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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...assembly. Genome Biol 24: 100. doi:10.1186/s13059-023-02919-8 ↵Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C, Human Pan Reference C, et al. 2023b. Gaps and complex structurally variant loci in phased assemblies. Genome Res 33: 496–510. doi:10.1101/gr...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...gaps. Nonetheless, with reduced sequencing cost, improved Nanopore read accuracy, and refined assembly algorithms, we anticipate more phased assemblies to be produced in the near future. Relatedly, Immuannot may misidentify a novel allele caused by base errors in contigs. Although, based...
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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
...—such as the IG heavy chain, light chains, and T cell receptor (TR) loci—encode the genes responsible for antibodies/B cell receptors as well as TRs. However, these contain many gene copies, are highly repetitive, and are host to a variety of structural variants (Watson and Breden 2012; Watson et al. 2013, 2017...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
..., and public HiFi data (set 2, see Methods); gnomAD v4 SV frequencies from 63,046 short-read samples (set 3, Collins et al. 2020); Human Genome Structural Variant Consortium phase 2 (HGSVC2) assembly-based calls from 18 HiFi samples (set 4, Ebert et al. 2021, https://ftp.1000s.ebi.ac.uk/vol1/ftp...
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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
...from use of long reads that can resolve their complex structures and improve haplotype phasing (Kolmogorov et al. 2023). However, individual single-cell transcriptomes have so far not been paired with germline assemblies from the same donor. Haplotyped structural variants and heterogeneity of IG V, D...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: tpastinen@cmh.edu, guil.bourque@mcgill.caAbstractStructural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation statuses are rarely characterized due to previous limitations in assembly...
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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...of 91.2% versus 91.2% (Hifi_L1), 90.1% versus 89.1% (CLR_L1), and 92.3% versus 90.2% (ONT_L1) (Supplemental Table S6). Overall, FocalSV demonstrated high phasing accuracy for both SNP phasing and local assemblies, while maintaining robust structural variant detection performance even in regions...
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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
...-quality assemblies from the Human Pan Reference Consortium (HPRC), we present a novel bioinformatic tool, the structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. In 47 HPRC-phased assemblies, SKIRT identifies a recurrent novel KIR2DS4/3DL1 fusion gene...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere assembly of C. elegans, generated from CGC1, an isogenic...
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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
...(Bloom 1970) is a space-efficient probabilistic data structure that is used to test whether an element is a member of a set and that may report false positives (with a small false-positive probability) but never false negatives. Given a , Genome (or its assembly), its Bloom filter is formed by Bloom...

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