Searching journal content for articles similar to Valenza-Schaerly et al. 11 (3): 382.

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  1. Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    ...of mutations.We performed -wide QTL mapping separately for each of these mutation phenotypes using R/qtl2 (Broman et al. 2019) and a set of 7101 LD-pruned SNPs (Fig. 2). To account for population structure, R/qtl2 uses a linear mixed model with a kinship matrix generated using the leave-one-chromosome...
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  2. 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
    ...sequences and their association with expression quantitative trait loci (eQTLs) to form the most comprehensive resource of this type, accessible through the UCSC Genome Browser. If your GOI and/or candidate TF are known to be expressed in human cancer, two useful tools that are relevant are DepMap, which...
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  3. Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
    • Shelley Reich,
    • Tobias Loschko,
    • Julie Jung,
    • Samantha Nestel,
    • Ralf J. Sommer,
    • and Michael S. Werner
    Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
    ...vary in the ratio of Eu to St animals even when grown under the same environmental conditions, indicating a strong effect of genetic background on mouth-form development (Ragsdale et al. 2013). A recent study employed recombinant inbred lines and QTL mapping with two strains from clade B (Dardiry et al...
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  4. Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
    • Montgomery Blencowe,
    • Xuqi Chen,
    • Yutian Zhao,
    • Yuichiro Itoh,
    • Caden N. McQuillen,
    • Yanjie Han,
    • Benjamin L. Shou,
    • Rebecca McClusky,
    • Karen Reue,
    • Arthur P. Arnold,
    • and Xia Yang
    Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
    ...the DEGs highlighted in the 1WA overlap with genes previously identified to have SNPs associated with human diseases/pathogenic traits by GWAS. In brief, we mapped each of the GWAS SNPs to genes using liver and adipose eQTLs to represent disease-associated genes informed by GWAS. The mouse orthologs...
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  5. Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
    • Benjamin P. Barré,
    • Johan Hallin,
    • Jia-Xing Yue,
    • Karl Persson,
    • Ekaterina Mikhalev,
    • Agurtzane Irizar,
    • Sylvester Holt,
    • Dawn Thompson,
    • Mikael Molin,
    • Jonas Warringer,
    • and Gianni Liti
    Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
    ...of the 1056 POLs separated according to genotype at the markers with highest LOD score in each of the two major QTLs: 394,381 kb in Chromosome IX (in FLO11) and 33,217 kb in Chromosome XV (in HPF1). (B) Schematic representation of the NA/WA reciprocal hemizygosity design used to validate the CLS effect...
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  6. Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
    • Maximilian O. Press,
    • Rajiv C. McCoy,
    • Ashley N. Hall,
    • Joshua M. Akey,
    • and Christine Queitsch
    Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
    ...(Kawakatsu et al. 2016), we also tested for associations between STR genotypes and expression of genes (i.e., eQTLs) (Supplemental Text), using a range of distances from genes. Although our power to detect eQTLs was limited by sample size, we detected 12 significant associations. The strongest association...
  7. Research: An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease
    • Farhoud Faraji,
    • Ying Hu,
    • Gang Wu,
    • Natalie E. Goldberger,
    • Renard C. Walker,
    • Jinghui Zhang,
    • and Kent W. Hunter
    Genome Res. February 2014 24: 227-240; Published in Advance December 9, 2013, doi:10.1101/gr.166223.113
    ...throughput sequence analysis of small RNAs derived from [AKXDn3 PyMT]F1 tumors (Fig. 1C) followed by eQTL analysis (Schadt et al. 2003) in the AKXD RI panel. Comparison of expression levels of significantly expressed miRNAs to the genetic map resulted in the detection of seven distinct eQTLs for 13 mi...
  8. REVIEW: Allelic variation and heterosis in maize: How do two halves make more than a whole?
    • Nathan M. Springer and
    • Robert M. Stupar
    Genome Res. March 2007 17: 264-275; Published in Advance January 25, 2007, doi:10.1101/gr.5347007
    ...not control all heterotic responses. Additionally, heterosis does not simply result from the overall genetic diversity within a hybrid, but is likely a reflection of diversity at specific, important genes that contribute to a particular trait. This view is supported by the ability to map QTLs that contribute...
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