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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...contributed equally to this work. Corresponding authors: ipm5219@psu.edu, izg5139@psu.eduAbstractDespite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying...
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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...bulls by leveraging the routine genotyping of their offspring for genomic evaluation and exploiting the assumed absence of linkage disequilibrium (LD) between markers from different chromosomes. In addition, we perform cytogenetic validation, long-read sequencing, and a series of complementary analyses...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...al. 2018, 2019) was made with the help of TRhist (Doi et al. 2014), an algorithm specifically developed to detect and correctly annotate TR expansions. Their identification of expanded TTTCA repeats within long TTTTA repeats causing BAFME1 was also facilitated by long-read sequencing technologies...
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Research: The Enterprise, a massive transposon carrying Spok meiotic drive genes
- Aaron A. Vogan,
- S. Lorena Ament-Velásquez,
- Eric Bastiaans,
- Ola Wallerman,
- Sven J. Saupe,
- Alexander Suh,
- and Hanna Johannesson
Genome Res. May 2021 31: 789-798; Published in Advance April 19, 2021, doi:10.1101/gr.267609.120
...killing approaches 100% as Spoks are located closer to centromeres) (Vogan et al. 2019), a given Spok gene may be able to increase its transmission distortion by relocating with the help of Enterprise. We have no direct evidence that this occurs, but Spok2 has a relatively low killing percentage (40...
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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
...with individual-level phenotype data are included in such studies, additional loci contributing to more nuanced parts of a phenotype will be found.View larger version: In this window In a new window Figure 1. Genomic analyses help resolve the genetics of shared human–canine traits. (A) Approximately 50...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
...sequences from families. Thus, our algorithm for localizing sequences is an orthogonal approach to the T2T's assembly strategy and can help validate the T2T's work. We also use our results to understand genetic diversity in relation to the T2T-CHM13 reference , especially in regions that were previously...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...genes are colored orange (ShxA), red (ShxB), green (ShxC), and blue (ShxD) in this figure and throughout the paper. (B) Genomic location of Hox genes in A. gamma with corresponding exon structures and genomic distances annotated below. Silhouette images of B. terrestris, T. castaneum, and D...
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Method: Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2
- Daniel N. Baker and
- Ben Langmead
Genome Res. July 2023 33: 1218-1227; Published in Advance July 6, 2023, doi:10.1101/gr.277655.123
...of the input items into account, namely, when using a weighted Jaccard coefficient as input to the Mash distance equation. This shows that multiplicities are helpful not only for quantitative applications but also in typical “flat” sketching scenarios. This motivates future study of sketch data structures...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...growing needs to directly compare and benchmark the T2T CHM13 assembly and other human assemblies.To meet the need to visualize genomic sequences and features at different scales in the genomic era, scientists developed browser/viewers to help interpret s. The UCSC Genome Browser, equipped...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...Rivera, and members of the Queitsch laboratory for technical assistance and important conversations. We thank Evan Boyle, Choli Lee, Matthew Snyder, and Jay Shendure for assistance and advice concerning MIP design and use. We thank the Dunham laboratory and the Fields laboratory for access to and help...

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