Searching journal content for articles similar to Kunyavskaya et al. 32 (6): 1137.

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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...Open Res 7: 297. doi:10.12688/wellcomeopenres.18646.1 ↵Kunyavskaya O, Dvorkina T, Bzikadze AV, Alexandrov IA, Pevzner PA. 2022. Automated annotation of human centromeres with HORmon. Genome Res 32: 1137–1151. doi:10.1101/gr.276362.121 Lawniczak MK, Darwin Tree of Life Barcoding collective, Wellcome...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...cultivated strawberry individuals are analyzed by whole sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 × 10−8–3.0 × 10−6 mutations per site. CG methylation shows a stable reduction (0...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...the de novo putative enhancer interactions (Supplemental Fig. S48A). The MYC de novo contacts are proximal to the DNAJC9 locus on Chromosome 10 (Fig. 4D), at which three putative cis regulatory elements (REs) enriched in ENCODE H3K27ac and annotated CREs are found (RE1–3) (Supplemental Fig. S48B...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...annotation using a combination of EDTA and RepeatModeler2 to identify repeats that were then further classified using DeepTE (Ou et al. 2019; Flynn et al. 2020; Yan et al. 2020).To explore the TE silencing landscape during Spirodela asexual clonal reproduction, we used Arabidopsis as a comparative system...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...–2476. doi:10.1093/gbe/evx154 ↵Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9: R7. doi:10.1186/gb-2008-9-1-r7 ↵Hu Q-L, Ye Y...
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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
...estimate that can be used in downstream analyses. We evaluated the strain-specific imputation accuracy on a “held-out” test set that was not used in the imputation process. We deliver these data in a harmonized, scalable, and programmatically accessible annotated variant resource, GenomeMUSter, which...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...-depth WGS. Hi-C libraries from control (maternal) and treated (daughter) clones are sequenced to identify acquired and drug-induced rearrangements. (B) Annotation of fragment size and edge positions. The latter is annotated at peaks of ectopic contacts between two distal sites. Duplicated regions...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...currently available conifer assembliesGenome annotation using evidence from Iso-Seq full-length cDNAs resulted in the identification of 39,659 gene models supported by the alignment of unique primary transcripts (Supplemental Data Set S1), and an additional 26,150 alternative transcripts. A total of 25...
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Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
- Shaleen Shrestha,
- Jared Allan Sewell,
- Clarissa Stephanie Santoso,
- Elena Forchielli,
- Sebastian Carrasco Pro,
- Melissa Martinez,
- and Juan Ignacio Fuxman Bass
Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
...nuclear hormone receptors and ETS factors, to the highly repetitive Alu elements. Further, we identified cancer-associated changes in TF binding, including gain of interactions involving ETS TFs and loss of interactions involving KLF TFs to different mutations in the TERT promoter, and gain of a MYB...
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Research: Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
- Felix Bemm,
- Dirk Becker,
- Christina Larisch,
- Ines Kreuzer,
- Maria Escalante-Perez,
- Waltraud X. Schulze,
- Markus Ankenbrand,
- Anna-Lena Van de Weyer,
- Elzbieta Krol,
- Khaled A. Al-Rasheid,
- Axel Mithöfer,
- Andreas P. Weber,
- Jörg Schultz,
- and Rainer Hedrich
Genome Res. June 2016 26: 812-825; Published in Advance May 4, 2016, doi:10.1101/gr.202200.115
...of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death–related genes...
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