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  1. ARTICLE: Single-tube nested PCR with room-temperature-stable reagents.
    • C Wolff,
    • D Hörnschemeyer,
    • D Wolff,
    • and K Kleesiek
    Genome Res. June 1995 4: 376-379
    ...K Kleesiek D Hörnschemeyer D, Hörnschemeyer Wolff D C Wolff Hornschemeyer Hörnschemeyer, D Kleesiek, K Wolff C K, Kleesiek Hörnschemeyer Wolff, D Wolff Wolff, C C, Wolff Hörnschemeyer D D, Wolff Kleesiek Kleesiek K D Wolff 1088-9051 genome;4/6/376 Single-tube nested PCR with room...
  2. REVIEW: Multiplex PCR: advantages, development, and applications.
    • M C Edwards and
    • R A Gibbs
    Genome Res. February 1994 3: S65-S75
    ...omp A DNA of the Chlamydia spp. J. Clin. Microbiol. 30 : 1098 – 1104 . 10.. Wilton, S. , Cousins. D. Wilton, S. and Cousins. D. 1992 . Detection and identification of multiple mycobacterial pathogens by DNA amplification in a single tube. PCR Methods Applic. 1 : 269 – 273 . 11.. Way, J.S., , Josephson...
  3. Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
    • Jacob Stewart-Ornstein,
    • Matthew J. Irby,
    • Marina K. Lilieholm,
    • Dylan Laprise,
    • Maria D. Collier,
    • Thomas Aunins,
    • Dewi Harjanto,
    • Aaron N. Chang,
    • Deepak Reyon,
    • and Jeremy S. Duffield
    Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
    ...ng of genomic DNA as input for the initial amplification. The first PCR consisted of 15 cycles using a target-specific primer and the Illumina P5 primer, followed by a 1.0× SPRIselect bead cleanup. The second PCR used a nested target-specific forward primer incorporating a 5′ Illumina Read 2 sequence...
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  4. REVIEW: The ligase chain reaction in a PCR world.
    • F Barany
    Genome Res. August 1991 1: 5-16; doi:10.1101/gr.1.1.5
    ...amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230 : 1350 – 1354 . 3. Erlich, H.A., ed. 1989. PCR technology: Principles and applications for DNA amplification . Stockton Press, New York. 4. Innis, M.A., D.H. Gelfand, J.J. Sninsky, and T...
  5. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...nested PCR or high-throughput sequencing (HTS), which may introduce bias and is restricted to detecting junctions between HBV and host s. Recently, the advancement of long-read sequencing has improved our understanding of HBV integration and its role in HCC development. HBV can integrate into the human...
  6. ARTICLE: Optimization and troubleshooting in PCR.
    • K H Roux
    Genome Res. April 1995 4: S185-S194
    ...-Y. and Ehrlich. M. 1994 . Detection and quantitation of low numbers of chromosomes containing bcl-2 oncogene translocations using semi-nested PCR. BioTechniques 16 : 502 – 507 . 25.. Zimmermann, K., , Pischinger, K. , Mannhalter. J.W. Zimmermann, K., Pischinger, K. and Mannhalter. J.W. 1994 . Nested primer PCR...
  7. REVIEW: RNA fingerprinting by arbitrarily primed PCR.
    • M McClelland and
    • J Welsh
    Genome Res. August 1994 4: S66-S81
    ...in a single tube in a few hours. Fragments of differentially expressed genes can be cloned directly from PCR-amplified products isolated from the gel. The method can provide a complex phenotype reflecting changes in the abundance of hundreds of RNAs under various conditions. Comparison of RNA fingerprints...
  8. REVIEW: Strategies for direct sequencing of PCR-amplified DNA.
    • V B Rao
    Genome Res. August 1994 4: S15-S23
    ...-amplified product is generated by choosing highly specific PCR primers with a GC content of >50%, using a high annealing temperature that is very close to the estimated Tm value of the primers (in the range of 50- 60~ initiating PCR by hot start, and if necessary, performing a second nested PCR with an internal set...
  9. Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
    • Brigitta Szabo,
    • Therese C. Mandl,
    • Bernhard Woldrich,
    • Gregor Diensthuber,
    • David Martin,
    • Michael F. Jantsch,
    • and Konstantin Licht
    Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
    ...a strong CMV promoter or a weak pGK promoter. The reporter constructs were transfected into HEK293 cells harboring or lacking a doxycycline-inducible FLAG-tagged Adarb1 (ADAR2) transgene. qPCR indicated that expression from the CMV promoter was typically 10–20 times stronger than expression from the p...
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  10. Research: Genomic context sensitivity of insulator function
    • André M. Ribeiro-dos-Santos,
    • Megan S. Hogan,
    • Raven D. Luther,
    • Ran Brosh,
    • and Matthew T. Maurano
    Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
    ...of sequencing libraries (Fig. 2A; Supplemental Fig. S4): an inverse PCR (iPCR) library to map reporter genomic insertion sites, a DNA library to determine their representation, and an RNA library to measure their expression. Sequencing libraries were constructed using a two-stage nested polymerase chain...
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