My NCBISign In
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes
Yang Liu, Paul M Harrison, Victor Kunin, Mark Gerstein
Genome Biol. 2004; 5(9): R64. Published online 2004 August 26. doi: 10.1186/gb-2004-5-9-r64
PMCID:
PMC522871
Abstract Full Text PDF–300K

Is Cited by the Following 40 Articles in this Archive:

Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments
Yong Wang, Jiang Ke Yang, On On Lee, Tie Gang Li, Abdulaziz Al-Suwailem, Antoine Danchin, Pei-Yuan Qian
PLoS One. 2011; 6(12): e29149. Published online 2011 December 21. doi: 10.1371/journal.pone.0029149
PMCID:
PMC3244439
Abstract Full Text PDF–601K Supplementary Material
Solving the Problem: Genome Annotation Standards before the Data Deluge
William Klimke, Claire O'Donovan, Owen White, J. Rodney Brister, Karen Clark, Boris Fedorov, Ilene Mizrachi, Kim D. Pruitt, Tatiana Tatusova
Stand Genomic Sci. 2011 October 15; 5(1): 168–193. Published online 2011 October 1. doi: 10.4056/sigs.2084864
PMCID:
PMC3236044
Abstract Full Text PDF–909K
An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes
Jia-Feng Yu, Ke Xiao, Dong-Ke Jiang, Jing Guo, Ji-Hua Wang, Xiao Sun
DNA Res. 2011 December; 18(6): 435–449. Published online 2011 September 8. doi: 10.1093/dnares/dsr030
PMCID:
PMC3223076
Abstract Full Text PDF–396K Supplementary Material
The mosaicism of plasmids revealed by atypical genes detection and analysis
Emanuele Bosi, Renato Fani, Marco Fondi
BMC Genomics. 2011; 12: 403. Published online 2011 August 8. doi: 10.1186/1471-2164-12-403
PMCID:
PMC3166947
Abstract Full Text PDF–812K Supplementary Material
Inferring functional modules of protein families with probabilistic topic models
Sebastian GA Konietzny, Laura Dietz, Alice C McHardy
BMC Bioinformatics. 2011; 12: 141. Published online 2011 May 9. doi: 10.1186/1471-2105-12-141
PMCID:
PMC3098182
Abstract Full Text PDF–1.4M Supplementary Material
Complete genome sequence of Cellulophaga lytica type strain (LIM-21T)
Amrita Pati, Birte Abt, Hazuki Teshima, Matt Nolan, Alla Lapidus, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Konstantinos Mavromatis, Galina Ovchinikova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, John C. Detter, Evelyne-Marie Brambilla, K. Palani Kannan, Manfred Rohde, Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Natalia Ivanova
Stand Genomic Sci. 2011 April 29; 4(2): 221–232. Published online 2011 April 29. doi: 10.4056/sigs.1774329
PMCID:
PMC3111997
Abstract Full Text PDF–2.4M
Marine integrons containing novel integrase genes, attachment sites, attI, and associated gene cassettes in polluted sediments from Suez and Tokyo Bays
Hosam Elsaied, Hatch W Stokes, Keiko Kitamura, Yasurou Kurusu, Yoichi Kamagata, Akihiko Maruyama
ISME J. 2011 July; 5(7): 1162–1177. Published online 2011 January 20. doi: 10.1038/ismej.2010.208
PMCID:
PMC3146285
Abstract Full Text PDF–2.8M Supplementary Material
Mycobacterium leprae: genes, pseudogenes and genetic diversity
Pushpendra Singh, Stewart T Cole
Future Microbiol. Author manuscript; available in PMC 2011 November 1.
Published in final edited form as: Future Microbiol. 2011 January; 6(1): 57–71. doi: 10.2217/fmb.10.153
PMCID:
PMC3076554
Abstract Full Text PDF–241K
The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons
Enrique M. Muro, Nancy Mah, Gabriel Moreno-Hagelsieb, Miguel A. Andrade-Navarro
Nucleic Acids Res. 2011 March; 39(5): 1732–1738. Published online 2010 November 4. doi: 10.1093/nar/gkq1067
PMCID:
PMC3061063
Abstract Full Text PDF–2.9M Supplementary Material
Inferring Bacterial Genome Flux While Considering Truncated Genes
Weilong Hao, G. Brian Golding
Genetics. 2010 September; 186(1): 411–426. doi: 10.1534/genetics.110.118448
PMCID:
PMC2940306
Abstract Full Text PDF–2.2M
Comparative Genome Biology of a Serogroup B Carriage and Disease Strain Supports a Polygenic Nature of Meningococcal Virulence
Biju Joseph, Susanne Schneiker-Bekel, Anja Schramm-Glück, Jochen Blom, Heike Claus, Burkhard Linke, Roland F. Schwarz, Anke Becker, Alexander Goesmann, Matthias Frosch, Christoph Schoen
J Bacteriol. 2010 October; 192(20): 5363–5377. Published online 2010 August 13. doi: 10.1128/JB.00883-10
PMCID:
PMC2950490
Abstract Full Text PDF–1.8M Supplementary Material
The Extinction Dynamics of Bacterial Pseudogenes
Chih-Horng Kuo, Howard Ochman
PLoS Genet. 2010 August; 6(8): e1001050. Published online 2010 August 5. doi: 10.1371/journal.pgen.1001050
PMCID:
PMC2916853
Abstract Full Text PDF–451K Supplementary Material
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies
Eugeni Belda, Andrés Moya, Stephen Bentley, Francisco J Silva
BMC Genomics. 2010; 11: 449. Published online 2010 July 22. doi: 10.1186/1471-2164-11-449
PMCID:
PMC3091646
Abstract Full Text PDF–1.1M Supplementary Material
Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes among Listeria monocytogenes Epidemic Clone I and Selected Strains of Serotype 1/2a
Suleyman Yildirim, Driss Elhanafi, Wen Lin, Anthony D. Hitchins, Robin M. Siletzky, S. Kathariou
Appl Environ Microbiol. 2010 August; 76(16): 5577–5584. Published online 2010 June 25. doi: 10.1128/AEM.00648-10
PMCID:
PMC2918945
Abstract Full Text PDF–700K
Visualizing high error levels during gene expression in living bacterial cells
Mor Meyerovich, Gideon Mamou, Sigal Ben-Yehuda
Proc Natl Acad Sci U S A. 2010 June 22; 107(25): 11543–11548. Published online 2010 June 7. doi: 10.1073/pnas.0912989107
PMCID:
PMC2895060
Abstract Full Text PDF–919K Supplementary Material
Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis
Ingrid Lafontaine, Bernard Dujon
BMC Genomics. 2010; 11: 260. Published online 2010 April 22. doi: 10.1186/1471-2164-11-260
PMCID:
PMC2876123
Abstract Full Text PDF–1.4M Supplementary Material
Implications of high level pseudogene transcription in Mycobacterium leprae
Diana L Williams, Richard A Slayden, Amol Amin, Alejandra N Martinez, Tana L Pittman, Alex Mira, Anirban Mitra, Valakunja Nagaraja, Norman E Morrison, Milton Moraes, Thomas P Gillis
BMC Genomics. 2009; 10: 397. Published online 2009 August 25. doi: 10.1186/1471-2164-10-397
PMCID:
PMC2753549
Abstract Full Text PDF–595K Supplementary Material
Genomic evidence for non-random endemic populations of decaying exons from mammalian genes
David DeLima Morais, Paul M Harrison
BMC Genomics. 2009; 10: 309. Published online 2009 July 13. doi: 10.1186/1471-2164-10-309
PMCID:
PMC2718932
Abstract Full Text PDF–1.1M Supplementary Material
Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle
Alice R. Wattam, Kelly P. Williams, Eric E. Snyder, Nalvo F. Almeida, Jr., Maulik Shukla, A. W. Dickerman, O. R. Crasta, R. Kenyon, J. Lu, J. M. Shallom, H. Yoo, T. A. Ficht, R. M. Tsolis, C. Munk, R. Tapia, C. S. Han, J. C. Detter, D. Bruce, T. S. Brettin, Bruno W. Sobral, Stephen M. Boyle, João C. Setubal
J Bacteriol. 2009 June; 191(11): 3569–3579. Published online 2009 April 3. doi: 10.1128/JB.01767-08
PMCID:
PMC2681906
Abstract Full Text PDF–1012K Supplementary Material
Whole-Genome Tiling Array Analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions
Takeshi Akama, Koichi Suzuki, Kazunari Tanigawa, Akira Kawashima, Huhehasi Wu, Noboru Nakata, Yasunori Osana, Yasubumi Sakakibara, Norihisa Ishii
J Bacteriol. 2009 May; 191(10): 3321–3327. Published online 2009 March 13. doi: 10.1128/JB.00120-09
PMCID:
PMC2687151
Abstract Full Text PDF–872K Supplementary Material
Pseudofam: the pseudogene families database
Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, Mark B. Gerstein
Nucleic Acids Res. 2009 January; 37(Database issue): D738–D743. Published online 2009 January. doi: 10.1093/nar/gkn758
PMCID:
PMC2686518
Abstract Full Text PDF–1.7M
The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients
Matthew T. G. Holden, Helena M. B. Seth-Smith, Lisa C. Crossman, Mohammed Sebaihia, Stephen D. Bentley, Ana M. Cerdeño-Tárraga, Nicholas R. Thomson, Nathalie Bason, Michael A. Quail, Sarah Sharp, Inna Cherevach, Carol Churcher, Ian Goodhead, Heidi Hauser, Nancy Holroyd, Karen Mungall, Paul Scott, Danielle Walker, Brian White, Helen Rose, Pernille Iversen, Dalila Mil-Homens, Eduardo P. C. Rocha, Arsenio M. Fialho, Adam Baldwin, Christopher Dowson, Bart G. Barrell, John R. Govan, Peter Vandamme, C. Anthony Hart, Eshwar Mahenthiralingam, Julian Parkhill
J Bacteriol. 2009 January; 191(1): 261–277. Published online 2008 October 17. doi: 10.1128/JB.01230-08
Correction in:
J Bacteriol. 2009 April; 191(8): 2907.
PMCID:
PMC2612433
Abstract Full Text PDF–1.2M Supplementary Material Correction
Insights and inferences about integron evolution from genomic data
Diana R Nemergut, Michael S Robeson, Robert F Kysela, Andrew P Martin, Steven K Schmidt, Rob Knight
BMC Genomics. 2008; 9: 261. Published online 2008 May 31. doi: 10.1186/1471-2164-9-261
PMCID:
PMC2426708
Abstract Full Text PDF–690K Supplementary Material
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli
Mark W. J. van Passel, Pradeep Reddy Marri, Howard Ochman
PLoS Comput Biol. 2008 April; 4(4): e1000059. Published online 2008 April 11. doi: 10.1371/journal.pcbi.1000059
PMCID:
PMC2275313
Abstract Full Text PDF–149K Supplementary Material
Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences
Caroline Deshayes, Emmanuel Perrodou, Daniel Euphrasie, Eric Frapy, Olivier Poch, Pablo Bifani, Odile Lecompte, Jean-Marc Reyrat
BMC Evol Biol. 2008; 8: 78. Published online 2008 March 6. doi: 10.1186/1471-2148-8-78
PMCID:
PMC2277376
Abstract Full Text PDF–395K Supplementary Material
Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis
Christoph Schoen, Jochen Blom, Heike Claus, Anja Schramm-Glück, Petra Brandt, Tobias Müller, Alexander Goesmann, Biju Joseph, Sebastian Konietzny, Oliver Kurzai, Corinna Schmitt, Torben Friedrich, Burkhard Linke, Ulrich Vogel, Matthias Frosch
Proc Natl Acad Sci U S A. 2008 March 4; 105(9): 3473–3478. Published online 2008 February 27. doi: 10.1073/pnas.0800151105
PMCID:
PMC2265139
Abstract Full Text PDF–467K Supplementary Material
Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction
Hans-Henrik Fuxelius, Alistair C Darby, Nam-Huyk Cho, Siv GE Andersson
Genome Biol. 2008; 9(2): R42. Published online 2008 February 26. doi: 10.1186/gb-2008-9-2-r42
PMCID:
PMC2374718
Abstract Full Text PDF–420K Supplementary Material
Distribution, Functional Expression, and Genetic Organization of Cif, a Phage-Encoded Type III-Secreted Effector from Enteropathogenic and Enterohemorrhagic Escherichia coli
Estelle Loukiadis, Rika Nobe, Sylvia Herold, Clara Tramuta, Yoshitoshi Ogura, Tadasuke Ooka, Stefano Morabito, Monique Kérourédan, Hubert Brugère, Herbert Schmidt, Tetsuya Hayashi, Eric Oswald
J Bacteriol. 2008 January; 190(1): 275–285. Published online 2007 September 14. doi: 10.1128/JB.00844-07
PMCID:
PMC2223761
Abstract Full Text PDF–3.3M
Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction
Laura Gómez-Valero, Eduardo P.C. Rocha, Amparo Latorre, Francisco J. Silva
Genome Res. 2007 August; 17(8): 1178–1185. doi: 10.1101/gr.6360207
PMCID:
PMC1933519
Abstract Full Text PDF–293K
Plasmids and Rickettsial Evolution: Insight from Rickettsia felis
Joseph J. Gillespie, Magda S. Beier, M. Sayeedur Rahman, Nicole C. Ammerman, Joshua M. Shallom, Anjan Purkayastha, Bruno S. Sobral, Abdu F. Azad
PLoS ONE. 2007; 2(3): e266. Published online 2007 March 7. doi: 10.1371/journal.pone.0000266
PMCID:
PMC1800911
Abstract Full Text PDF–604K Supplementary Material
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