Genome-wide analyses

The genome sequence

Daniel R Zeigler
The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics.
Microbiology (Reading): 2011, 157(Pt 7);2033-2041
[PubMed:21527469] [WorldCat.org] [DOI] (I p)

Valérie Barbe, Stéphane Cruveiller, Frank Kunst, Patricia Lenoble, Guillaume Meurice, Agnieszka Sekowska, David Vallenet, Tingzhang Wang, Ivan Moszer, Claudine Médigue, Antoine Danchin
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later.
Microbiology (Reading): 2009, 155(Pt 6);1758-1775
[PubMed:19383706] [WorldCat.org] [DOI] (P p)

Daniel R Zeigler, Zoltán Prágai, Sabrina Rodriguez, Bastien Chevreux, Andrea Muffler, Thomas Albert, Renyuan Bai, Markus Wyss, John B Perkins
The origins of 168, W23, and other Bacillus subtilis legacy strains.
J Bacteriol: 2008, 190(21);6983-95
[PubMed:18723616] [WorldCat.org] [DOI] (I p)

F Kunst, N Ogasawara, I Moszer, A M Albertini, G Alloni, V Azevedo, M G Bertero, P Bessières, A Bolotin, S Borchert, R Borriss, L Boursier, A Brans, M Braun, S C Brignell, S Bron, S Brouillet, C V Bruschi, B Caldwell, V Capuano, N M Carter, S K Choi, J J Codani, I F Connerton, N J Cummings, R A Daniel, F Denizot, K M Devine, A Düsterhöft, S D Ehrlich, P T Emmerson, K D Entian, J Errington, C Fabret, E Ferrari, D Foulger, C Fritz, M Fujita, Y Fujita, S Fuma, A Galizzi, N Galleron, S Y Ghim, P Glaser, A Goffeau, E J Golightly, G Grandi, G Guiseppi, B J Guy, K Haga, J Haiech, C R Harwood, A Hènaut, H Hilbert, S Holsappel, S Hosono, M F 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, S M Lee, A Levine, H Liu, S Masuda, C Mauël, C Médigue, N Medina, R P Mellado, M Mizuno, D Moestl, S Nakai, M Noback, D Noone, M O'Reilly, K Ogawa, A Ogiwara, B Oudega, S H Park, V Parro, T M Pohl, D Portetelle, S Porwollik, A M 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 Scanlan, S Schleich, R Schroeter, F Scoffone, J Sekiguchi, A Sekowska, S J Seror, P Serror, B S 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, H Wedler, T Weitzenegger, P Winters, A Wipat, H Yamamoto, K Yamane, K Yasumoto, K Yata, K Yoshida, H F Yoshikawa, E Zumstein, H Yoshikawa, A Danchin
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Nature: 1997, 390(6657);249-56
[PubMed:9384377] [WorldCat.org] [DOI] (P p)

Transcript analysis

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

Evert-Jan Blom, Anja N J A Ridder, Andrzej T Lulko, Jos B T M Roerdink, Oscar P Kuipers
Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis.
PLoS One: 2011, 6(11);e27160
[PubMed:22087258] [WorldCat.org] [DOI] (I p)

Kai Song
Recognition of prokaryotic promoters based on a novel variable-window Z-curve method.
Nucleic Acids Res: 2012, 40(3);963-71
[PubMed:21954440] [WorldCat.org] [DOI] (I p)

Andreas Otto, Jörg Bernhardt, Hanna Meyer, Marc Schaffer, Florian-A Herbst, Juliane Siebourg, Ulrike Mäder, Michael Lalk, Michael Hecker, Dörte Becher
Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis.
Nat Commun: 2010, 1;137
[PubMed:21266987] [WorldCat.org] [DOI] (I p)

Simon Rasmussen, Henrik Bjørn Nielsen, Hanne Jarmer
The transcriptionally active regions in the genome of Bacillus subtilis.
Mol Microbiol: 2009, 73(6);1043-57
[PubMed:19682248] [WorldCat.org] [DOI] (I p)