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Vol. 11, Issue 4, 614-625, April 2001
METHODS
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  M. Naito, H. Hirakawa, A. Yamashita, N. Ohara, M. Shoji, H. Yukitake, K. Nakayama, H. Toh, F. Yoshimura, S. Kuhara, et al. Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis DNA Res, June 3, 2008; (2008) dsn013v1. [Abstract] [Full Text] [PDF]
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H. Morita, H. Toh, S. Fukuda, H. Horikawa, K. Oshima, T. Suzuki, M. Murakami, S. Hisamatsu, Y. Kato, T. Takizawa, et al. Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production DNA Res, May 16, 2008; (2008) dsn009v1. [Abstract] [Full Text] [PDF]
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 N. Warthmann, S. Das, C. Lanz, and D. Weigel Comparative Analysis of the MIR319a MicroRNA Locus in Arabidopsis and Related Brassicaceae Mol. Biol. Evol., May 1, 2008; 25(5): 892 - 902. [Abstract] [Full Text] [PDF]
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 K.-H. Gartemann, B. Abt, T. Bekel, A. Burger, J. Engemann, M. Flugel, L. Gaigalat, A. Goesmann, I. Grafen, J. Kalinowski, et al. The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity J. Bacteriol., March 15, 2008; 190(6): 2138 - 2149. [Abstract] [Full Text] [PDF]
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 J. F. Storz, F. G. Hoffmann, J. C. Opazo, and H. Moriyama Adaptive Functional Divergence Among Triplicated {alpha}-Globin Genes in Rodents Genetics, March 1, 2008; 178(3): 1623 - 1638. [Abstract] [Full Text] [PDF]
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T. Goto, A. Yamashita, H. Hirakawa, M. Matsutani, K. Todo, K. Ohshima, H. Toh, K. Miyamoto, S. Kuhara, M. Hattori, et al. Complete Genome Sequence of Finegoldia magna, an Anaerobic Opportunistic Pathogen DNA Res, February 7, 2008; (2008) dsm030v1. [Abstract] [Full Text] [PDF]
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 C. M. Albert, E. G. Nam, E. B. Rimm, H. W. Jin, R. J. Hajjar, D. J. Hunter, C. A. MacRae, and P. T. Ellinor Cardiac Sodium Channel Gene Variants and Sudden Cardiac Death in Women Circulation, January 1, 2008; 117(1): 16 - 23. [Abstract] [Full Text] [PDF]
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 R. Sorek, Y. Zhu, C. J. Creevey, M. P. Francino, P. Bork, and E. M. Rubin Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer Science, November 30, 2007; 318(5855): 1449 - 1452. [Abstract] [Full Text] [PDF]
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 A. Schluter, I. Krahn, F. Kollin, G. Bonemann, M. Stiens, R. Szczepanowski, S. Schneiker, and A. Puhler IncP-1{beta} Plasmid pGNB1 Isolated from a Bacterial Community from a Wastewater Treatment Plant Mediates Decolorization of Triphenylmethane Dyes Appl. Envir. Microbiol., October 15, 2007; 73(20): 6345 - 6350. [Abstract] [Full Text] [PDF]
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 N. Yuhki, T. Beck, R. Stephens, B. Neelam, and S. J. O'Brien Comparative Genomic Structure of Human, Dog, and Cat MHC: HLA, DLA, and FLA J. Hered., August 3, 2007; (2007) esm056v1. [Abstract] [Full Text] [PDF]
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A. Schluter, R. Szczepanowski, N. Kurz, S. Schneiker, I. Krahn, and A. Puhler Erythromycin Resistance-Conferring Plasmid pRSB105, Isolated from a Sewage Treatment Plant, Harbors a New Macrolide Resistance Determinant, an Integron-Containing Tn402-Like Element, and a Large Region of Unknown Function Appl. Envir. Microbiol., March 15, 2007; 73(6): 1952 - 1960. [Abstract] [Full Text] [PDF]
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 R. Szczepanowski, I. Krahn, N. Bohn, A. Puhler, and A. Schluter Novel Macrolide Resistance Module Carried by the IncP-1{beta} Resistance Plasmid pRSB111, Isolated from a Wastewater Treatment Plant Antimicrob. Agents Chemother., February 1, 2007; 51(2): 673 - 678. [Abstract] [Full Text] [PDF]
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 L. Rohmer, M. Brittnacher, K. Svensson, D. Buckley, E. Haugen, Y. Zhou, J. Chang, R. Levy, H. Hayden, M. Forsman, et al. Potential Source of Francisella tularensis Live Vaccine Strain Attenuation Determined by Genome Comparison Infect. Immun., December 1, 2006; 74(12): 6895 - 6906. [Abstract] [Full Text] [PDF]
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T. Hain, C. Steinweg, C. T. Kuenne, A. Billion, R. Ghai, S. S. Chatterjee, E. Domann, U. Karst, A. Goesmann, T. Bekel, et al. Whole-Genome Sequence of Listeria welshimeri Reveals Common Steps in Genome Reduction with Listeria innocua as Compared to Listeria monocytogenes J. Bacteriol., November 1, 2006; 188(21): 7405 - 7415. [Abstract] [Full Text] [PDF]
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K. Smalla, A. S. Haines, K. Jones, E. Krogerrecklenfort, H. Heuer, M. Schloter, and C. M. Thomas Increased Abundance of IncP-1{beta} Plasmids and Mercury Resistance Genes in Mercury-Polluted River Sediments: First Discovery of IncP-1{beta} Plasmids with a Complex mer Transposon as the Sole Accessory Element Appl. Envir. Microbiol., November 1, 2006; 72(11): 7253 - 7259. [Abstract] [Full Text] [PDF]
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 M. Stapleton, J. W. Carlson, and S. E. Celniker RNA editing in Drosophila melanogaster: New targets and functional consequences RNA, November 1, 2006; 12(11): 1922 - 1932. [Abstract] [Full Text] [PDF]
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 A. Dokras, J. Coffin, L. Field, A. Frakes, H. Lee, A. Madan, T. Nelson, G.-Y. Ryu, J.-G. Yoon, and A. Madan Epigenetic regulation of maspin expression in the human placenta Mol. Hum. Reprod., October 1, 2006; 12(10): 611 - 617. [Abstract] [Full Text] [PDF]
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 D. M. Bulach, R. L. Zuerner, P. Wilson, T. Seemann, A. McGrath, P. A. Cullen, J. Davis, M. Johnson, E. Kuczek, D. P. Alt, et al. Genome reduction in Leptospira borgpetersenii reflects limited transmission potential PNAS, September 26, 2006; 103(39): 14560 - 14565. [Abstract] [Full Text] [PDF]
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G. Bonemann, M. Stiens, A. Puhler, and A. Schluter Mobilizable IncQ-Related Plasmid Carrying a New Quinolone Resistance Gene, qnrS2, Isolated from the Bacterial Community of a Wastewater Treatment Plant. Antimicrob. Agents Chemother., September 1, 2006; 50(9): 3075 - 3080. [Abstract] [Full Text] [PDF]
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 V. M. Deyde, M. L. Khristova, P. E. Rollin, T. G. Ksiazek, and S. T. Nichol Crimean-congo hemorrhagic Fever virus genomics and global diversity. J. Virol., September 1, 2006; 80(17): 8834 - 8842. [Abstract] [Full Text] [PDF]
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 A. S. Haines, P. Akhtar, E. R. Stephens, K. Jones, C. M. Thomas, C. D. Perkins, J. R. Williams, M. J. Day, and J. C. Fry Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype. Microbiology, September 1, 2006; 152(Pt 9): 2689 - 2701. [Abstract] [Full Text] [PDF]
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S. L. Dellaporta, A. Xu, S. Sagasser, W. Jakob, M. A. Moreno, L. W. Buss, and B. Schierwater Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum PNAS, June 6, 2006; 103(23): 8751 - 8756. [Abstract] [Full Text] [PDF]
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M. Stiens, S. Schneiker, M. Keller, S. Kuhn, A. Puhler, and A. Schluter Sequence Analysis of the 144-Kilobase Accessory Plasmid pSmeSM11a, Isolated from a Dominant Sinorhizobium meliloti Strain Identified during a Long-Term Field Release Experiment. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3662 - 3672. [Abstract] [Full Text] [PDF]
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M. Gaillard, T. Vallaeys, F. J. Vorholter, M. Minoia, C. Werlen, V. Sentchilo, A. Puhler, and J. R. van der Meer The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties. J. Bacteriol., March 1, 2006; 188(5): 1999 - 2013. [Abstract] [Full Text] [PDF]
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 H. Toh, B. L. Weiss, S. A.H. Perkin, A. Yamashita, K. Oshima, M. Hattori, and S. Aksoy Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host Genome Res., February 1, 2006; 16(2): 149 - 156. [Abstract] [Full Text] [PDF]
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P. F. Cliften, R. S. Fulton, R. K. Wilson, and M. Johnston After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes Genetics, February 1, 2006; 172(2): 863 - 872. [Abstract] [Full Text] [PDF]
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Y. Azuma, H. Hirakawa, A. Yamashita, Y. Cai, M. A. Rahman, H. Suzuki, S. Mitaku, H. Toh, S. Goto, T. Murakami, et al. Genome Sequence of the Cat Pathogen, Chlamydophila felis DNA Res, January 1, 2006; 13(1): 15 - 23. [Abstract] [Full Text] [PDF]
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 R. A. Hoskins, M. Stapleton, R. A. George, C. Yu, K. H. Wan, J. W. Carlson, and S. E. Celniker Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP) Nucleic Acids Res., December 2, 2005; 33(21): e185 - e185. [Abstract] [Full Text] [PDF]
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K. V. Krutovsky and D. B. Neale Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir Genetics, December 1, 2005; 171(4): 2029 - 2041. [Abstract] [Full Text] [PDF]
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F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Buttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, et al. Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence J. Bacteriol., November 1, 2005; 187(21): 7254 - 7266. [Abstract] [Full Text] [PDF]
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S. N. Gardner, M. W. Lam, J. R. Smith, C. L. Torres, and T. R. Slezak Draft versus finished sequence data for DNA and protein diagnostic signature development Nucleic Acids Res., October 20, 2005; 33(18): 5838 - 5850. [Abstract] [Full Text] [PDF]
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 A. M. Likos, S. A. Sammons, V. A. Olson, A. M. Frace, Y. Li, M. Olsen-Rasmussen, W. Davidson, R. Galloway, M. L. Khristova, M. G. Reynolds, et al. A tale of two clades: monkeypox viruses J. Gen. Virol., October 1, 2005; 86(10): 2661 - 2672. [Abstract] [Full Text] [PDF]
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M. Kuroda, A. Yamashita, H. Hirakawa, M. Kumano, K. Morikawa, M. Higashide, A. Maruyama, Y. Inose, K. Matoba, H. Toh, et al. Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection PNAS, September 13, 2005; 102(37): 13272 - 13277. [Abstract] [Full Text] [PDF]
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S. Reslewic, S. Zhou, M. Place, Y. Zhang, A. Briska, S. Goldstein, C. Churas, R. Runnheim, D. Forrest, A. Lim, et al. Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum Appl. Envir. Microbiol., September 1, 2005; 71(9): 5511 - 5522. [Abstract] [Full Text] [PDF]
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C. K. Raymond, A. Kas, M. Paddock, R. Qiu, Y. Zhou, S. Subramanian, J. Chang, A. Palmieri, E. Haugen, R. Kaul, et al. Ancient haplotypes of the HLA Class II region Genome Res., September 1, 2005; 15(9): 1250 - 1257. [Abstract] [Full Text] [PDF]
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A. S. Haines, K. Jones, M. Cheung, and C. M. Thomas The IncP-6 Plasmid Rms149 Consists of a Small Mobilizable Backbone with Multiple Large Insertions J. Bacteriol., July 15, 2005; 187(14): 4728 - 4738. [Abstract] [Full Text] [PDF]
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B. Negre, S. Casillas, M. Suzanne, E. Sanchez-Herrero, M. Akam, M. Nefedov, A. Barbadilla, P. de Jong, and A. Ruiz Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex Genome Res., May 1, 2005; 15(5): 692 - 700. [Abstract] [Full Text] [PDF]
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E. E. Smith, E. H. Sims, D. H. Spencer, R. Kaul, and M. V. Olson Evidence for Diversifying Selection at the Pyoverdine Locus of Pseudomonas aeruginosa J. Bacteriol., March 15, 2005; 187(6): 2138 - 2147. [Abstract] [Full Text] [PDF]
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R. W. Blakesley, N. F. Hansen, J. C. Mullikin, P. J. Thomas, J. C. McDowell, B. Maskeri, A. C. Young, B. Benjamin, S. Y. Brooks, B. I. Coleman, et al. An intermediate grade of finished genomic sequence suitable for comparative analyses Genome Res., November 1, 2004; 14(11): 2235 - 2244. [Abstract] [Full Text] [PDF]
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E. L. Hendrickson, R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J. A. Dodsworth, W. Gillett, D. E. Graham, et al. Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis J. Bacteriol., October 15, 2004; 186(20): 6956 - 6969. [Abstract] [Full Text] [PDF]
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J. Ishikawa, A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori The complete genomic sequence of Nocardia farcinica IFM 10152 PNAS, October 12, 2004; 101(41): 14925 - 14930. [Abstract] [Full Text] [PDF]
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K. Ueda, A. Yamashita, J. Ishikawa, M. Shimada, T.-o Watsuji, K. Morimura, H. Ikeda, M. Hattori, and T. Beppu Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism Nucleic Acids Res., September 21, 2004; 32(16): 4937 - 4944. [Abstract] [Full Text] [PDF]
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K. V. Krutovsky, M. Troggio, G. R. Brown, K. D. Jermstad, and D. B. Neale Comparative Mapping in the Pinaceae Genetics, September 1, 2004; 168(1): 447 - 461. [Abstract] [Full Text] [PDF]
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T. Domazet-Loso and D. Tautz An Evolutionary Analysis of Orphan Genes in Drosophila Genome Res., October 1, 2003; 13(10): 2213 - 2219. [Abstract] [Full Text] [PDF]
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C. Baar, M. Eppinger, G. Raddatz, J. Simon, C. Lanz, O. Klimmek, R. Nandakumar, R. Gross, A. Rosinus, H. Keller, et al. Complete genome sequence and analysis of Wolinella succinogenes PNAS, September 30, 2003; 100(20): 11690 - 11695. [Abstract] [Full Text] [PDF]
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P. Cliften, P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting Science, July 4, 2003; 301(5629): 71 - 76. [Abstract] [Full Text] [PDF]
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N. Yuhki, T. Beck, R. M. Stephens, Y. Nishigaki, K. Newmann, and S. J. O'Brien Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region Genome Res., June 1, 2003; 13(6): 1169 - 1179. [Abstract] [Full Text] [PDF]
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B. J. Williams, M. Golomb, T. Phillips, J. Brownlee, M. V. Olson, and A. L. Smith Bacteriophage HP2 of Haemophilus influenzae J. Bacteriol., December 15, 2002; 184(24): 6893 - 6905. [Abstract] [Full Text] [PDF]
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Y. Sasaki, J. Ishikawa, A. Yamashita, K. Oshima, T. Kenri, K. Furuya, C. Yoshino, A. Horino, T. Shiba, T. Sasaki, et al. The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans Nucleic Acids Res., December 1, 2002; 30(23): 5293 - 5300. [Abstract] [Full Text] [PDF]
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E. Wienholds, S. Schulte-Merker, B. Walderich, and R. H. A. Plasterk Target-Selected Inactivation of the Zebrafish rag1 Gene Science, July 5, 2002; 297(5578): 99 - 102. [Abstract] [Full Text] [PDF]
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C. K. Raymond, E. H. Sims, A. Kas, D. H. Spencer, T. V. Kutyavin, R. G. Ivey, Y. Zhou, R. Kaul, J. B. Clendenning, and M. V. Olson Genetic Variation at the O-Antigen Biosynthetic Locus in Pseudomonas aeruginosa J. Bacteriol., July 1, 2002; 184(13): 3614 - 3622. [Abstract] [Full Text] [PDF]
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Y. S. N. Butterfield, M. A. Marra, J. K. Asano, S. Y. Chan, R. Guin, M. I. Krzywinski, S. S. Lee, K. W. K. MacDonald, C. A. Mathewson, T. E. Olson, et al. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones Nucleic Acids Res., June 1, 2002; 30(11): 2460 - 2468. [Abstract] [Full Text] [PDF]
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A. I. Slesarev, K. V. Mezhevaya, K. S. Makarova, N. N. Polushin, O. V. Shcherbinina, V. V. Shakhova, G. I. Belova, L. Aravind, D. A. Natale, I. B. Rogozin, et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens PNAS, April 2, 2002; 99(7): 4644 - 4649. [Abstract] [Full Text] [PDF]
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J. C. Smoot, K. D. Barbian, J. J. Van Gompel, L. M. Smoot, M. S. Chaussee, G. L. Sylva, D. E. Sturdevant, S. M. Ricklefs, S. F. Porcella, L. D. Parkins, et al. Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks PNAS, March 21, 2002; (2002) 62526099. [Abstract] [Full Text] [PDF]
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once with each method. This comparison
shows that the Autofinish-Hybrid method saves many hours
over a human finisher alone, while using roughly the same number and
type of reads and closing gaps at roughly the same rate.
Autofinish currently is in production use at several large
sequencing centers. It is designed to be adaptable to the finishing
strategy of the lab