Searching journal content for articles similar to Band et al. 10 (9): 1359.

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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...Taurine pan uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle Sotiria Milia1,4, Alexander S. Leonard1,4, Xena Marie Mapel1, Sandra Milena Bernal Ulloa2, Cord Drögemüller3 and Hubert Pausch1 1Animal Genomics, ETH Zurich, Zurich 8092, Switzerland...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...SNVs in specific genomic contexts, suggesting that the observed rate increase in ART-derived mice is a general -wide phenomenon. Together, our findings show that ART is moderately mutagenic in house mice and motivate future work to define the procedure(s) associated with this increased mutational vulnerability...
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Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
- Xiran Liu,
- Lorin Crawford,
- and Sohini Ramachandran
Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
...using neural networks. We then cluster variant associations among multiple traits via variational inference. We compare the performance of shrinkage via neural networks to regularized regression and fine-mapping, two approaches used for addressing inflated effects but dealing with variants in focal...
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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
...and accessibility of assemblies for global cattle breeds and other bovine species. Genome Biol 24: 139. doi:10.1186/s13059-023-02975-0 ↵Tavakoli N, Gibney D, Aluru S. 2022. Haplotype-aware variant selection for graphs. In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...phases into biological questions to provide insight into DV's behavior. For example, as with prior nonmammalian approaches, our training strategy during the first two phases focuses on creating a “cattle-specific” model, using data typical for domesticated animal genomics. Training begins with six cattle...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
...Pan-genotyped structural variation improves molecular phenotype mapping in cattle Alexander S. Leonard, Xena M. Mapel and Hubert Pausch Animal Genomics, ETH Zurich, 8092 Zurich, Switzerland Corresponding authors: alleonard@ethz.ch, hubert.pausch@usys.ethz.chAbstractExpression and splicing...
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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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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
..., the heart and lung were considered as one class and the lymph node, thymus, and spleen as another class, and each of the other tissues was treated as a separate class. MAP calculates for each gene the average precision within its K ordered nearest neighbors (Supplemental Note 4). We obtained a tissue...
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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...) optimize nanopore adaptive sampling with the GNASTy algorithm to improve pneumococcal serotype surveillance for epidemiological studies. Milia et al. (2025) present a pan-wide association mapping approach to link SVs to cattle breed traits. Paniagua et al. (2025) evaluate long-read RNA-seq strategies...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...seven species, the total size of which is 33.1% longer than that of a single cichlid . Approximately 4.73% to 9.86% of the assembly lengths are estimated as interspecies structural variation between cichlids, suggesting substantial genomic diversity underappreciated in SNP studies. Although coding...
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