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Versatile and open software for comparing large genomes
Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg
Genome Biol. 2004; 5(2): R12. Published online 2004 January 30. doi: 10.1186/gb-2004-5-2-r12
PMCID:
PMC395750
Abstract Full Text PDF–1.2M

Is Cited by the Following 347 Articles in this Archive:

Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome
Jian Li, R. Alan Harris, Sau Wai Cheung, Cristian Coarfa, Mira Jeong, Margaret A. Goodell, Lisa D. White, Ankita Patel, Sung-Hae Kang, Chad Shaw, A. Craig Chinault, Tomasz Gambin, Anna Gambin, James R. Lupski, Aleksandar Milosavljevic
PLoS Genet. 2012 May; 8(5): e1002692. Published online 2012 May 17. doi: 10.1371/journal.pgen.1002692
PMCID:
PMC3355074
Abstract Full Text PDF–1.0M Supplementary Material
Edwardsiella Comparative Phylogenomics Reveal the New Intra/Inter-Species Taxonomic Relationships, Virulence Evolution and Niche Adaptation Mechanisms
Minjun Yang, Yuanzhi Lv, Jingfan Xiao, Haizhen Wu, Huajun Zheng, Qin Liu, Yuanxing Zhang, Qiyao Wang
PLoS One. 2012; 7(5): e36987. Published online 2012 May 10. doi: 10.1371/journal.pone.0036987
PMCID:
PMC3349661
Abstract Full Text PDF–1.6M Supplementary Material
Genome Sequence of Erythromelalgia-Related Poxvirus Identifies it as an Ectromelia Virus Strain
Jorge D. Mendez-Rios, Craig A. Martens, Daniel P. Bruno, Stephen F. Porcella, Zhi-Ming Zheng, Bernard Moss
PLoS One. 2012; 7(4): e34604. Published online 2012 April 27. doi: 10.1371/journal.pone.0034604
PMCID:
PMC3338725
Abstract Full Text PDF–1.7M Supplementary Material
Comparative Genomics Reveals Adaptation by Alteromonas sp. SN2 to Marine Tidal-Flat Conditions: Cold Tolerance and Aromatic Hydrocarbon Metabolism
Renukaradhya K. Math, Hyun Mi Jin, Jeong Myeong Kim, Yoonsoo Hahn, Woojun Park, Eugene L. Madsen, Che Ok Jeon
PLoS One. 2012; 7(4): e35784. Published online 2012 April 26. doi: 10.1371/journal.pone.0035784
PMCID:
PMC3338528
Abstract Full Text PDF–3.1M Supplementary Material
Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia
Manuel Martinez-Garcia, David M. Brazel, Brandon K. Swan, Carol Arnosti, Patrick S. G. Chain, Krista G. Reitenga, Gary Xie, Nicole J. Poulton, Monica Lluesma Gomez, Dashiell E. D. Masland, Brian Thompson, Wendy K. Bellows, Kai Ziervogel, Chien-Chi Lo, Sanaa Ahmed, Cheryl D. Gleasner, Chris J. Detter, Ramunas Stepanauskas
PLoS One. 2012; 7(4): e35314. Published online 2012 April 20. doi: 10.1371/journal.pone.0035314
PMCID:
PMC3335022
Abstract Full Text PDF–1.8M Supplementary Material
Complete Genome and Transcriptomes of Streptococcus parasanguinis FW213: Phylogenic Relations and Potential Virulence Mechanisms
Jianing Geng, Cheng-Hsun Chiu, Petrus Tang, Yaping Chen, Hui-Ru Shieh, Songnian Hu, Yi-Ywan M. Chen
PLoS One. 2012; 7(4): e34769. Published online 2012 April 18. doi: 10.1371/journal.pone.0034769
PMCID:
PMC3329508
Abstract Full Text PDF–1.0M Supplementary Material
Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-Step Model of Paleohexaploidy
Haibao Tang, Margaret R. Woodhouse, Feng Cheng, James C. Schnable, Brent S. Pedersen, Gavin Conant, Xiaowu Wang, Michael Freeling, J. Chris Pires
Genetics. 2012 April; 190(4): 1563–1574. doi: 10.1534/genetics.111.137349
PMCID:
PMC3316664
Free in PMC on 2013/04/01
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
Amine Namouchi, Xavier Didelot, Ulrike Schöck, Brigitte Gicquel, Eduardo P.C. Rocha
Genome Res. 2012 April; 22(4): 721–734. doi: 10.1101/gr.129544.111
PMCID:
PMC3317154
Free in PMC on 2012/10/01
Draft Genome Sequence of the Nontoxigenic Clostridium difficile Strain CD37
Michael S. M. Brouwer, Elaine Allan, Peter Mullany, Adam P. Roberts
J Bacteriol. 2012 April; 194(8): 2125–2126. doi: 10.1128/JB.00122-12
PMCID:
PMC3318468
Free in PMC on 2012/10/01
Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage
Jennifer L. Kyle, Craig A. Cummings, Craig T. Parker, Beatriz Quiñones, Paolo Vatta, Elizabeth Newton, Steven Huynh, Michelle Swimley, Lovorka Degoricija, Melissa Barker, Samar Fontanoz, Kimberly Nguyen, Ronak Patel, Rixun Fang, Robert Tebbs, Olga Petrauskene, Manohar Furtado, Robert E. Mandrell
J Bacteriol. 2012 April; 194(8): 1885–1896. doi: 10.1128/JB.00120-12
PMCID:
PMC3318487
Free in PMC on 2012/10/01
Novel Plasmids and Resistance Phenotypes in Yersinia pestis: Unique Plasmid Inventory of Strain Java 9 Mediates High Levels of Arsenic Resistance
Mark Eppinger, Lyndsay Radnedge, Gary Andersen, Nicholas Vietri, Grant Severson, Sherry Mou, Jacques Ravel, Patricia L. Worsham
PLoS One. 2012; 7(3): e32911. Published online 2012 March 30. doi: 10.1371/journal.pone.0032911
PMCID:
PMC3316555
Abstract Full Text PDF–619K Supplementary Material
Genome Sequence and Transcriptome Analysis of the Radioresistant Bacterium Deinococcus gobiensis: Insights into the Extreme Environmental Adaptations
Menglong Yuan, Ming Chen, Wei Zhang, Wei Lu, Jin Wang, Mingkun Yang, Peng Zhao, Ran Tang, Xinna Li, Yanhua Hao, Zhengfu Zhou, Yuhua Zhan, Haiying Yu, Chao Teng, Yongliang Yan, Shuzhen Ping, Yingdian Wang, Min Lin
PLoS One. 2012; 7(3): e34458. Published online 2012 March 28. doi: 10.1371/journal.pone.0034458
PMCID:
PMC3314630
Abstract Full Text PDF–723K Supplementary Material
Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing
Ronnie de Jonge, H. Peter van Esse, Karunakaran Maruthachalam, Melvin D. Bolton, Parthasarathy Santhanam, Mojtaba Keykha Saber, Zhao Zhang, Toshiyuki Usami, Bart Lievens, Krishna V. Subbarao, Bart P. H. J. Thomma
Proc Natl Acad Sci U S A. 2012 March 27; 109(13): 5110–5115. Published online 2012 March 13. doi: 10.1073/pnas.1119623109
PMCID:
PMC3323992
Abstract Full Text PDF–799K Supplementary Material
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
Bernadette C. Young, Tanya Golubchik, Elizabeth M. Batty, Rowena Fung, Hanna Larner-Svensson, Antonina A. Votintseva, Ruth R. Miller, Heather Godwin, Kyle Knox, Richard G. Everitt, Zamin Iqbal, Andrew J. Rimmer, Madeleine Cule, Camilla L. C. Ip, Xavier Didelot, Rosalind M. Harding, Peter Donnelly, Tim E. Peto, Derrick W. Crook, Rory Bowden, Daniel J. Wilson
Proc Natl Acad Sci U S A. 2012 March 20; 109(12): 4550–4555. Published online 2012 March 5. doi: 10.1073/pnas.1113219109
PMCID:
PMC3311376
Abstract Full Text PDF–472K Supplementary Material
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg, Adam M. Phillippy, Aleksey Zimin, Daniela Puiu, Tanja Magoc, Sergey Koren, Todd J. Treangen, Michael C. Schatz, Arthur L. Delcher, Michael Roberts, Guillaume Marçais, Mihai Pop, James A. Yorke
Genome Res. 2012 March; 22(3): 557–567. doi: 10.1101/gr.131383.111
PMCID:
PMC3290791
Free in PMC on 2012/09/01
Complete Genome Sequence of Lactococcus lactis subsp. cremoris A76
Alexander Bolotin, Benoit Quinquis, Stanislas Dusko Ehrlich, Alexei Sorokin
J Bacteriol. 2012 March; 194(5): 1241–1242. doi: 10.1128/JB.06629-11
PMCID:
PMC3294806
Free in PMC on 2012/09/01
Draft Genome Sequence of Paenibacillus peoriae Strain KCTC 3763T
Haeyoung Jeong, Soo-Keun Choi, Soo-Young Park, Sun Hong Kim, Seung-Hwan Park
J Bacteriol. 2012 March; 194(5): 1237–1238. doi: 10.1128/JB.06577-11
PMCID:
PMC3294820
Free in PMC on 2012/09/01
Complete Genome Sequence of the Highly Hemolytic Strain Bacillus cereus F837/76
Sandrine Auger, Nathalie Galleron, Béatrice Ségurens, Carole Dossat, Alexander Bolotin, Patrick Wincker, Alexei Sorokin
J Bacteriol. 2012 March; 194(6): 1630. doi: 10.1128/JB.06719-11
PMCID:
PMC3294841
Free in PMC on 2012/09/01
Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103
Stefan Weidner, Anke Becker, Ildefonso Bonilla, Sebastian Jaenicke, Javier Lloret, Isabel Margaret, Alfred Pühler, José E. Ruiz-Sainz, Susanne Schneiker-Bekel, Rafael Szczepanowski, José María Vinardell, Susanne Zehner, Michael Göttfert
J Bacteriol. 2012 March; 194(6): 1617–1618. doi: 10.1128/JB.06729-11
PMCID:
PMC3294874
Free in PMC on 2012/09/01
Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis Strain LK5
L. Farris Hanna, T. David Matthews, Elizabeth A. Dinsdale, David Hasty, Robert A. Edwards
Appl Environ Microbiol. 2012 March; 78(6): 1785–1793. doi: 10.1128/AEM.07241-11
PMCID:
PMC3298174
Free in PMC on 2012/09/01
Patterns of Gene Flow Define Species of Thermophilic Archaea
Hinsby Cadillo-Quiroz, Xavier Didelot, Nicole L. Held, Alfa Herrera, Aaron Darling, Michael L. Reno, David J. Krause, Rachel J. Whitaker
PLoS Biol. 2012 February; 10(2): e1001265. Published online 2012 February 21. doi: 10.1371/journal.pbio.1001265
PMCID:
PMC3283564
Abstract Full Text PDF–573K Supplementary Material
High-Resolution Single Nucleotide Polymorphism Analysis Distinguishes Recrudescence and Reinfection in Recurrent Invasive Nontyphoidal Salmonella Typhimurium Disease
Chinyere K. Okoro, Robert A. Kingsley, Michael A. Quail, Anstead M. Kankwatira, Nicholas A. Feasey, Julian Parkhill, Gordon Dougan, Melita A. Gordon
Clin Infect Dis. 2012 April 1; 54(7): 955–963. Published online 2012 February 7. doi: 10.1093/cid/cir1032
PMCID:
PMC3297646
Abstract Full Text PDF–270K Supplementary Material
Physical and Linkage Maps for Drosophila serrata, a Model Species for Studies of Clinal Adaptation and Sexual Selection
Ann J. Stocker, Bosco B. Rusuwa, Mark J. Blacket, Francesca D. Frentiu, Mitchell Sullivan, Bradley R. Foley, Scott Beatson, Ary A. Hoffmann, Stephen F. Chenoweth
G3 (Bethesda) 2012 February; 2(2): 287–297. Published online 2012 February 1. doi: 10.1534/g3.111.001354
PMCID:
PMC3284336
Abstract Full Text PDF–2.1M
A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation
Jingwei Jiang, Jun Li, Hoi Shan Kwan, Chun Hang Au, Patrick Tik Wan Law, Lei Li, Kai Man Kam, Julia Mei Lun Ling, Frederick C Leung
BMC Res Notes. 2012; 5: 80. Published online 2012 January 31. doi: 10.1186/1756-0500-5-80
PMCID:
PMC3296665
Abstract Full Text PDF–468K Supplementary Material
Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach
Ze Peng, Zhiying Zhao, Nandita Nath, Jeff L. Froula, Alicia Clum, Tao Zhang, Jan-fang Cheng, Alex C. Copeland, Len A. Pennacchio, Feng Chen
PLoS One. 2012; 7(1): e29437. Published online 2012 January 9. doi: 10.1371/journal.pone.0029437
PMCID:
PMC3253782
Abstract Full Text PDF–319K Supplementary Material
Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7
Minjung Park, Ju-Hoon Lee, Hakdong Shin, Minsik Kim, Jeongjoon Choi, Dong-Hyun Kang, Sunggi Heu, Sangryeol Ryu
Appl Environ Microbiol. 2012 January; 78(1): 58–69. doi: 10.1128/AEM.06231-11
PMCID:
PMC3255626
Free in PMC on 2012/07/01
Genome Shrinkage and Loss of Nutrient-Providing Potential in the Obligate Symbiont of the Primitive Termite Mastotermes darwiniensis
Zakee L. Sabree, Charlie Ye Huang, Gaku Arakawa, Gaku Tokuda, Nathan Lo, Hirofumi Watanabe, Nancy A. Moran
Appl Environ Microbiol. 2012 January; 78(1): 204–210. doi: 10.1128/AEM.06540-11
PMCID:
PMC3255634
Free in PMC on 2012/07/01
A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle
Joseph J. Gillespie, Vinita Joardar, Kelly P. Williams, Timothy Driscoll, Jessica B. Hostetler, Eric Nordberg, Maulik Shukla, Brian Walenz, Catherine A. Hill, Vishvanath M. Nene, Abdu F. Azad, Bruno W. Sobral, Elisabet Caler
J Bacteriol. 2012 January; 194(2): 376–394. doi: 10.1128/JB.06244-11
PMCID:
PMC3256634
Abstract Full Text PDF–2.4M Supplementary Material
Identification of Substrain-Specific Mutations by Massively Parallel Whole-Genome Resequencing of Synechocystis sp. PCC 6803
Yu Kanesaki, Yuh Shiwa, Naoyuki Tajima, Marie Suzuki, Satoru Watanabe, Naoki Sato, Masahiko Ikeuchi, Hirofumi Yoshikawa
DNA Res. 2012 February; 19(1): 67–79. Published online 2011 December 22. doi: 10.1093/dnares/dsr042
PMCID:
PMC3276265
Abstract Full Text PDF–405K Supplementary Material
The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway
Shelley D. Copley, Joseph Rokicki, Pernilla Turner, Hajnalka Daligault, Matt Nolan, Miriam Land
Genome Biol Evol. 2012; 4(2): 184–198. Published online 2011 December 16. doi: 10.1093/gbe/evr137
PMCID:
PMC3318906
Abstract Full Text PDF–1.0M
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