Searching journal content for articles similar to Wall et al..

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  1. Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
    • Shaoqiang Hu,
    • Xiangguo Zeng,
    • Yuguo Liu,
    • Yongping Li,
    • Minghao Qu,
    • Wen-Biao Jiao,
    • Yongchao Han,
    • and Chunying Kang
    Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
    ...the tissue culture process of cultivated strawberry to reveal features of somaclonal variation. DNA mutation and methylation changes were analyzed at single base resolution in regenerated plants obtained at two hormone levels and two culture times. We chose the strawberry cultivar “Beni hoppe” to assemble...
  2. Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
    • Yang Zhou,
    • Lv Yang,
    • Xiaotao Han,
    • Jiazheng Han,
    • Yan Hu,
    • Fan Li,
    • Han Xia,
    • Lingwei Peng,
    • Clarissa Boschiero,
    • Benjamin D. Rosen,
    • Derek M. Bickhart,
    • Shujun Zhang,
    • Aizhen Guo,
    • Curtis P. Van Tassell,
    • Timothy P.L. Smith,
    • Liguo Yang,
    • and George E. Liu
    Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
    ...al. 2015b). The known mechanisms of SV formation include nonallelic homologous recombination, nonhomologous end joining (NHEJ), mobile element insertion (MEI), microhomology-mediated break-induced replication (MMBIR), and fork stalling and template switching (FoSTeS) during DNA replication (Zhang et...
  3. Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
    • PingHsun Hsieh,
    • August E. Woerner,
    • Jeffrey D. Wall,
    • Joseph Lachance,
    • Sarah A. Tishkoff,
    • Ryan N. Gutenkunst,
    • and Michael F. Hammer
    Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
    ...(2006) recently analyzed patterns of divergence and linkage disequilibrium (LD) in DNA sequence polymorphism data from extant modern humans. Their summary statistic, S∗, exploits the fact that recently introgressed lineages from long-isolated archaic humans show increased divergence and extensive LD...
  4. Method: Discriminating somatic and germline mutations in tumor DNA samples without matching normals
    • Saskia Hiltemann,
    • Guido Jenster,
    • Jan Trapman,
    • Peter van der Spek,
    • and Andrew Stubbs
    Genome Res. September 2015 25: 1382-1390; Published in Advance July 24, 2015, doi:10.1101/gr.183053.114
    ...left alignment is by far the most commonly used. However, the HGVS recommendations urge “for all descriptions [to use] themost 3′ position possible,”whichwould imply right alignment of variants on forward strand genes (http://www.hgvs.org/ mutnomen/recs-DNA.html). Another example, and one of the most...
  5. Research: Comprehensive identification and analysis of human accelerated regulatory DNA
    • Rachel M. Gittelman,
    • Enna Hun,
    • Ferhat Ay,
    • Jennifer Madeoy,
    • Len Pennacchio,
    • William S. Noble,
    • R. David Hawkins,
    • and Joshua M. Akey
    Genome Res. September 2015 25: 1245-1255; Published in Advance June 23, 2015, doi:10.1101/gr.192591.115
    ...Comprehensive identification and analysis of human accelerated regulatory DNA Rachel M. Gittelman 1 , Enna Hun 2 , Ferhat Ay 1 , Jennifer Madeoy 1 , Len Pennacchio 3 , William S. Noble 1 , R. David Hawkins 1 , 2...
  6. Letter: Darwinian and demographic forces affecting human protein coding genes
    • Rasmus Nielsen,
    • Melissa J. Hubisz,
    • Ines Hellmann,
    • Dara Torgerson,
    • Aida M. Andrés,
    • Anders Albrechtsen,
    • Ryan Gutenkunst,
    • Mark D. Adams,
    • Michele Cargill,
    • Adam Boyko,
    • Amit Indap,
    • Carlos D. Bustamante,
    • and Andrew G. Clark
    Genome Res. May 2009 19: 838-849; Published in Advance March 11, 2009, doi:10.1101/gr.088336.108
    ...analyzed here is the first comprehensive data set of variability in human protein-coding genes that is not based on SNP data, but is based on directly sequenced DNA. The problems associated with ascertainment biases in SNP data are, therefore, avoided. We cannot exclude the possibility that there are other...
  7. Research: Reconstructing ancient mitochondrial DNA links between Africa and Europe
    • María Cerezo,
    • Alessandro Achilli,
    • Anna Olivieri,
    • Ugo A. Perego,
    • Alberto Gómez-Carballa,
    • Francesca Brisighelli,
    • Hovirag Lancioni,
    • Scott R. Woodward,
    • Manuel López-Soto,
    • Ángel Carracedo,
    • Cristian Capelli,
    • Antonio Torroni,
    • and Antonio Salas
    Genome Res. May 2012 22: 821-826; Published in Advance March 27, 2012, doi:10.1101/gr.134452.111
    ...sub-Saharan mtDNA variability. In Europe, these mtDNAs account for <1% of the total but, when analyzed at the level of control region, they show no signals of having evolved within the European continent, an observation that is compatible with a recent arrival from the African continent. To further...
  8. Research: Degrees of convergent evolution in rodent adaptations to arid environments
    • Domitille Chalopin,
    • Carine Rey,
    • Jeremy Ganofsky,
    • Juliana Blin,
    • Pascale Chevret,
    • Marion Mouginot,
    • Laurent Guéguen,
    • Bastien Boussau,
    • Sophie Pantalacci,
    • and Marie Sémon
    Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
    ...for the kidney. We combined publicly available data (cDNA from published s and kidney RNA-seq data) with newly generated RNA-seq data to obtain coding sequence and expression data in a variety of rodents, ensuring a reasonable overlap between the two types of data (12 families, 48 species out of which 33 species...
    OPEN ACCESS ARTICLE
  9. METHODS: SNPSTRs: Empirically Derived, Rapidly Typed, Autosomal Haplotypes for Inference of Population History and Mutational Processes
    • Joanna L. Mountain,
    • Alec Knight,
    • Matthew Jobin,
    • Christopher Gignoux,
    • Adam Miller,
    • Alice A. Lin,
    • and Peter A. Underhill
    Genome Res. November 1, 2002 12: 1766-1772; doi:10.1101/gr.238602
    ...organism has a separate history reflecting part of the evolutionary history of that organism. Uniparentally or clonally inherited DNA segments such as the mitochondrial and chloroplast genomes and the nonrecombining portion of the Y chromosome have provided, to date, most of the known data regarding...
  10. Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
    ...; Braaker and Heckel 2009; Martínková et al. 2013; Lischer et al. 2014; Wang et al. 2023). New resequencing was performed for four samples. Sequence data from all samples are available at NCBI BioProject (https://www.ncbi.nlm.nih.gov/bioproject) under accession number PRJNA963218.DNA extraction...
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