Searching journal content for articles similar to Porubský et al. 26 (11): 1565.

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Method: Sequencing of isolated sperm cells for direct haplotyping of a human genome
- Ewen F. Kirkness,
- Rashel V. Grindberg,
- Joyclyn Yee-Greenbaum,
- Christian R. Marshall,
- Stephen W. Scherer,
- Roger S. Lasken,
- and J. Craig Venter
Genome Res. May 2013 23: 826-832; Published in Advance January 2, 2013, doi:10.1101/gr.144600.112
...heterozygous SNPs). The remaining 90% of heterozygous SNPs in the HuRef cannot be genotyped using commercial arrays, and incorporation of these variants into a comprehensive haplotype map requires direct sequencing of sperm DNA. Currently, sequencing of whole s from single cells can be challenging due...
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Method: Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
- Dongqing Shi,
- Jun Wu,
- Haibao Tang,
- Hao Yin,
- Hongtao Wang,
- Ran Wang,
- Runze Wang,
- Ming Qian,
- Juyou Wu,
- Kaijie Qi,
- Zhihua Xie,
- Zhiwen Wang,
- Xiang Zhao,
- and Shaoling Zhang
Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
...for linking s to life and the environment. Nucleic Acids Res 36: D480–D484. doi:10.1093/nar/gkm882 ↵Kirkness EF, Grindberg RV, Yee-Greenbaum J, Marshall CR, Scherer SW, Lasken RS, Venter JC. 2013. Sequencing of isolated sperm cells for direct haplotyping of a human . Genome Res 23: 826–832. doi:10.1101/gr...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...of CHROMOSOME_I and CHROMOSOME_III. For C. elegans to have a completely accurate reference , the N2 reference assembly needed to be replaced, but the VC2010 assembly could not fully replace it.View this table: In this window In a new window Table 1. Chromosome lengths and tandem repeat lengths of different C...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...al. 2023). However, for most domestic species, low-pass WGS (coverage < 5×) is the preferred strategy (Fig. 2B), as lower sequencing costs allow for additional resources to be directed toward bolstering sample sizes. This widely employed strategy is effective for population genetic analysis...
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Method: Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos
- Daniel Ariad,
- Svetlana Madjunkova,
- Mitko Madjunkov,
- Siwei Chen,
- Rina Abramov,
- Clifford Librach,
- and Rajiv C. McCoy
Genome Res. January 2024 34: 70-84; Published in Advance December 1, 2023, doi:10.1101/gr.278168.123
...). At such coverages, direct comparison of haplotypes is not possible, as a small minority of the is covered by any sequencing reads, and positions of aligned reads from samples under comparison rarely overlap. We circumvent this challenge based on patterns of LD, whereby observations of a set of alleles from one...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...studies as it reflects the direction of change in an evolutionary context. The takin and goat s were used as outgroups for whole- alignments. The ancestral state of each SV was determined by estimating the size of the region in outgroups that was homologous to the region that encompassed the ovine SV (Fig...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...(Bretani et al. 2020; Ebert et al. 2021). Inference and characterization of SVs representing a derived state in sheep The ancestral state of a variant is critical in population genetic studies as it reflects the direction of change in an evolutionary context. The takin and goat s were used as outgroups...
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Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
...was the number of TF combinatorial programs, which was consistent with number of TF modules in C and number of cell type/states for single-cell data. K could be determined in two ways. First, if we had prior knowledge about the number of TF modules or cell types, we could direct assign this number to K. Second...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...-renewing stem cell lineage (Varley et al. 2023), compared with the three self-renewing lineages found in Hydra (interstitial, endodermal, and ectodermal). There are also salient differences in their life cycles, with Hydractinia undergoing metamorphosis from the larval to adult form, whereas Hydra shows direct...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...haplotype 1 or 2 (blue, H1; yellow, H2) using single-nucleotide polymorphisms phased using trio information (1000 Genomes Project panel) with respect to the reference (GRCh38). (C) A barplot reporting the percentage of base pairs in an opposite (reverse) orientation in contrast to the expected (direct...
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