Searching journal content for articles similar to Mikelov et al. 34 (12): 2293.

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  1. Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...(⁄ . 449 8 450 The model was studied by simulation with a custom script (aev_sim.py). 451 Indel allele count benchmarking 452 21 The Sequencing Quality Control Phase 2 (SEQC2) Consortium established a reference somatic 453 call set from the HCC1395 breast cancer cell line and the HCC1395BL cell line, which...
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  2. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...Dayea Park and Can Cenik Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Corresponding author: ccenik@austin.utexas.eduAbstractLong-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights...
  3. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    ...are problematic, there are alternative methods available. Germline genotype inference using adaptive immune receptor repertoire sequencing (AIRR-Seq) is an established approach, with many published bespoke tools (Corcoran et al. 2016; Gadala-Maria et al. 2019; Peres et al. 2019; Ralph and Matsen IV 2019). Another...
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  4. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...-mer counts in the sequencing data to calculate likelihoods of reference and alternative alleles. Pangenie and KAGE also use the long-range haplotype information available in the haplotype-resolved pan references. The other approach used in methods such as Giraffe (Sirén et al. 2021) and Graphtyper...
  5. 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
    ...effector proteins essential for host infection. Rust effectors are under strong selection pressure to diversify into nonrecognized virulence alleles because they can be recognized by cognate immune receptors encoded by wheat resistance genes (Chen et al. 2017; Salcedo et al. 2017; Ortiz et al. 2022...
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  6. Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
    ...from our reference set but differed from the IMGT allele owing to the A330V and W334G substitutions.To determine the extent to which both copies of the duplicated genes were expressed in the BCR repertoire, we performed near-full-length adaptive immune receptor repertoire sequencing (FLAIRR...
  7. Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
    • Ran Zhang,
    • Chengxiang Qiu,
    • Galina N. Filippova,
    • Gang Li,
    • Jay Shendure,
    • Jean-Philippe Vert,
    • Xinxian Deng,
    • William Stafford Noble,
    • and Christine M. Disteche
    Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
    ...to be immensely valuable, they suffer from a fundamental limitation: Because sequencing measurements are usually disruptive, it is impossible to trace a given cell's behavior across time. In addition, single-cell profile inference suffers from heterogeneity of biological samples (e.g., female vs. male, disease vs...
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  8. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...alterations in transcriptomes or epis and cannot simultaneously capture genomic and epigenomic variations, which further hinders the phasing of methylation and the detection of allele-specific methylation (ASM).Addressing these challenges, long-read sequencing technologies, such as Pacific Biosciences (Pac...
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  9. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ...of development, aging, and cancer. Cell lineage trees represent the evolutionary history of cells sampled from an organism. Recent developments in single-cell sequencing have greatly facilitated the inference of cell lineage trees. However, single-cell data are sparse and noisy, and the size of single-cell data...
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  10. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...; 4Rice Synthetic Biology Institute, Rice University, Houston, Texas 77005, USA ↵5 These authors contributed equally to this work. Corresponding author: vy@rice.eduAbstractAs sequencing techniques advance in precision, affordability, and diversity, an abundance of heterogeneous sequencing data has...
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