Searching journal content for articles similar to Kuronen et al. 34 (7): 1081.

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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere assembly, phasing, and scaffolding Dmitry Antipov1,4, Mikko Rautiainen2,4, Sergey Nurk3, Brian P. Walenz1, Steven J. Solar1, Adam M. Phillippy1 and Sergey Koren1 1Genome Informatics Section...
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RECOMB 2022 Special/Methods: Lossless indexing with counting de Bruijn graphs
- Mikhail Karasikov,
- Harun Mustafa,
- Gunnar Rätsch,
- and André Kahles
Genome Res. September 2022 32: 1754-1764; Published in Advance May 24, 2022, doi:10.1101/gr.276607.122
...for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated (or colored) de Bruijn graphs for efficiently indexing k-mer sets. However, approaches for representing quantitative...
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Method: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
- Andrea Cracco and
- Alexandru I. Tomescu
Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
...Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a collection of sequences and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...Haplotype-aware sequence alignment to pan graphs Ghanshyam Chandra1, Daniel Gibney2 and Chirag Jain1 1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore Karnataka 560012, India; 2Department of Computer Science, The University of Texas at Dallas, Richardson, Texas...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...Strain-level metagenomic profiling using pan graphs with PanTax Wenhai Zhang1,2,5, Yuansheng Liu3,5, Guangyi Li2,5, Jialu Xu2, Enlian Chen2, Alexander Schönhuth4 and Xiao Luo1,2 1Hunan Research Center of the Basic Discipline for Cell Signaling, Hunan University, Changsha, Hunan 410082, China; 2...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...that arise from recent demographic events, patterns that are crucial for understanding rare variant effects. To address this challenge, we propose a novel method called spectral components (SPCs), which leverages identity-by-descent (IBD) graphs to capture and transform local, nonlinear fine-scale population...
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Method: Aligning distant sequences to graphs using long seed sketches
- Amir Joudaki,
- Alexandru Meterez,
- Harun Mustafa,
- Ragnar Groot Koerkamp,
- André Kahles,
- and Gunnar Rätsch
Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
...of finding accurate alignments. Methods that use de Bruijn graphs (DBGs) as a graph model (Bowe et al. 2012) or use an auxiliary index (Sirén 2017) are restricted to finding seeds of minimum length k. To find seeds when the query has a high edit distance relative to the reference sequences, sequence-to-graph...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...High resolution s of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis Yuan Lu1,9, Edward Rice2,9, Kang Du1, Susanne Kneitz3, Magali Naville4, Corentin Dechaud4, Jean-Nicolas Volff4, Mikki Boswell1, William Boswell1, LaDeana Hillier5, Chad...
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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
...Interactive visualization and interpretation of pan graphs by linear reference–based coordinate projection and annotation integration Zepu Miao and Jia-Xing Yue State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong...
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RECOMB 2022 Special/Methods: Assembler artifacts include misassembly because of unsafe unitigs and underassembly because of bidirected graphs
- Amatur Rahman and
- Paul Medvedev
Genome Res. September 2022 32: 1746-1753; Published in Advance July 27, 2022, doi:10.1101/gr.276601.122
...graph are different from those of a doubled de Bruijn graph and, contrary to our expectations, result in underassembly. Using experimental simulations, we then confirm that these two artifacts exist not only in theory but also in the output of widely used assemblers. In particular, when coverage is low...

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