Pangenome graphs improve the analysis of structural variants in rare genetic diseases
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DOI: 10.1038/s41467-024-44980-2
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- Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
- Ryan L. Collins & Harrison Brand & Konrad J. Karczewski & Xuefang Zhao & Jessica Alföldi & Laurent C. Francioli & Amit V. Khera & Chelsea Lowther & Laura D. Gauthier & Harold Wang & Nicholas A. Watts , 2020. "A structural variation reference for medical and population genetics," Nature, Nature, vol. 581(7809), pages 444-451, May.
- Mitchell R. Vollger & Philip C. Dishuck & William T. Harvey & William S. DeWitt & Xavi Guitart & Michael E. Goldberg & Allison N. Rozanski & Julian Lucas & Mobin Asri & Katherine M. Munson & Alexandra, 2023. "Increased mutation and gene conversion within human segmental duplications," Nature, Nature, vol. 617(7960), pages 325-334, May.
- Wen-Wei Liao & Mobin Asri & Jana Ebler & Daniel Doerr & Marina Haukness & Glenn Hickey & Shuangjia Lu & Julian K. Lucas & Jean Monlong & Haley J. Abel & Silvia Buonaiuto & Xian H. Chang & Haoyu Cheng , 2023. "A draft human pangenome reference," Nature, Nature, vol. 617(7960), pages 312-324, May.
- Andrea Guarracino & Silvia Buonaiuto & Leonardo Gomes Lima & Tamara Potapova & Arang Rhie & Sergey Koren & Boris Rubinstein & Christian Fischer & Jennifer L. Gerton & Adam M. Phillippy & Vincenza Colo, 2023. "Recombination between heterologous human acrocentric chromosomes," Nature, Nature, vol. 617(7960), pages 335-343, May.
- Joel Armstrong & Glenn Hickey & Mark Diekhans & Ian T. Fiddes & Adam M. Novak & Alden Deran & Qi Fang & Duo Xie & Shaohong Feng & Josefin Stiller & Diane Genereux & Jeremy Johnson & Voichita Dana Mari, 2020. "Progressive Cactus is a multiple-genome aligner for the thousand-genome era," Nature, Nature, vol. 587(7833), pages 246-251, November.
- Alex Diaz-Papkovich & Luke Anderson-Trocmé & Chief Ben-Eghan & Simon Gravel, 2019. "UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts," PLOS Genetics, Public Library of Science, vol. 15(11), pages 1-24, November.
- Hannes P. Eggertsson & Snaedis Kristmundsdottir & Doruk Beyter & Hakon Jonsson & Astros Skuladottir & Marteinn T. Hardarson & Daniel F. Gudbjartsson & Kari Stefansson & Bjarni V. Halldorsson & Pall Me, 2019. "GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
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- Cristian Groza & Xun Chen & Travis J. Wheeler & Guillaume Bourque & Clément Goubert, 2024. "A unified framework to analyze transposable element insertion polymorphisms using graph genomes," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
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