Searching journal content for articles similar to Haff 3 (6): 332.

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  1. Method: Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants
    • Iraad F. Bronner,
    • Thomas D. Otto,
    • Min Zhang,
    • Kenneth Udenze,
    • Chengqi Wang,
    • Michael A. Quail,
    • Rays H.Y. Jiang,
    • John H. Adams,
    • and Julian C. Rayner
    Genome Res. July 2016 26: 980-989; Published in Advance May 10, 2016, doi:10.1101/gr.200279.115
    ...because the number of reads from sequences that did not arise from a transposon integration site is reduced by the nested PCR step in QIseq. This is a significant improvement compared to other methods utilizing the Roche 454sequencing platform (Uren et al. 2009; Rad et al. 2010). Onemoderate limitation...
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  2. Methods: Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
    • Katherine Elena Varley and
    • Robi David Mitra
    Genome Res. November 2008 18: 1844-1850; Published in Advance October 10, 2008, doi:10.1101/gr.078204.108
    ...Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes Katherine Elena Varley and Robi David Mitra 1 Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri 63108, USA...
  3. Resource: A quantitative atlas of polyadenylation in five mammals
    • Adnan Derti,
    • Philip Garrett-Engele,
    • Kenzie D. MacIsaac,
    • Richard C. Stevens,
    • Shreedharan Sriram,
    • Ronghua Chen,
    • Carol A. Rohl,
    • Jason M. Johnson,
    • and Tomas Babak
    Genome Res. June 2012 22: 1173-1183; Published in Advance March 27, 2012, doi:10.1101/gr.132563.111
    ...was used to reveal thousands of novel polyA sites in C. elegans, but requires many steps during library construction and has not been shown to be quantitative. Lastly, PAS-seq is similar to MAPS in that a universal sequence is upstream of the T20VN, which enables direct amplification by serving as a PCR...
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  4. Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
    • Jingwei Zhou,
    • Yuhong Huang,
    • Huan Ma,
    • Yiqian Chen,
    • Chuanye Chen,
    • Fangpu Han,
    • and Handong Su
    Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
    ...amplifications observed (Fig. 2A–C). These copy number increases were quantified using resequencing data and validated by quantitative PCR (Fig. 2E,F). These subtelomeric duplications were aligned with the hallmark of BFB cycles or the break-induced replication (BIR) model (Kim et al. 2021; Showman et al. 2024...
  5. 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
    ...- agents to permit quantitative PCR. TABLE 4 Lower Detection Limits of CMV-, HCV-, and HIV 1-specific single-tube Nested PCR Copy number of Positive reactions Control DNA template DNA in 10 PCR assays (no.) CMV (plasmid pRR47) HCV (purified first-round PCR product) HIV 1 (purifed first-round PCR product...
  6. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...replicate and used for RNA sequencing and quantitative PCR (qPCR). The gut of each honeybee was collected for 16S rRNA sequencing. The detailed experimental procedures regarding the first and second batches of sequencing data are described in the Supplemental Methods. Acquisition of public data...
  7. Method: Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples
    • Katherine Elena Varley and
    • Robi David Mitra
    Genome Res. September 2010 20: 1279-1287; Published in Advance July 13, 2010, doi:10.1101/gr.101212.109
    ...in tumors are often detected in peripheral samples (e.g., blood or stool) and may serve as diagnostic or prognostic biomarkers (Laird 2005). Many techniques have been developed to detect DNA methylation, includingmethods based onmicroarrays (Ushijima 2005), quantitative PCR (Eads et al. 2000), mass...
  8. REVIEW: Multiplex PCR: advantages, development, and applications.
    • M C Edwards and
    • R A Gibbs
    Genome Res. February 1994 3: S65-S75
    ...phosphoribosyltransferase gene in Lesch-Nyhan families. Genomics 7 : 235 – 244 . 16.. Abbs, S. , Bobrow. M. Abbs, S. and Bobrow. M. 1992 . Analysis of quantitative PCR for the diagnosis of deletion and duplication carriers in the dystrophin gene. J. Med. Genet. 29 : 191 – 196 . 17.. Ioannou, P., , Christopoulos, G...
  9. Methods: Quantitative phenotyping via deep barcode sequencing
    • Andrew M. Smith,
    • Lawrence E. Heisler,
    • Joseph Mellor,
    • Fiona Kaper,
    • Michael J. Thompson,
    • Mark Chee,
    • Frederick P. Roth,
    • Guri Giaever,
    • and Corey Nislow
    Genome Res. October 2009 19: 1836-1842; Published in Advance July 21, 2009, doi:10.1101/gr.093955.109
    ...to quantitative -scale fitness profiling of yeast deletion pools to characterize gene–environment interactions and drug mechanisms of action. In addition, we used NGS to re-sequence the barcodes and common priming sites and showed that it improved the results obtained from Sanger sequencing and the data collected...
  10. 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...
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