Searching journal content for articles similar to Gur-Arie et al. 10 (1): 62.

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  1. LETTER: Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species
    • Tony Le Gall,
    • Pierre Darlu,
    • Patricia Escobar-Páramo,
    • Bertrand Picard,
    • and Erick Denamur
    Genome Res. February 2005 15: 260-268; doi:10.1101/gr.2405905
    ...Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species Tony Le Gall 1 , 2 , Pierre Darlu 3 , Patricia Escobar-Páramo 1 , Bertrand Picard 2 , and Erick Denamur 1 , 4 1 Institut National de la...
  2. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...), these repeats have elevated germline mutation and polymorphism rates. After a certain threshold length, STRs are termed microsatellites (Kelkar et al. 2010; Ananda et al. 2013). The high level of polymorphismmakes microsatellites attractive markers for population and conservation genetics studies (Jarne...
  3. LETTER: Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties
    • Albino Bacolla,
    • Jacquelynn E. Larson,
    • Jack R. Collins,
    • Jian Li,
    • Aleksandar Milosavljevic,
    • Peter D. Stenson,
    • David N. Cooper,
    • and Robert D. Wells
    Genome Res. October 2008 18: 1545-1553; Published in Advance August 7, 2008, doi:10.1101/gr.078303.108
    ...– 2675 . ↵ Bowater, R.P. , Jaworski, A. , Larson, J.E. , Parniewski, P. , Wells, R.D. ( 1997 ) Transcription increases the deletion frequency of long CTG.CAG triplet repeats from plasmids in Escherichia coli . Nucleic Acids Res. 25 : 2861 – 2868 . ↵ Cantor, C.R. , Schimmel, P.R. ( 1980 ) Biophysical...
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  4. LETTER: Predicting Human Minisatellite Polymorphism
    • France Denoeud,
    • Gilles Vergnaud,
    • and Gary Benson
    Genome Res. May 1, 2003 13: 856-867; Published in Advance April 14, 2003, doi:10.1101/gr.574403
    ...processes. That %GC correlates with polymorphism is in agreement with earlier observations. Some of the first minisatellites to be characterized were detected via a shared 10- to 15-bp “core” sequence similar to the generalized recombination signal (χ) of Escherichia coli (GCTGTGG; Jeffreys et al. 1985...
  5. Letter: Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
    • Tadasuke Ooka,
    • Yoshitoshi Ogura,
    • Md Asadulghani,
    • Makoto Ohnishi,
    • Keisuke Nakayama,
    • Jun Terajima,
    • Haruo Watanabe,
    • and Tetsuya Hayashi
    Genome Res. October 2009 19: 1809-1816; Published in Advance June 29, 2009, doi:10.1101/gr.089615.108
    ...Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes Tadasuke Ooka 1 , Yoshitoshi Ogura 1 , 2 , Md Asadulghani 2 , Makoto...
  6. LETTER: Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
    • Mikael Brandström and
    • Hans Ellegren
    Genome Res. June 2008 18: 881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
    ...1997 ) as well as in in vivo studies of Escherichia coli and Saccharomyces cerevisiae ( Lenzmeier and Freudenreich 2003 ). For motifs less likely to form hairpins the same trend as for di- and tetranucleotide repeats was observed, with AT-rich repeats showing the highest variability. In contrast...
  7. LETTER: Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
    • Austen R.D. Ganley and
    • Takehiko Kobayashi
    Genome Res. February 2007 17: 184-191; Published in Advance January 2, 2007, doi:10.1101/gr.5457707
    .... ( 1984 ) in Cell biology monographs , The nucleolus and ribosome biogenesis , ed Alfert, M. , et al. ( Springer-Verlag Wien , New York ), 12 . ↵ Hoffman, C.S. , Winston, F. ( 1987 ) A ten-minute preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli . Gene...
  8. METHODS: Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation
    • Charles A. Mein,
    • Bryan J. Barratt,
    • Michael G. Dunn,
    • Thorsten Siegmund,
    • Annabel N. Smith,
    • Laura Esposito,
    • Sarah Nutland,
    • Helen E. Stevens,
    • Amanda J. Wilson,
    • Michael S. Phillips,
    • Nancy Jarvis,
    • Scott Law,
    • Monika de Arruda,
    • and John A. Todd
    Genome Res. March 1, 2000 10: 330-343; doi:10.1101/gr.10.3.330
    ...-walled polycarbonate microtiter plates (Corning Costar). PCR product was dried for 15 min at 80°C. Five microliters of Invader mix, consisting of 4% PEG8000, 10 mM MOPS, 0.025 µM Invader oligonucleotide, 0.25 µM secondary target oligonucleotide, 0.5 µM FRET probe, 5 ng/µl Escherichia coli genomic DNA as a carrier, 0...
  9. INSIGHT/OUTLOOK: The Beautifully Simple but Intriguingly Complex World of Small Genomes
    • Sandra W. Clifton and
    • Bruce A. Roe
    Genome Res. April 1, 1998 8: 331-333; doi:10.1101/gr.8.4.331
    ..., The University of Oklahoma, Norman, Oklahoma 73017 USA I n his review of the Small Genome Meeting in 1997, Eugene Koonin remarked that we have quite a bit of “... ignorance about the simple cell ( Escherichia coli ) that has been the primary object of molecular biology for several decades.” This message...
  10. Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
    • Ulrich Omasits,
    • Adithi R. Varadarajan,
    • Michael Schmid,
    • Sandra Goetze,
    • Damianos Melidis,
    • Marc Bourqui,
    • Olga Nikolayeva,
    • Maxime Québatte,
    • Andrea Patrignani,
    • Christoph Dehio,
    • Juerg E. Frey,
    • Mark D. Robinson,
    • Bernd Wollscheid,
    • and Christian H. Ahrens
    Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
    ..., Bradyrhizobium diazoefficiens and Escherichia coli and the software to generate both proteogenomics search databases and integrated annotation files that can be viewed in a browser for any prokaryote.Advances in next-generation sequencing technology and assembly algorithms have fueled an exponential growth...
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