Searching journal content for articles similar to Clayton 11 (5): 659.

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  1. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    .... length ±1bp). Without SNVs, STRkit achieves a lower seq. MI rate of 93.64% (95.58% seq. len., 98.42% ±1 bp). LongTR and TRGT again perform almost as well as STRkit with HiFi data; LongTR achieves a seq. MI rate of 94.52% (94.85% seq. len., 97.54% ±1 bp), and TRGT achieves a seq. MI rate of 94.77% (97...
  2. Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    • Xue Dong,
    • Mengzhu Hu,
    • Xiaonan Cui,
    • Wenjian Zhou,
    • Jingtao Cai,
    • Guangyao Mao,
    • and Weiyang Shi
    Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
    ...), to identify the eye region. PAX6-positive and PAX6-negative domains were independently photo-illuminated using a 20× objective lens (Supplemental Fig. 3A). Following lysis, cDNA libraries were amplified and sequenced. At an average sequencing depth of 7.3 million read pairs per sample, we detected an average...
  3. Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
    • Ali Azizpour,
    • Advait Balaji,
    • Todd J. Treangen,
    • and Santiago Segarra
    Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
  4. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M. Riley,
    • Randa Elsayed,
    • Mark D. Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C. Nelson
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...discrete regions containing the zebrafish and human HCNE (i5zHCNE and i5hHCNE, respectively). We also tested the upstream accessible region (Enh –3 kb). Each reporter construct also contained the crystallin, alpha a (cryaa) promoter upstream of gfp. This drives GFP expression in the lens of the eye, thus...
  5. Research: Large haplotypes highlight a complex age structure within the maize pan-genome
    • Jianing Liu and
    • R. Kelly Dawe
    Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
    ...of anchor i in the first round was calculated as f(i) = max{f(j) + len(i) × log10(q(i) + 0.001) − gap(i, j)/100}, i > j > 1, where len(i) and q(i) are, respectively, the length and the mapping quality of anchor i. Gap (i,j) is the distance between anchors i and j, which was computed as abs (ix − jy), and x...
  6. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    OPEN ACCESS ARTICLE
  7. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...BLASTN (v2.12.0) (Chen et al. 2015) with the consensus sequence (len = 32 bp): “gatatttccatgtttatacagatagcggtgta.” BLAST hits with >90% of the consensus (>28 bp) were recovered. The individual pCht unit was classified into different types based on the variants (small INS, DEL, or substitution). The SD...
    OPEN ACCESS ARTICLE
  8. Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
    • Sophia N. Lee,
    • Erin C. Banda,
    • Lu Qiao,
    • Sarah L. Thompson,
    • Karan Singh,
    • Ryan A. Hagenson,
    • Teresa Davoli,
    • Stefan F. Pinter,
    • and Jason M. Sheltzer
    Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
  9. Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
    • Wiesław Babik,
    • Katarzyna Dudek,
    • Gemma Palomar,
    • Marzena Marszałek,
    • Grzegorz Dubin,
    • Maximina H. Yun,
    • and Magdalena Migalska
    Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
  10. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...splice-site variations involving complex combinations. The ENACT algorithm systematically addresses these splicing complexities through exon architecture representation for genes after processing exonic loci in isoforms and their variations (see Methods) (Box 1).Box 1. ENACT AlgorithmFunctions:len...
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