Searching journal content for articles similar to Henikoff and Henikoff 10 (4): 543.

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  1. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...efficient than hifiasm when handling Drosophila highly repetitive regions. The remaining eight autosomal genes (JYalpha, Marf1, DIP-lambda, CG42402, Myo81F, Pzl, Gpa2, and klhl10) had satellite blocks near the exons either within introns or in flanking intergenic regions, which were associated with clear...
  2. 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
    ..., and Arabidopsis thaliana. It can further map annotation effectively across species pairs as far apart as mouse and rat or Drosophila melanogaster and Drosophila erecta.Recent advancements in sequencing technologies have resulted in an exponential increase in available assemblies. Long-read sequencing technology...
  3. Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
    • Zepu Miao and
    • Jia-Xing Yue
    Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
    ..., centromere, and telomere annotations were extracted from the NCBI RefSeq GFF3 file (https://ftp.ncbi.nlm.nih.gov/s/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.gff.gz). The subtelomere annotation was extracted from the GFF3 file retrieved from the ScRAPdb database (Miao et al. 2024...
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  4. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...initial data processing to variant calling and annotation, focusing on how these methods improve our ability to interpret a wide array of genomic variants. Additionally, we discuss the current challenges, limitations, and future directions in the field, offering a detailed examination of the state...
  5. Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
    • Harsh G. Shukla,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
    ...on mutational processes shaping two functionally important tandem arrays in the Drosophila .ResultsGenome assembliesThe strains selected include the Drosophila community's reference strain (iso-1) (Adams et al. 2000) and two strains from the Drosophila Synthetic Population Resource (A3 and A4) (King et al. 2012...
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  6. Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
    • John S. Sproul,
    • Scott Hotaling,
    • Jacqueline Heckenhauer,
    • Ashlyn Powell,
    • Dez Marshall,
    • Amanda M. Larracuente,
    • Joanna L. Kelley,
    • Steffen U. Pauls,
    • and Paul B. Frandsen
    Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
    ...” following automated annotation, compared with only ∼13% in Drosophila species. Although the diversity of available insect s has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We...
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  7. Method: Evaluation of N6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes
    • Brian M. Debo,
    • Benjamin J. Mallory,
    • and Andrew B. Stergachis
    Genome Res. March 2023 33: 427-434; Published in Advance February 14, 2023, doi:10.1101/gr.276696.122
    ...(Stergachis et al. 2020). Genome builds used were dm6 (D. melanogaster), TAIR9 (A. thaliana), and creinhardtii_281_v5.0 (C. reinhardtii). Signal tracks were generated using BEDOPS (Neph et al. 2012), and signal was normalized to 1 million reads. For the Drosophila S2 samples, DNA-m6A peaks were identified...
  8. Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
    • Junling Shi,
    • Jiaqi Xu,
    • Jun Ma,
    • and Feng He
    Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
    ...are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which...
  9. Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
    • Peter O. Mulhair,
    • Liam Crowley,
    • Douglas H. Boyes,
    • Amber Harper,
    • Owen T. Lewis,
    • Darwin Tree of Life Consortium,
    • and Peter W.H. Holland
    Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
    ...generally comprises 10 homeobox genes arranged in a specific order reflecting their evolutionary origin by tandem gene duplication: lab, pb, zen, Dfd, Scr, Antp, ftz, Ubx, abd-A, and Abd-B. The cluster may be split, as in many Drosophila species (Duboule 2007; Negre and Ruiz 2007), individual genes may...
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  10. Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
    • Aleix Palahí i Torres,
    • Lars Höök,
    • Karin Näsvall,
    • Daria Shipilina,
    • Christer Wiklund,
    • Roger Vila,
    • Peter Pruisscher,
    • and Niclas Backström
    Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
    ...of, but not within, coding and regulatory regions. The slightly elevated recombination rate in introns is consistent with findings in the holocentric nematode C. elegans (Prachumwat et al. 2004), but opposed to observations in Drosophila (Carvalho and Clark 1999) and humans (Comeron and Kreitman 2000...
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