Searching journal content for articles similar to Haas et al. 21 (3): 494.

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  1. Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
    • Ariadna Picart-Picolo,
    • Stefan Grob,
    • Nathalie Picault,
    • Michal Franek,
    • Christel Llauro,
    • Thierry Halter,
    • Tom R. Maier,
    • Edouard Jobet,
    • Julie Descombin,
    • Panpan Zhang,
    • Vijayapalani Paramasivan,
    • Thomas J. Baum,
    • Lionel Navarro,
    • Martina Dvořáčková,
    • Marie Mirouze,
    • and Frédéric Pontvianne
    Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
    ...and names of each chromosome rearrangement identified are represented by blue (TDDO) and orange (deletion) arrows along chromosomes. Characteristics of each TDDO can be found in Supplemental Table S2. (B) CNV of genes present or not in TDDO3 and of rRNA genes were determined by quantitative PCR...
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  2. Research: Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
    • Aleksandar D. Kostic,
    • Dirk Gevers,
    • Chandra Sekhar Pedamallu,
    • Monia Michaud,
    • Fujiko Duke,
    • Ashlee M. Earl,
    • Akinyemi I. Ojesina,
    • Joonil Jung,
    • Adam J. Bass,
    • Josep Tabernero,
    • José Baselga,
    • Chen Liu,
    • Ramesh A. Shivdasani,
    • Shuji Ogino,
    • Bruce W. Birren,
    • Curtis Huttenhower,
    • Wendy S. Garrett,
    • and Matthew Meyerson
    Genome Res. February 2012 22: 292-298; Published in Advance October 18, 2011, doi:10.1101/gr.126573.111
    ...16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494–504. ↵ Han YW, Shi W, Huang GT, Kinder Haake S, Park NH, Kuramitsu H, Genco RJ Han YW, Shi W, Huang GT, Kinder Haake S, Park NH, Kuramitsu H, Genco RJ. 2000. Interactions between periodontal...
  3. LETTER: Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm
    • Bernard La Scola,
    • Khalid Elkarkouri,
    • Wenjun Li,
    • Tara Wahab,
    • Ghislain Fournous,
    • Jean-Marc Rolain,
    • Silpak Biswas,
    • Michel Drancourt,
    • Catherine Robert,
    • Stéphane Audic,
    • Sven Löfdahl,
    • and Didier Raoult
    Genome Res. May 2008 18: 742-750; Published in Advance April 11, 2008, doi:10.1101/gr.071266.107
    ..., contigs with sizes of 605–46,278 bp (URFT1 strain), rRNA operons, and CDSs (LVS strain). On the other hand, a total of 377 short remaining contigs (81–425 bp) were rejected by the bioinformatic tools used for the four Francisella s. However, using BLASTN analysis ( E -value = 10 −4 ), a first subset...
  4. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...-range PCR step to generate an amplicon target for long-read sequencing. The 16S rRNA gene is a conserved genetic marker that is present in nearly all bacteria and archaea, and its sequencing allows for the identification of microorganisms based on the sequence similarity of their 16S rRNA gene (Tringe...
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  5. Next-Generation DNA Sequencing/Review: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
    • Micah Hamady and
    • Rob Knight
    Genome Res. July 2009 19: 1141-1152; Published in Advance April 21, 2009, doi:10.1101/gr.085464.108
    ...an exceptional bargain compared to Sanger sequencing of full-length amplicons. However, to define new bacterial phyla, or in cases in which the sequences obtained are highly divergent from related sequences in the reference databases, obtaining the full-length sequence (e.g., by repeating the PCR using a very...
  6. PERSPECTIVE: Application of sequence-based methods in human microbial ecology
    • Li Weng,
    • Edward M. Rubin,
    • and James Bristow
    Genome Res. March 2006 16: 316-322; Published in Advance February 6, 2006, doi:10.1101/gr.3676406
    ...the highly conserved regions used for primer design may amplify less efficiently or not amplify at all. For example, the 16S rRNA gene sequence of the Nanoarchaeota is so divergent that PCR with the “universal” primers failed to detect this species even from cultured organisms ( Huber et al. 2002 ). Second...
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