Searching journal content for articles similar to Birchler 7 (11): 1035.

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  1. Research: Identification and characterization of centromeric sequences in Xenopus laevis
    • Owen K. Smith,
    • Charles Limouse,
    • Kelsey A. Fryer,
    • Nicole A. Teran,
    • Kousik Sundararajan,
    • Rebecca Heald,
    • and Aaron F. Straight
    Genome Res. June 2021 31: 958-967; Published in Advance April 19, 2021, doi:10.1101/gr.267781.120
    ...and Chr 8S (Supplemental Fig. S6E). This indicates that, for this Xenopus laevis chromosome, the centromere can be assembled and maintained on nonrepetitive DNA.We have evaluated the k-mer content of each Xenopus laevis chromosome; however, to understand which 174-bp monomer sequences make up...
  2. Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
    ...of the centromere-specific histone H3 variant Cse4p/CENPA, while the pericentric sequence is dominated by normal histone H3 (Burrack et al. 2011). Centromeres frequently harbor repetitive sequences and complex chromatin structures that make the centromere especially susceptible to double-stranded breaks...
  3. Research: Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
    • Josh T. Cuperus,
    • Benjamin Groves,
    • Anna Kuchina,
    • Alexander B. Rosenberg,
    • Nebojsa Jojic,
    • Stanley Fields,
    • and Georg Seelig
    Genome Res. December 2017 27: 2015-2024; Published in Advance November 2, 2017, doi:10.1101/gr.224964.117
    .... By making sequential single base changes, we were able to track how sequence features changed over the course of evolution. We continued making changes until the predicted expression of each 5′ UTR plateaued (Fig. 4A; Supplemental Fig. S7A).View larger version: In this window In a new window Figure 4. Model...
  4. Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
    • Rita Tam,
    • Mareike Möller,
    • Runpeng Luo,
    • Zhenyan Luo,
    • Ashley Jones,
    • Sambasivam Periyannan,
    • John P. Rathjen,
    • and Benjamin Schwessinger
    Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
    ...without predicted transmembrane domain.ONT direct cDNA sequencing has demonstrated quantitative power consistent with short-read RNA-seq, making it suitable for differential expression analysis (Sessegolo et al. 2019; Grünberger et al. 2022; Pardo-Palacios et al. 2024). We performed differential...
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  5. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...using SPA to yield haploid recombinant strains. To establish CRI-SPA-Map, we mate a 22 W303 SPA strain to 92 strains from the BY4742 yeast knockout collection that carry gene 23 deletion cassettes on the left arm of chromosome XIV and create 1,451 recombinant isolates. 24 Whole- sequencing verified...
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  6. Method: Automated annotation of human centromeres with HORmon
    • Olga Kunyavskaya,
    • Tatiana Dvorkina,
    • Andrey V. Bzikadze,
    • Ivan A. Alexandrov,
    • and Pavel A. Pevzner
    Genome Res. June 2022 32: 1137-1151; Published in Advance May 11, 2022, doi:10.1101/gr.276362.121
    ...tandem repeat formed by various monomers. The vast majority of units in cenX correspond to the canonical HOR, which is formed by 12 monomers (shown by 12 different colors). The figure on top represents the dot plot of the nucleotide sequence of the canonical HOR that reveals 12 monomers. Although...
  7. Method: Fast and accurate mapping of long reads to complete genome assemblies with VerityMap
    • Andrey V. Bzikadze,
    • Alla Mikheenko,
    • and Pavel A. Pevzner
    Genome Res. November/December 2022 32: 2107-2118; Published in Advance November 15, 2022, doi:10.1101/gr.276871.122
    ...), whereas Winnowmap2 and minimap2 extend them through it.View larger version: In this window In a new window Figure 3. Visualization of VerityMap, Winnowmap2, and minimap2 alignments of simulated reads from the CenX-Diploid data set to the CenX-Diploid-Switch sequence using the IGV browser (Robinson et al...
  8. Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
    • Damira Veseljak,
    • Evelin Despot-Slade,
    • Marin Volarić,
    • Lucija Horvat,
    • Tanja Vojvoda Zeljko,
    • Nevenka Meštrović,
    • and Brankica Mravinac
    Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
    ...repetitive, tandemly organized DNA sequences whose contiguous arrays make up extensive regions in many eukaryotic s. The repetitive organization has hampered their study in the past and made them the most challenging regions to assemble in sequenced s. They were initially considered “junk DNA” due...
  9. Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
    ...scenario. After making these adjustments, LiftOn evaluates the differences between the reference and target transcripts and, similarly to LiftoffTools (Shumate and Salzberg 2022), produces a mutation report. Transcripts are deemed “identical” when their target and reference gene DNA sequences are entirely...
  10. LETTER: Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
    • Ines Hellmann,
    • Yuan Mang,
    • Zhiping Gu,
    • Peter Li,
    • Francisco M. de la Vega,
    • Andrew G. Clark,
    • and Rasmus Nielsen
    Genome Res. July 2008 18: 1020-1029; Published in Advance April 14, 2008, doi:10.1101/gr.074187.107
    ..., Cornell University, Ithaca, New York 14853, USA Abstract We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity θ from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one...
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