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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...) to identify putative CREs that have evolved from TE-derived sequences. We then combine these TE-CRE annotations with analyses of the temporal dynamics of TE activity, analyses of gene coexpression, and massive parallel reporter assays. Our results support a link between WGD and TE-CRE evolution and support...
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Commentary: The Atacama skeleton
- Garry Nolan and
- Atul Butte
Genome Res. May 2018 28: 607-608; Published in Advance March 30, 2018, doi:10.1101/gr.237834.118
...E , Asadi NB , et al. 2018 . Whole- sequencing of Atacama skeleton shows novel mutations linked with dysplasia . Genome Res 28 : 423 – 431 . ↵ Callaway E . 2018 . Divided by DNA: the uneasy relationship between archaeology and ancient genomics . Nature 555 : 573 – 576 . ↵ Greer S , Virk R...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...Whole- long-read sequencing downsampling and its effect on variant-calling precision and recall William T. Harvey1, Peter Ebert2,3,4, Jana Ebler2,4, Peter A. Audano5, Katherine M. Munson1, Kendra Hoekzema1, David Porubsky1, Christine R. Beck5,6, Tobias Marschall2,4, Kiran Garimella7 and Evan E...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...was produced from a variety of sequencing techniques including short-read, linked-read, and long-read sequencing, as well as optical mapping (Zook et al. 2020), making it more suited to measuring recall.Data accessAll crossovers detected in the SSC data set are available as Supplemental Data S1. The 1-Mbp...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...Evidence for selfing in a vertebrate from whole- sequencing Astrid Böhne1, Zeynep Oğuzhan1, Ioannis Chrysostomakis1, Simon Vitt2, Denis Meuthen2,3, Sebastian Martin1, Sandra Kukowka1 and Timo Thünken2 1Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
..., the clearest one against GA-rich repeats in the human . However, our study reveals a systematic failure of both technologies to sequence and assemble specific exons of Drosophila melanogaster genes, indicating an overlooked limitation. Namely, multiple Y-linked exons are nearly or completely absent from raw...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...-Cancer Analysis of Whole Genomes Consortium 2020), across approximately 2700 tumor samples.One major limitation of MuSE 1, like many other mutation callers (Koboldt et al. 2012; Larson et al. 2012; Cibulskis et al. 2013), is the computational speed. It takes 2–3 d to finish running the WGS data of a tumor...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
.... A uniform recombination rate of 1.0 × 10−8 has been assumed in all simulations as well as a mutation rate of 2.36 × 10−8 (Tennessen et al. 2012) for a sequence of 1.0 × 109 bases.Simulation 1 has the following population split times: t1 = 100, t2 = 60, t3 = 40, and t4 = 20 with an assumed constant...
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Editorial: A statement about the publication describing genome sequencing of the Atacama skeleton Genome Res. May 2018 28: xiv; Published in Advance March 30, 2018, doi:10.1101/gr.237842.118

...-Arcos MC, Ji X, Smith E, Asadi NB, et al. 2018. Whole- sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Res 28: 423–431. ↵Nolan G, Butte A. 2018. The Atacama skeleton. Genome Res (this issue) 28: 607–608. A statement about the publication describing sequencing...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...are typically subclonal and have been linked to disease progression and shorter survival (Wan and Wu 2013; Landau et al. 2015). On the other hand, SF3B1 mutations in MDS patients have been associated with specific disease phenotypes that show erythroid dysplasia with ring sideroblasts and ineffective...
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