Searching journal content for articles similar to Gornitzka et al. 35 (10): 2240.

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  1. Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
    • Inswasti Cahyani,
    • John Tyson,
    • Nadine Holmes,
    • Josh Quick,
    • Chris Moore,
    • Nick Loman,
    • and Matthew Loose
    Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
    ...techniques.The first ultra-long (UL) sequencing protocols on nanopore sequencing instruments resulted in highly contiguous human assemblies (Jain et al. 2018a; Quick 2018). Later, some methods improved on these assemblies through increased yields (Miga et al. 2020; Logsdon et al. 2021). Oxford Nanopore...
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  2. Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
    • Yali Zhang,
    • Yayi Zhou,
    • Yangyang Chen,
    • Xueyu Wang,
    • Boyan Hu,
    • Shahid Siddique,
    • Romnick A. Latina,
    • Veronica I. Casey,
    • Dexin Bo,
    • Yucheng Liao,
    • Min Zhang,
    • Ming Sun,
    • Fengjuan Zhang,
    • and Dadong Dai
    Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
    ...al. 2014). This strategy substantially reduced sequencing errors and ensured a high-quality assembly.3D constructionTo reconstruct the 3D chromosomal maps of each haplotype, we used HiC-Pro (Servant et al. 2015) to generate interaction matrices for each haplotype's nine chromosomes at resolutions...
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  3. Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    • Enzo Battistella,
    • Anant Maheshwari,
    • Barış Ekim,
    • Bonnie Berger,
    • and Victoria Popic
    Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
    ...of sequencing errors, however, the problem of read-based haplotype assembly is computationally intractable. Numerous formulations for this problem have been proposed to date (Panconesi and Sozio 2004; Levy et al. 2007; Bansal and Bafna 2008; Duitama et al. 2010; Aguiar and Istrail 2012; Berger et al. 2014, 2020...
  4. Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
    • Julie A. Karl,
    • Trent M. Prall,
    • Hailey E. Bussan,
    • Joshua M. Varghese,
    • Aparna Pal,
    • Roger W. Wiseman,
    • and David H. O'Connor
    Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
    ...haplotypes. The MHC class I region, in contrast, contains 13 MHC-B genes, four MHC-A genes, and three MHC-E genes (vs. 19 MHC-B, two MHC-A, and one MHC-E in the previously sequenced haplotype). These results provide an unambiguously assembled single contiguous cynomolgus macaque MHC haplotype with fully...
  5. Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    ...transcriptome characterization of each cell, as well as highly accurate consensus sequences for the somatically rearranged and hypermutated light and heavy chain IG transcripts. A subset of antibodies synthesized based on their consensus heavy and light chain transcript sequences demonstrate binding to measles...
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  6. Research: Ultra-long-range interactions between active regulatory elements
    • Elias T. Friman,
    • Ilya M. Flyamer,
    • Davide Marenduzzo,
    • Shelagh Boyle,
    • and Wendy A. Bickmore
    Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
    ...Fig. S4B). Analysis of Micro-C data at 100-bp resolution within the 10-kb region surrounding TSSs showed that enriched interactions are centered at the TSS (Fig. 2C).View larger version: In this window In a new window Figure 2. Ultra-long-range interactions (ULIs) between active promoters and distal...
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  7. Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
    • Tsung-Kai Hung,
    • Wan-Chi Liu,
    • Sheng-Kai Lai,
    • Hui-Wen Chuang,
    • Yi-Che Lee,
    • Hong-Ye Lin,
    • Chia-Lang Hsu,
    • Chien-Yu Chen,
    • Ya-Chien Yang,
    • Jacob Shujui Hsu,
    • and Pei-Lung Chen
    Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
    ...haplotypes in contigs assembled from probe-captured Pacific Biosciences (PacBio) CCS long-read sequencing data (Roe et al. 2020). Assembly quality, including completeness and contiguity, largely depends on the sensitivity and specificity of the in vitro and in silico probes and the assembly algorithm...
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  8. Method: Gene prediction in the immunoglobulin loci
    • Vikram Sirupurapu,
    • Yana Safonova,
    • and Pavel A. Pevzner
    Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
    ...tasks (Das et al. 2012; Pettinello and Dooley 2014).Mammalian s have three IG loci—heavy chain (IGH), kappa light chain (IGK), and lambda light chain (IGL)—as well as four T-cell antigen receptor (TCR) loci (TRA, TRB, TRG, and TRD). In this work, we mainly focus on the IGH locus. The V, D, and J genes...
  9. 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
    ...) and clique enumeration to resolve ambiguous read assignments across highly similar gene sequences. Our previous work employed a similar framework to genotype germline IG heavy-chain variable (IGHV) genes using long-read WGS (Ford et al. 2020) and short-read WGS (Ford et al. 2022), implemented in the Immuno...
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  10. 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
    ...sequencing. This began in 2020 with the publication of the first gapless assembly of the human X Chromosome using ultra-long-read nanopore sequencing (Miga et al. 2020). Then in 2022, the consortium published T2T-CHM13 as the first fully gapless human assembled primarily from PacBio HiFi and ONT Ultralong...
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