Searching journal content for articles similar to Walsh et al. 1 (4): 241.

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  1. Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
    • Xuyan Liu,
    • Lin Xia,
    • Yixin Qiao,
    • Yang Li,
    • Yan Huang,
    • Bingyan Yue,
    • Xi Liang,
    • Xin Yang,
    • Honghui Zhang,
    • Jiaxun Zhang,
    • Xiao Chen,
    • Dan Xie,
    • and Jifeng Liu
    Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
    ...sequences identical to flanking repeats (Supplemental Fig. S4G). A 323 representative case in simple repeats demonstrated a 12-fold amplification of the 324 reference TTCT motif in tumor samples (Supplemental Fig. S4H), indicating that 325 somatic INS preferentially propagate existing repetitive...
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  2. GENOME METHODS: Overlapping PCR for Bidirectional PCR Amplification of Specific Alleles: A Rapid One-Tube Method for Simultaneously Differentiating Homozygotes and Heterozygotes
    • Qiang Liu,
    • Erik C. Thorland,
    • John A. Heit,
    • and Steve S. Sommer
    Genome Res. April 1, 1997 7: 389-398; doi:10.1101/gr.7.4.389
    ...-specific PCR, and amplification refractory mutation system (ARMS) ( Newton et al. 1989 ; Nichols et al. 1989 ; Wu et al. 1989 ). For this technique, an oligonucleotide primer is designed to match one allele perfectly but mismatch the other allele at or near the 3′ end, thereby preferentially amplifying one...
  3. Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
    • Sudeshna Majumdar,
    • Lakshmi Sowjanya Bammidi,
    • Hemant C. Naik,
    • Avinchal Manhas,
    • Runumi Baro,
    • Akash Kalita,
    • Amlan Jyoti Naskar,
    • Sundarraj Nidharshan,
    • Girija S. Bariha,
    • Dimple Notani,
    • and Srimonta Gayen
    Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
    .... sgRNA binding sites: g1 and g2. PCR primers F2 and R2, and F1 and R1 shown as gray arrows used for amplification of the wild-type allele and the allele with deletion, respectively. (B) PCR-based identification of clones having the deletion of the Xist upstream region (D1) on the paternal allele (top...
  4. ARTICLES: Effect of freezing of the PCR buffer on the amplification specificity: allelic exclusion and preferential amplification of contaminating molecules.
    • C Y Hu,
    • M Allen,
    • and U Gyllensten
    Genome Res. November 1992 2: 182-183; doi:10.1101/gr.2.2.182
    ...Effect of freezing of the PCR buffer on the amplification specificity: allelic exclusion and preferential amplification of contaminating molecules. C Y Hu , M Allen , and U Gyllensten Department of Medical Genetics, University of Uppsala, Sweden...
  5. Method: High-fidelity, large-scale targeted profiling of microsatellites
    • Caitlin A. Loh,
    • Danielle A. Shields,
    • Adam Schwing,
    • and Gilad D. Evrony
    Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
    ...; Bhargava and Fuentes 2010). This same process occurs during in vitro amplification of microsatellites, for example, in PCR. This produces an artifact pattern called “stutter” in which the final population of amplified molecules has a distribution of repeat unit counts with a peak at the true repeat unit...
  6. Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    ...capable of binding a vast array of possible antigens. However, the antibody repertoire is fundamentally limited by the set of variable (V), diversity (D), and joining (J) alleles present in the germline IG loci. To better understand how the germline IG haplotypes contribute to the expressed antibody...
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  7. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...within that droplet. The absolute number of target molecules is calculated using Poisson statistics, bypassing the need for standard curves and making ddPCR advantageous for low-abundance targets or small fold-changes that may fall below the detection limits of qRT-PCR. Because each amplification occurs...
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  8. REVIEW: Multiplex PCR: advantages, development, and applications.
    • M C Edwards and
    • R A Gibbs
    Genome Res. February 1994 3: S65-S75
    ...for multiplex pur- poses, such as allele-specific PCR, (21'22) restriction site-generating PeR, (23-25) amplification refractory mutation system (ARMS), (2~ color complementa- tion assay, (3~ and nested PCR. (6'31'32) For deletion assays of genes with many exons, the amplicons can be distributed to scan a wide...
  9. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...and 9 bp UMI adapters, and one cycle of PCR amplification. Library quality was assessed using the D5000 screentape (Agilent Technologies), and concentration was determined by a Qubit dsDNA HS assay (Thermo Fisher Scientific).The initial set of paired-end 150 bp Illumina libraries was prepared...
  10. 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
    ...-read target enrichment (Hodges et al. 2007; Turner et al. 2009; Mertes et al. 2011; Altmüller et al. 2014; Ballester et al. 2016) and typically rely on multiplexed PCR amplification (Jones et al. 2008; Tewhey et al. 2009) or oligonucleotide-based DNA hybridization capture (Albert et al. 2007; Hodges et al...
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