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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
..., this could lead to stable founder subpopulations potentially driving population divergence and diversification. In contrast to clonal reproduction, selfing allows recombination with the associated selective benefits, which may facilitate the establishment of stable populations. The before-mentioned P...
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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
...TE annotation from Lien et al. (2016). The total TE annotation covered 51.92% of the . Consistent with previous findings (Goodier and Davidson 1994; Lien et al. 2016), the dominating TE group was DNA transposons from the Tc1-Mariner superfamily with more than 655,000 copies, covering 327 million base...
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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
...the paternal copies, and red and pink represent the maternal copies.PhasingFamilies assumes that the input data are not phased. The input to our algorithm is a VCF file containing genetic data along with a PED file specifying familial relationships. We do not incorporate population allele frequency. We rely...
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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
...the sensitivity of structural variant (SV) discovery by ∼threefold by providing access to repetitive regions of s typically masked or excluded as part of short-read sequencing analyses (Chaisson et al. 2015, 2019; Audano et al. 2019) and by providing breakpoint resolution of variants previously inferred...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...CNAs occurred randomly in lymphocytesWe further analyzed CNA profile similarities between cells to try to capture clonal amplification signatures. Dimension-reduction analysis of single-cell copy number profiles produced a few clusters based on large-CNA patterns (Fig. 2A; Supplemental Fig. S5A...
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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
...in the haplotypes. We have also tested different window sizes (L = {512, 1024, 2048}) to evaluate their effect on the inference of global population structure. Lastly, we have also tested a simpler version of our model architecture in which we only use the categorical latent variable with a linear decoder...
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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
...in the human MHC. Int J Biochem Cell Biol 131: 105882. doi:10.1016/j.biocel.2020.105882 ↵Dilthey A, Cox C, Iqbal Z, Nelson MR, McVean G. 2015. Improved inference in the MHC using a population reference graph. Nat Genet 47: 682–688. doi:10.1038/ng.3257 ↵Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D...
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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
...as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project (Ellrott et al. 2018), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC-PCAWG) initiative (The ICGC/TCGA Pan...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...more general single-cell genotypes and mutation models remains a research question.Applying ScisTree2 in studies of cancer biology and stem cell biologyInference of the cell lineage tree is very relevant to single-cell cancer genomics. For example, finding clonal populations is a common problem...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...as the fraction of species that retained the genes in two copies after the duplication). Specifically, ProfileNJ rearranges subtrees below these poorly supported nodes to make them more parsimonious in terms of inferred duplications and losses. Finally, we ran SCORPiOs (version v1.1.0) to account for several...

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