, H Liu, S Masuda, C Mauël, C Médigue, N Medina, RP Mellado, M Mizuno, D Moesti, S Nakai, M Noback, D Noone, M O'Reilly, K Ogawa, A Ogiwara, B Oudega, SH Park, V Parro, TM Pohl, D Portetelle, S Porwollik, AM Prescott, E Presecan, P Pujic, B purnelle, G Rapoport, M Rey, S Reynolds, M Rieger, C Rivolta, E Rocha, B Roche, M Rose, Y Sadaie, T Sato, E Scalan, S Schleich, R Schroeter, F Scoffone, J Sekiguchi, A Sekowska, SJ Seror, P Serror, BS Shin, B Soldo, A Sorokin, E Tacconi, T Takagi, H Takahashi, K Takemaru, M Takeuchi, A Tamakoshi, T Tanaka, P Terpstra, A Tognoni, V Tosato, S Uchiyama, M Vandenbol, F Vannier, A Vassarotti, A Viari, R Wambutt, E Wedler, T Weitzenegger, P Winters, A Wipat, H Yamamoto, K Yamane, K Yasumoto, K Yata, K Yoshida, HF Yoshikawa, E Zumstein, H Yoshikawa, A Danchin
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
Nature (1997) 390: 249-256

     

V Barbe, S Cruveiller, F Kunst, P Lenoble, G Meurice, A Sekowska, D Vallenet, T Wang, I Moszer, 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 pubmed
pdf

 

 

    Data organisation for the genome sequence and annotation of Escherichia coli

C Médigue, JP Bouché, A Hénaut, A Danchin
Mapping of sequenced genes (700 kbp) in the restriction map of the Escherichia coli chromosome
Mol Microbiol (1990) 4: 169-187

C Médigue, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1000 kbp): update I
Mol Microbiol (1990) 4: 1443-1454

C Médigue, A Viari, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1500 kbp): update II
Mol Microbiol (1991) 5: 2629-2640

C Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654

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

    Cet article montre, pour la première fois, que dans le génome de la bactérie la mieux connue, Escherichia coli, un sixième des gènes provient d'ailleurs. Ce résultat, qui démontre l'importance considérable du transfert génétique latéral chez les bactéries, montre aussi que la fidélité de la réplication n'est pas le caractère premier des espèces, mais que les gènes de correction des erreurs se propagent par transfert horizontal.  

M Borodovsky, JD McIninch, EV Koonin, KE Rudd, C Médigue, A Danchin
Detection of new genes in a bacterial genome using Markov models for three gene classes
Nucleic Acids Res (1995) 23: 3554-3562

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 coli in silico
In: Escherichia coli and Salmonella, Cellular and Molecular Biology (Editor in Chief: Frederick C Neidhardt) vol. 1, chap 114, pp 2047-2065

P Guerdoux-Jamet, A Hénaut, P Nitschké, JL Risler, A Danchin
Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes?
DNA Res (1997) 4: 257-265

     

    1998 - 2009

     

    Photorhabdus luminescens TT01

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
Nat Biotechnol (2003) 21: 1307-1313

      Leptospira interrogans Lai               L P S N

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 Zha
Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing
Nature (2003) 422: 888-893

      Staphylococcus epidermidis ATCC 12228

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

Pseudoalteromonas haloplanktis TAC125      L P S N

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
PubMed TAC125

Herminiimonas arsenicoxydans

    (previously known as Cenibacter arsenoxidans, Caenibacter arsenoxydans, Cenibacterium arsenoxidans)

    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
    PubMed codon usage

    Psychromonas ingrahamii

    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 (2008) 9: 210
     PubMed  BMC HA F1000

    Escherichia fergusonii and various Escherichia coli strains

    The ColiScope project

    M Touchon, C Hoede, O Tenaillon, V Barbe, S Baeriswyl, P Bidet, E Bingen, S Bonacorsi, C Bouchier, O Bouvet, A Calteau, H Chiapello, O Clermont, S Cruveiller, A Danchin, M Diard, C Dossat, M El Karoui, E Frapy, L Garry, JM Ghigo, AM Gilles, J Johnson, C Le Bouguénec, M Lescat, S Mangenot, V Martinez-Jéhanne, I Matic, X Nassif, S Oztas, MA Petit, C Pichon, Z Rouy, C Saint Ruf, D Schneider, J Tourret, B Vacherie, D Vallenet, 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
    PubMed

 

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