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Evidence for symmetric chromosomal inversions around the replication origin in bacteria
Jonathan A Eisen, John F Heidelberg, Owen White, Steven L Salzberg
Genome Biol. 2000; 1(6): research0011.1–11.9. Published online 2000 December 4.
PMCID:
PMC16139
Abstract Full Text PDF–200K
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 Is Cited by the Following 45 Articles in this Archive:
The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes
John M. Chaston, Garret Suen, Sarah L. Tucker, Aaron W. Andersen, Archna Bhasin, Edna Bode, Helge B. Bode, Alexander O. Brachmann, Charles E. Cowles, Kimberly N. Cowles, Creg Darby, Limaris de Léon, Kevin Drace, Zijin Du, Alain Givaudan, Erin E. Herbert Tran, Kelsea A. Jewell, Jennifer J. Knack, Karina C. Krasomil-Osterfeld, Ryan Kukor, Anne Lanois, Phil Latreille, Nancy K. Leimgruber, Carolyn M. Lipke, Renyi Liu, Xiaojun Lu, Eric C. Martens, Pradeep R. Marri, Claudine Médigue, Megan L. Menard, Nancy M. Miller, Nydia Morales-Soto, Stacie Norton, Jean-Claude Ogier, Samantha S. Orchard, Dongjin Park, Youngjin Park, Barbara A. Qurollo, Darby Renneckar Sugar, Gregory R. Richards, Zoé Rouy, Brad Slominski, Kathryn Slominski, Holly Snyder, Brian C. Tjaden, Ransome van der Hoeven, Roy D. Welch, Cathy Wheeler, Bosong Xiang, Brad Barbazuk, Sophie Gaudriault, Brad Goodner, Steven C. Slater, Steven Forst, Barry S. Goldman, Heidi Goodrich-Blair
PLoS One. 2011; 6(11): e27909. Published online 2011 November 18. doi: 10.1371/journal.pone.0027909
PMCID:
PMC3220699
Abstract Full Text PDF–826K Supplementary Material
Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
Ole Skovgaard, Mads Bak, Anders Løbner-Olesen, Niels Tommerup
Genome Res. 2011 August; 21(8): 1388–1393. doi: 10.1101/gr.117416.110
PMCID:
PMC3149504
Abstract Full Text PDF–543K
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T
Karin Schwibbert, Alberto Marin-Sanguino, Irina Bagyan, Gabriele Heidrich, Georg Lentzen, Harald Seitz, Markus Rampp, Stephan C Schuster, Hans-Peter Klenk, Friedhelm Pfeiffer, Dieter Oesterhelt, Hans Jörg Kunte
Environ Microbiol. 2011 August; 13(8): 1973–1994. doi: 10.1111/j.1462-2920.2010.02336.x
PMCID:
PMC3187862
Abstract Full Text PDF–1.6M Supplementary Material
Genome-level homology and phylogeny of Shewanella (Gammaproteobacteria: lteromonadales: Shewanellaceae)
Rebecca B Dikow
BMC Genomics. 2011; 12: 237. Published online 2011 May 12. doi: 10.1186/1471-2164-12-237
PMCID:
PMC3107185
Abstract Full Text PDF–3.2M
Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements
Hanna Skarin, Therese Håfström, Josefina Westerberg, Bo Segerman
BMC Genomics. 2011; 12: 185. Published online 2011 April 12. doi: 10.1186/1471-2164-12-185
PMCID:
PMC3098183
Abstract Full Text PDF–5.5M Supplementary Material
New Implications on Genomic Adaptation Derived from the Helicobacter pylori Genome Comparison
Edgar Eduardo Lara-Ramírez, Aldo Segura-Cabrera, Xianwu Guo, Gongxin Yu, Carlos Armando García-Pérez, Mario A. Rodríguez-Pérez
PLoS One. 2011; 6(2): e17300. Published online 2011 February 28. doi: 10.1371/journal.pone.0017300
Correction in:
PLoS One. 2011; 6(3): 10.1371/annotation/d8fae120-5f86-4df7-8e53-46afa9c01be0.
Correction in:
PLoS One. 2011; 6(3): 10.1371/annotation/2f2953da-1918-4068-a730-46660d43e6b5.
PMCID:
PMC3046158
Abstract Full Text PDF–900K Supplementary Material Correction Correction
Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans
Weerayuth Kittichotirat, Roger Bumgarner, Casey Chen
BMC Genomics. 2010; 11: 489. Published online 2010 September 8. doi: 10.1186/1471-2164-11-489
PMCID:
PMC2996985
Abstract Full Text PDF–3.1M Supplementary Material
Constraints and plasticity in genome and molecular-phenome evolution
Eugene V. Koonin, Yuri I. Wolf
Nat Rev Genet. Author manuscript; available in PMC 2012 February 6.
Published in final edited form as: Nat Rev Genet. 2010 July; 11(7): 487–498. doi: 10.1038/nrg2810
PMCID:
PMC3273317
Abstract Full Text PDF–992K
Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen
Paul W O'Toole, William J Snelling, Carlos Canchaya, Brian M Forde, Kim R Hardie, Christine Josenhans, Robert LJ Graham, Geoff McMullan, Julian Parkhill, Eugenio Belda, Stephen D Bentley
BMC Genomics. 2010; 11: 164. Published online 2010 March 10. doi: 10.1186/1471-2164-11-164
PMCID:
PMC2846917
Abstract Full Text PDF–2.5M Supplementary Material
The Genome of Streptococcus mitis B6 - What Is a Commensal?
Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, Rolf Wambutt, Regine Hakenbeck
PLoS One. 2010; 5(2): e9426. Published online 2010 February 25. doi: 10.1371/journal.pone.0009426
PMCID:
PMC2828477
Abstract Full Text PDF–1.0M Supplementary Material
High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak
Matthew W Gilmour, Morag Graham, Gary Van Domselaar, Shaun Tyler, Heather Kent, Keri M Trout-Yakel, Oscar Larios, Vanessa Allen, Barbara Lee, Celine Nadon
BMC Genomics. 2010; 11: 120. Published online 2010 February 18. doi: 10.1186/1471-2164-11-120
PMCID:
PMC2834635
Abstract Full Text PDF–1.6M Supplementary Material
Conditions for the Evolution of Gene Clusters in Bacterial Genomes
Sara Ballouz, Andrew R. Francis, Ruiting Lan, Mark M. Tanaka
PLoS Comput Biol. 2010 February; 6(2): e1000672. Published online 2010 February 12. doi: 10.1371/journal.pcbi.1000672
PMCID:
PMC2820515
Abstract Full Text PDF–596K
Co-Orientation of Replication and Transcription Preserves Genome Integrity
Anjana Srivatsan, Ashley Tehranchi, David M. MacAlpine, Jue D. Wang
PLoS Genet. 2010 January; 6(1): e1000810. Published online 2010 January 15. doi: 10.1371/journal.pgen.1000810
PMCID:
PMC2797598
Abstract Full Text PDF–662K Supplementary Material
The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity
Marco Ventura, Francesca Turroni, Aldert Zomer, Elena Foroni, Vanessa Giubellini, Francesca Bottacini, Carlos Canchaya, Marcus J. Claesson, Fei He, Maria Mantzourani, Laura Mulas, Alberto Ferrarini, Beile Gao, Massimo Delledonne, Bernard Henrissat, Pedro Coutinho, Marco Oggioni, Radhey S. Gupta, Ziding Zhang, David Beighton, Gerald F. Fitzgerald, Paul W. O'Toole, Douwe van Sinderen
PLoS Genet. 2009 December; 5(12): e1000785. Published online 2009 December 24. doi: 10.1371/journal.pgen.1000785
PMCID:
PMC2788695
Abstract Full Text PDF–1.2M Supplementary Material
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content
Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa
BMC Genomics. 2009; 10: 358. Published online 2009 August 5. doi: 10.1186/1471-2164-10-358
PMCID:
PMC2907686
Abstract Full Text PDF–1.5M Supplementary Material
Hidden Chromosome Symmetry: In Silico Transformation Reveals Symmetry in 2D DNA Walk Trajectories of 671 Chromosomes
Maria S. Poptsova, Sergei A. Larionov, Eugeny V. Ryadchenko, Sergei D. Rybalko, Ilya A. Zakharov, Alexander Loskutov
PLoS One. 2009; 4(7): e6396. Published online 2009 July 28. doi: 10.1371/journal.pone.0006396
PMCID:
PMC2712679
Abstract Full Text PDF–800K Supplementary Material
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea
Yvan Zivanovic, Jean Armengaud, Arnaud Lagorce, Christophe Leplat, Philippe Guérin, Murielle Dutertre, Véronique Anthouard, Patrick Forterre, Patrick Wincker, Fabrice Confalonieri
Genome Biol. 2009; 10(6): R70. Published online 2009 June 26. doi: 10.1186/gb-2009-10-6-r70
PMCID:
PMC2718504
Abstract Full Text PDF–1.2M Supplementary Material
Genome Sequence of Azotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes
João C. Setubal, Patricia dos Santos, Barry S. Goldman, Helga Ertesvåg, Guadelupe Espin, Luis M. Rubio, Svein Valla, Nalvo F. Almeida, Divya Balasubramanian, Lindsey Cromes, Leonardo Curatti, Zijin Du, Eric Godsy, Brad Goodner, Kaitlyn Hellner-Burris, José A. Hernandez, Katherine Houmiel, Juan Imperial, Christina Kennedy, Timothy J. Larson, Phil Latreille, Lauren S. Ligon, Jing Lu, Mali Mærk, Nancy M. Miller, Stacie Norton, Ina P. O'Carroll, Ian Paulsen, Estella C. Raulfs, Rebecca Roemer, James Rosser, Daniel Segura, Steve Slater, Shawn L. Stricklin, David J. Studholme, Jian Sun, Carlos J. Viana, Erik Wallin, Baomin Wang, Cathy Wheeler, Huijun Zhu, Dennis R. Dean, Ray Dixon, Derek Wood
J Bacteriol. 2009 July; 191(14): 4534–4545. Published online 2009 May 8. doi: 10.1128/JB.00504-09
PMCID:
PMC2704721
Abstract Full Text PDF–1.8M Supplementary Material
Conservation in the face of diversity: multistrain analysis of an intracellular bacterium
Michael J Dark, David R Herndon, Lowell S Kappmeyer, Mikel P Gonzales, Elizabeth Nordeen, Guy H Palmer, Donald P Knowles, Jr, Kelly A Brayton
BMC Genomics. 2009; 10: 16. Published online 2009 January 11. doi: 10.1186/1471-2164-10-16
PMCID:
PMC2649000
Abstract Full Text PDF–2.8M Supplementary Material
The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome
D. A. Sela, J. Chapman, A. Adeuya, J. H. Kim, F. Chen, T. R. Whitehead, A. Lapidus, D. S. Rokhsar, C. B. Lebrilla, J. B. German, N. P. Price, P. M. Richardson, D. A. Mills
Proc Natl Acad Sci U S A. 2008 December 2; 105(48): 18964–18969. Published online 2008 November 24. doi: 10.1073/pnas.0809584105
PMCID:
PMC2596198
Abstract Full Text PDF–600K Supplementary Material
Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes
Pavel S. Novichkov, Yuri I. Wolf, Inna Dubchak, Eugene V. Koonin
J Bacteriol. 2009 January; 191(1): 65–73. Published online 2008 October 31. doi: 10.1128/JB.01237-08
PMCID:
PMC2612427
Abstract Full Text PDF–906K
Genome Sequence of a Lancefield Group C Streptococcus zooepidemicus Strain Causing Epidemic Nephritis: New Information about an Old Disease
Stephen B. Beres, Ricardo Sesso, Sergio Wyton L. Pinto, Nancy P. Hoe, Stephen F. Porcella, Frank R. DeLeo, James M. Musser
PLoS ONE. 2008; 3(8): e3026. Published online 2008 August 21. doi: 10.1371/journal.pone.0003026
PMCID:
PMC2516327
Abstract Full Text PDF–666K Supplementary Material
Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation
Sheri L Simmons, Genevieve DiBartolo, Vincent J Denef, Daniela S. Aliaga Goltsman, Michael P Thelen, Jillian F Banfield
PLoS Biol. 2008 July; 6(7): e177. Published online 2008 July 22. doi: 10.1371/journal.pbio.0060177
PMCID:
PMC2475542
Abstract Full Text PDF–954K Supplementary Material
Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea Iron Reducing Bacterium Shewanella piezotolerans WP3
Fengping Wang, Jianbin Wang, Huahua Jian, Bing Zhang, Shengkang Li, Feng Wang, Xiaowei Zeng, Lei Gao, Douglas Hoyt Bartlett, Jun Yu, Songnian Hu, Xiang Xiao
PLoS ONE. 2008; 3(4): e1937. Published online 2008 April 9. doi: 10.1371/journal.pone.0001937
Correction in:
PLoS ONE. 2008; 3(5): 10.1371/annotation/744d7c8d-db8a-4ad4-aec5-62549b1dbefe.
PMCID:
PMC2276687
Abstract Full Text PDF–1.2M Correction
Chromosome Structuring Limits Genome Plasticity in Escherichia coli
Emilie Esnault, Michèle Valens, Olivier Espéli, Frédéric Boccard
PLoS Genet. 2007 December; 3(12): e226. Prepublished online 2007 November 6. Published online 2007 December 14. doi: 10.1371/journal.pgen.0030226
PMCID:
PMC2134941
Abstract Full Text PDF–1.2M Supplementary Material
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks
Kira S. Makarova, Marina V. Omelchenko, Elena K. Gaidamakova, Vera Y. Matrosova, Alexander Vasilenko, Min Zhai, Alla Lapidus, Alex Copeland, Edwin Kim, Miriam Land, Konstantinos Mavromatis, Samuel Pitluck, Paul M. Richardson, Chris Detter, Thomas Brettin, Elizabeth Saunders, Barry Lai, Bruce Ravel, Kenneth M. Kemner, Yuri I. Wolf, Alexander Sorokin, Anna V. Gerasimova, Mikhail S. Gelfand, James K. Fredrickson, Eugene V. Koonin, Michael J. Daly
PLoS ONE. 2007; 2(9): e955. Published online 2007 September 26. doi: 10.1371/journal.pone.0000955
PMCID:
PMC1978522
Abstract Full Text PDF–850K Supplementary Material
Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum
Marco Ventura, Carlos Canchaya, Andreas Tauch, Govind Chandra, Gerald F. Fitzgerald, Keith F. Chater, Douwe van Sinderen
Microbiol Mol Biol Rev. 2007 September; 71(3): 495–548. doi: 10.1128/MMBR.00005-07
PMCID:
PMC2168647
Abstract Full Text PDF–1.5M Supplementary Material
Chromosomal periodicity of evolutionarily conserved gene pairs
Matthew A. Wright, Peter Kharchenko, George M. Church, Daniel Segrè
Proc Natl Acad Sci U S A. 2007 June 19; 104(25): 10559–10564. Published online 2007 June 11. doi: 10.1073/pnas.0610776104
PMCID:
PMC1890563
Abstract Full Text PDF–1.8M Supplementary Material
Reductive Genome Evolution from the Mother of Rickettsia
Guillaume Blanc, Hiroyuki Ogata, Catherine Robert, Stéphane Audic, Karsten Suhre, Guy Vestris, Jean-Michel Claverie, Didier Raoult
PLoS Genet. 2007 January; 3(1): e14. Published online 2007 January 19. doi: 10.1371/journal.pgen.0030014
PMCID:
PMC1779305
Abstract Full Text PDF–590K Supplementary Material
Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a
Huan Nie, Fan Yang, Xiaobing Zhang, Jian Yang, Lihong Chen, Jing Wang, Zhaohui Xiong, Junping Peng, Lilian Sun, Jie Dong, Ying Xue, Xingye Xu, Shuxia Chen, Zhijian Yao, Yan Shen, Qi Jin
BMC Genomics. 2006; 7: 173. Published online 2006 July 6. doi: 10.1186/1471-2164-7-173
PMCID:
PMC1550401
Abstract Full Text PDF–483K Supplementary Material
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