Cited by ..

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-21^T)

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