Ravel J, Fraser CM: Genomics at the genus scale. Trends Microbiol. 2005, 13 (3): 95-97. 10.1016/j.tim.2005.01.004.
Article
CAS
PubMed
Google Scholar
Earl AM, Losick R, Kolter R: Ecology and genomics of Bacillus subtilis. Trends Microbiol. 2008, 16 (6): 269-275. 10.1016/j.tim.2008.03.004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Merrill L, Dunbar J, Richardson J, Kuske CR: Composition of Bacillus Species in Aerosols from 11 U.S. Cities. Journal of Forensic Sciences. 2006, 51 (3): 559-565. 10.1111/j.1556-4029.2006.00132.x.
Article
CAS
PubMed
Google Scholar
Hugenholtz P: Exploring prokaryotic diversity in the genomic era. Genome Biol. 2002, 3 (2): REVIEWS0003-10.1186/gb-2002-3-2-reviews0003.
Article
PubMed Central
PubMed
Google Scholar
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O: Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009, 5 (1): e1000344-10.1371/journal.pgen.1000344.
Article
PubMed Central
PubMed
Google Scholar
Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T: Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis. FEMS Microbiol Lett. 2005, 250 (2): 175-184. 10.1016/j.femsle.2005.07.008.
Article
CAS
PubMed
Google Scholar
Priest FG, Barker M, Baillie LWJ, Holmes EC, Maiden MCJ: Population Structure and Evolution of the Bacillus cereus Group. J Bacteriol. 2004, 186 (23): 7959-7970. 10.1128/JB.186.23.7959-7970.2004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Helgason E, Tourasse NJ, Meisal R, Caugant DA, Kolsto A-B: Multilocus Sequence Typing Scheme for Bacteria of the Bacillus cereus Group. Appl Environ Microbiol. 2004, 70 (1): 191-201. 10.1128/AEM.70.1.191-201.2004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A: Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003, 423 (6935): 87-91. 10.1038/nature01582.
Article
CAS
PubMed
Google Scholar
Takami H, Takaki Y, Chee GJ, Nishi S, Shimamura S, Suzuki H, Matsui S, Uchiyama I: Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res. 2004, 32 (21): 6292-6303. 10.1093/nar/gkh970.
Article
CAS
PubMed Central
PubMed
Google Scholar
Takami H, Takaki Y, Uchiyama I: Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res. 2002, 30 (18): 3927-3935. 10.1093/nar/gkf526.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997, 390 (6657): 249-256. 10.1038/36786.
Article
CAS
PubMed
Google Scholar
Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, de Leon Lopez A, Xiang H, Gusti V, Clausen IG: Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol. 2004, 5 (10): R77-10.1186/gb-2004-5-10-r77.
Article
PubMed Central
PubMed
Google Scholar
Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N: Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res. 2000, 28 (21): 4317-4331. 10.1093/nar/28.21.4317.
Article
CAS
PubMed Central
PubMed
Google Scholar
Siefert JL, Larios-Sanz M, Nakamura LK, Slepecky RA, Paul JH, Moore ER, Fox GE, Jurtshuk P: Phylogeny of marine Bacillus isolates from the Gulf of Mexico. Curr Microbiol. 2000, 41 (2): 84-88. 10.1007/s002840010098.
Article
CAS
PubMed
Google Scholar
Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernandez G, Cruz A, Ramirez E, Putonti C, Jimenez B, Martinez E: The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment. Proc Natl Acad Sci USA. 2008, 105 (15): 5803-5808. 10.1073/pnas.0800981105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci USA. 2005, 102 (39): 13950-13955. 10.1073/pnas.0506758102.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tettelin H, Riley D, Cattuto C, Medini D: Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008, 11 (5): 472-477. 10.1016/j.mib.2008.09.006.
Article
CAS
PubMed
Google Scholar
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R: The microbial pan-genome. Curr Opin Genet Dev. 2005, 15 (6): 589-594. 10.1016/j.gde.2005.09.006.
Article
CAS
PubMed
Google Scholar
Uchiyama I: Multiple genome alignment for identifying the core structure among moderately related microbial genomes. BMC Genomics. 2008, 9: 515-10.1186/1471-2164-9-515.
Article
PubMed Central
PubMed
Google Scholar
Cortez D, Forterre P, Gribaldo S: A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biology. 2009, 10 (6): R65-10.1186/gb-2009-10-6-r65.
Article
PubMed Central
PubMed
Google Scholar
Harris JK, Kelley ST, Spiegelman GB, Pace NR: The genetic core of the universal ancestor. Genome Res. 2003, 13 (3): 407-412. 10.1101/gr.652803.
Article
CAS
PubMed Central
PubMed
Google Scholar
Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, Paulsen IT, de Marsac NT, Wincker P, Dossat C: Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 2008, 9 (5): R90-10.1186/gb-2008-9-5-r90.
Article
PubMed Central
PubMed
Google Scholar
Konstantinidis KT, Tiedje JM: Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol. 2007, 10 (5): 504-509. 10.1016/j.mib.2007.08.006.
Article
CAS
PubMed
Google Scholar
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Peer Van de Y, Vandamme P, Thompson FL: Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol. 2005, 3 (9): 733-739. 10.1038/nrmicro1236.
Article
CAS
PubMed
Google Scholar
Cerritos R, Vinuesa P, Eguiarte LE, Herrera-Estrella L, Alcaraz-Peraza LD, Arvizu-Gomez JL, Olmedo G, Ramirez E, Siefert JL, Souza V: Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Cienegas Valley in Coahuila, Mexico. Int J Syst Evol Microbiol. 2008, 58 (Pt 4): 919-923. 10.1099/ijs.0.64959-0.
Article
CAS
PubMed
Google Scholar
Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E, Edwards R, Souza V, Rohwer F, Hollander D: Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cienegas, Mexico. Environ Microbiol. 2009, 11 (1): 16-34. 10.1111/j.1462-2920.2008.01725.x.
Article
CAS
PubMed
Google Scholar
Dyhrman ST, Chappell PD, Haley ST, Moffett JW, Orchard ED, Waterbury JB, Webb EA: Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nature. 2006, 439 (7072): 68-71. 10.1038/nature04203.
Article
CAS
PubMed
Google Scholar
Van Mooy BAS, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, Koblizek M, Lomas MW, Mincer TJ, Moore LR, Moutin T: Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature. 2009, 458 (7234): 69-72. 10.1038/nature07659.
Article
CAS
PubMed
Google Scholar
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC: The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008, D475-479. 36 Database
Rasko DA, Ravel J, Okstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV: The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucl Acids Res. 2004, 32 (3): 977-988. 10.1093/nar/gkh258.
Article
CAS
PubMed Central
PubMed
Google Scholar
Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003, 423 (6935): 81-86. 10.1038/nature01586.
Article
CAS
PubMed
Google Scholar
Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O: Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis. J Bacteriol. 2006, 188 (9): 3382-3390. 10.1128/JB.188.9.3382-3390.2006.
Article
PubMed Central
PubMed
Google Scholar
Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM: The complete genome sequence of Bacillus anthracis Ames "Ancestor". J Bacteriol. 2009, 191 (1): 445-446. 10.1128/JB.01347-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Challacombe JF, Altherr MR, Xie G, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O: The complete genome sequence of Bacillus thuringiensis Al Hakam. J Bacteriol. 2007, 189 (9): 3680-3681. 10.1128/JB.00241-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W: Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032. PLoS ONE. 2007, 2 (9): e928-10.1371/journal.pone.0000928.
Article
PubMed Central
PubMed
Google Scholar
Moreno-Hagelsieb G, Janga SC: Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles. Proteins. 2008, 70 (2): 344-352. 10.1002/prot.21564.
Article
CAS
PubMed
Google Scholar
Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol. 2001, 1: 8-10.1186/1471-2148-1-8.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009, 462 (7276): 1056-1060. 10.1038/nature08656.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P: Toward automatic reconstruction of a highly resolved tree of life. Science. 2006, 311 (5765): 1283-1287. 10.1126/science.1123061.
Article
CAS
PubMed
Google Scholar
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN: The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003, 4: 41-10.1186/1471-2105-4-41.
Article
PubMed Central
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP: Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes. PLoS Comput Biol. 2007, 3 (9): e175-10.1371/journal.pcbi.0030175.
Article
PubMed Central
Google Scholar
Helgason E, Okstad OA, Caugant DA, Johansen HA, Fouet A, Mock M, Hegna I, Kolsto AB: Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis--one species on the basis of genetic evidence. Appl Environ Microbiol. 2000, 66 (6): 2627-2630. 10.1128/AEM.66.6.2627-2630.2000.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hu X, Auwera Van der G, Timmery S, Zhu L, Mahillon J: Distribution, Diversity, and Potential Mobility of Extrachromosomal Elements Related to the Bacillus anthracis pXO1 and pXO2 Virulence Plasmids. Appl Environ Microbiol. 2009, 75 (10): 3016-3028. 10.1128/AEM.02709-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Luna VA, King DS, Gulledge J, Cannons AC, Amuso PT, Cattani J: Susceptibility of Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus pseudomycoides and Bacillus thuringiensis to 24 antimicrobials using Sensititre(R) automated microbroth dilution and Etest(R) agar gradient diffusion methods. J Antimicrob Chemother. 2007, 60 (3): 555-567. 10.1093/jac/dkm213.
Article
CAS
PubMed
Google Scholar
Schuch R, Fischetti VA: Detailed Genomic Analysis of the W{beta} and {gamma} Phages Infecting Bacillus anthracis: Implications for Evolution of Environmental Fitness and Antibiotic Resistance. J Bacteriol. 2006, 188 (8): 3037-3051. 10.1128/JB.188.8.3037-3051.2006.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mira A, Pushker R, Rodriguez-Valera F: The Neolithic revolution of bacterial genomes. Trends Microbiol. 2006, 14 (5): 200-206. 10.1016/j.tim.2006.03.001.
Article
CAS
PubMed
Google Scholar
Dufresne A, Garczarek L, Partensky F: Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 2005, 6 (2): R14-10.1186/gb-2005-6-2-r14.
Article
PubMed Central
PubMed
Google Scholar
Pushker R, Mira A, Rodriguez-Valera F: Comparative genomics of gene-family size in closely related bacteria. Genome Biol. 2004, 5 (4): R27-10.1186/gb-2004-5-4-r27.
Article
PubMed Central
PubMed
Google Scholar
Moran NA, Mira A: The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2001, 2 (12): RESEARCH0054-10.1186/gb-2001-2-12-research0054.
Article
CAS
PubMed Central
PubMed
Google Scholar
Setlow P: Spores of Bacillus subtilis: their resistance to and killing by radiation, heat and chemicals. Journal of Applied Microbiology. 2006, 101 (3): 514-525. 10.1111/j.1365-2672.2005.02736.x.
Article
CAS
PubMed
Google Scholar
Kageyama Y, Takaki Y, Shimamura S, Nishi S, Nogi Y, Uchimura K, Kobayashi T, Hitomi J, Ozaki K, Kawai S: Intragenomic diversity of the V1 regions of 16S rRNA genes in high-alkaline protease-producing Bacillus clausii spp. Extremophiles. 2007, 11 (4): 597-603. 10.1007/s00792-007-0074-1.
Article
CAS
PubMed
Google Scholar
Makihara F, Tsuzuki M, Sato K, Masuda S, Nagashima KV, Abo M, Okubo A: Role of trehalose synthesis pathways in salt tolerance mechanism of Rhodobacter sphaeroides f. sp. denitrificans IL106. Arch Microbiol. 2005, 184 (1): 56-65. 10.1007/s00203-005-0012-5.
Article
CAS
PubMed
Google Scholar
Mira A, Pushker R: The silencing of pseudogenes. Mol Biol Evol. 2005, 22 (11): 2135-2138. 10.1093/molbev/msi209.
Article
CAS
PubMed
Google Scholar
Mira A, Klasson L, Andersson SG: Microbial genome evolution: sources of variability. Curr Opin Microbiol. 2002, 5 (5): 506-512. 10.1016/S1369-5274(02)00358-2.
Article
CAS
PubMed
Google Scholar
Mira A, Ochman H, Moran NA: Deletional bias and the evolution of bacterial genomes. Trends Genet. 2001, 17 (10): 589-596. 10.1016/S0168-9525(01)02447-7.
Article
CAS
PubMed
Google Scholar
Chen I, Dubnau D: DNA uptake during bacterial transformation. Nat Rev Micro. 2004, 2 (3): 241-249. 10.1038/nrmicro844.
Article
CAS
Google Scholar
Kramer N, Hahn J, Dubnau D: Multiple interactions among the competence proteins of Bacillus subtilis. Mol Microbiol. 2007, 65 (2): 454-464. 10.1111/j.1365-2958.2007.05799.x.
Article
CAS
PubMed
Google Scholar
Maamar H, Dubnau D: Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol. 2005, 56 (3): 615-624. 10.1111/j.1365-2958.2005.04592.x.
Article
CAS
PubMed
Google Scholar
Earl AM, Losick R, Kolter R: Bacillus subtilis genome diversity. J Bacteriol. 2007, 189 (3): 1163-1170. 10.1128/JB.01343-06.
Article
CAS
PubMed Central
PubMed
Google Scholar
Paredes CJ, Alsaker KV, Papoutsakis ET: A comparative genomic view of clostridial sporulation and physiology. Nat Rev Micro. 2005, 3 (12): 969-978. 10.1038/nrmicro1288.
Article
CAS
Google Scholar
Piggot PJ, Hilbert DW: Sporulation of Bacillus subtilis. Curr Opin Microbiol. 2004, 7 (6): 579-586. 10.1016/j.mib.2004.10.001.
Article
CAS
PubMed
Google Scholar
Hilbert DW, Piggot PJ: Compartmentalization of gene expression during Bacillus subtilis spore formation. Microbiol Mol Biol Rev. 2004, 68 (2): 234-262. 10.1128/MMBR.68.2.234-262.2004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Errington J: Regulation of endospore formation in Bacillus subtilis. Nat Rev Microbiol. 2003, 1 (2): 117-126. 10.1038/nrmicro750.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T: KEGG for linking genomes to life and the environment. Nucl Acids Res. 2008, 36 (suppl_1): D480-484.
CAS
PubMed Central
PubMed
Google Scholar
Perego M: Kinase-phosphatase competition regulates Bacillus subtilis development. Trends Microbiol. 1998, 6 (9): 366-370. 10.1016/S0966-842X(98)01350-X.
Article
CAS
PubMed
Google Scholar
Scaramozzino F, White A, Perego M, Hoch JA: A unique GTP-dependent sporulation sensor histidine kinase in Bacillus anthracis. J Bacteriol. 2009, 191 (3): 687-692. 10.1128/JB.01184-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bauer T, Little S, Stover AG, Driks A: Functional Regions of the Bacillus subtilis Spore Coat Morphogenetic Protein CotE. J Bacteriol. 1999, 181 (22): 7043-7051.
CAS
PubMed Central
PubMed
Google Scholar
Pelczar PL, Igarashi T, Setlow B, Setlow P: Role of GerD in Germination of Bacillus subtilis Spores. J Bacteriol. 2007, 189 (3): 1090-1098. 10.1128/JB.01606-06.
Article
CAS
PubMed Central
PubMed
Google Scholar
Daniel JR, Michael YG: Sequence analysis of GerM and SpoVS, uncharacterized bacterial sporulation proteins with widespread phylogenetic distribution. Bioinformatics. 2008, 24 (16): 1793-1797. 10.1093/bioinformatics/btn314.
Article
Google Scholar
Orsburn B, Sucre K, Popham DL, Melville SB: The SpmA/B and DacF proteins of Clostridium perfringens play important roles in spore heat resistance. FEMS Microbiology Letters. 2009, 291 (2): 188-194. 10.1111/j.1574-6968.2008.01454.x.
Article
CAS
PubMed
Google Scholar
Paredes-Sabja D, Sarker N, Setlow B, Setlow P, Sarker MR: Roles of DacB and Spm Proteins in Clostridium perfringens Spore Resistance to Moist Heat, Chemicals, and UV Radiation. Appl Environ Microbiol. 2008, 74 (12): 3730-3738. 10.1128/AEM.00169-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ehling-Schulz M, Svensson B, Guinebretiere M-H, Lindback T, Andersson M, Schulz A, Fricker M, Christiansson A, Granum PE, Martlbauer E: Emetic toxin formation of Bacillus cereus is restricted to a single evolutionary lineage of closely related strains. Microbiology. 2005, 151 (1): 183-197. 10.1099/mic.0.27607-0.
Article
CAS
PubMed
Google Scholar
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP: The bacterial species challenge: making sense of genetic and ecological diversity. Science. 2009, 323 (5915): 741-746. 10.1126/science.1159388.
Article
CAS
PubMed
Google Scholar
Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM, Rooney AP, Brambilla E, Connor N, Ratcliff RM: Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics. Proceedings of the National Academy of Sciences. 2008, 105 (7): 2504-2509. 10.1073/pnas.0712205105.
Article
CAS
Google Scholar
Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P: Essential Bacillus subtilis genes. Proc Natl Acad Sci USA. 2003, 100 (8): 4678-4683. 10.1073/pnas.0730515100.
Article
CAS
PubMed Central
PubMed
Google Scholar
Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J: Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. J Bacteriol. 2006, 188 (9): 3382-3390. 10.1128/JB.188.9.3382-3390.2006.
Article
PubMed Central
PubMed
Google Scholar
Earl AM, Losick R, Kolter R: Ecology and genomics of Bacillus subtilis. Trends in Microbiology. 2008, 16 (6): 269-275. 10.1016/j.tim.2008.03.004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, Vallenet D, Wang T, Moszer I, Medigue C: From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology. 2009, 155 (Pt 6): 1758-1775. 10.1099/mic.0.027839-0.
Article
CAS
PubMed Central
PubMed
Google Scholar
Moreno-Hagelsieb G, Latimer K: Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics. 2008, 24 (3): 319-324. 10.1093/bioinformatics/btm585.
Article
CAS
PubMed
Google Scholar
Castillo-Ramirez S, Gonzalez V: Factors affecting the concordance between orthologous gene trees and species tree in bacteria. BMC Evolutionary Biology. 2008, 8 (1): 300-10.1186/1471-2148-8-300.
Article
PubMed Central
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797. 10.1093/nar/gkh340.
Article
CAS
PubMed Central
PubMed
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52 (5): 696-704. 10.1080/10635150390235520.
Article
PubMed
Google Scholar
Li KB: ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics. 2003, 19 (12): 1585-1586. 10.1093/bioinformatics/btg192.
Article
PubMed
Google Scholar
Team RDC: Development Core Team, R: A language and environment for statistical computing. 2008, R Foundation for Statistical Computing, Vienna, Austria
Google Scholar
Gregory R, Warnes BBaTL: gplots: Various R programming tools for plotting data. R package version 2.6.0. 2008
Google Scholar
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G: Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 2008, 24 (24): 2818-2824. 10.1093/bioinformatics/btn548.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8 (3): 186-194.
Article
CAS
PubMed
Google Scholar
Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007, btm009
Google Scholar
Lukashin AV, Borodovsky M: GeneMark.hmm: new solutions for gene finding. Nucl Acids Res. 1998, 26 (4): 1107-1115. 10.1093/nar/26.4.1107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS: BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005, W455-459. 10.1093/nar/gki593. 33 Web Server