Searching journal content for articles similar to Yu et al. 12 (8): 1185.

Displaying results 1-10 of 46

For checked items

view abstracts
download to citation manager

Select this article
Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...artifacts of incomplete transcripts derived from intronic SINEs (Fig. 1E; Supplemental Fig. S2A; Sela et al. 2007; Elbarbary et al. 2016; Shao and Wang 2021; Gualandi et al. 2022). Across all three transcript tiers, we observed similar subfamily enrichment, particularly with LTRs like ERV1, suggesting...
OPEN ACCESS ARTICLE
Select this article
Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...was followed (e.g., DRB1, DRB3). The first two or three digits designate the lineage number, whereas the digits after the first colon label the allelic variation (e.g., DRB1*01:01). A third and a fourth set of digits assign synonymous and intronic variations, respectively. Additional suffixes may be used...
OPEN ACCESS ARTICLE
Select this article
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
...; Bradamante et al. 2023; Incarbone et al. 2023), and in monocots, AGO5 participates in anther development and TE silencing during male gametogenesis (Zhai et al. 2015; Fei et al. 2016; Lee et al. 2021).Regarding the RdDM pathway, Spirodela contains the minimal set of its components, either...
OPEN ACCESS ARTICLE
Select this article
Resource: Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
- Wankun Deng,
- Citu Citu,
- Andi Liu,
- and Zhongming Zhao
Genome Res. October 2024 34: 1687-1699; Published in Advance October 18, 2024, doi:10.1101/gr.279363.124
...unknown. This lack of knowledge is because of the low complexity of their sequences and abundance in the (Copley and Shorter 2023), making their precise mapping of short reads to the challenging (Zhao and Han 2009; Wells and Feschotte 2020). TEs have long been categorized as “junk” sequences in the (Orgel...
Select this article
Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
.... This was done to remove the effects of transcription delays due to gene length. We note that, for all other analyses, pre-mRNA expression was measured using the first 10 kb of intron sequence from the TSS, excluding any exon sequences. Model parameters were selected as those minimizing the difference between...
OPEN ACCESS ARTICLE
Select this article
ARTICLE: A region of mouse chromosome 16 is syntenic to the DiGeorge, velocardiofacial syndrome minimal critical region.
- N Galili,
- H S Baldwin,
- J Lund,
- R Reeves,
- W Gong,
- Z Wang,
- B A Roe,
- B S Emanuel,
- S Nayak,
- C Mickanin,
- M L Budarf,
- and C A Buck
Genome Res. January 1997 7: 17-26; doi:10.1101/gr.7.1.17
...A region of mouse chromosome 16 is syntenic to the DiGeorge, velocardiofacial syndrome minimal critical region. N Galili , H S Baldwin , J Lund , R Reeves , W Gong , Z Wang , B A Roe , B S Emanuel , S Nayak...
Select this article
Research: Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
- Marta Coronado-Zamora and
- Josefa González
Genome Res. September 2023 33: 1541-1553; Published in Advance October 4, 2023, doi:10.1101/gr.277565.122
...assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene–TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference s available. We found that ∼19% of body part...
Select this article
Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...(623 deletions), intronic sequence (4990), or flanking sequence (1585). The numbers of deletions of each category and ploidy were similar across all samples, with more homozygous deletions than heterozygous in each category. This is consistent with the high homogeneity of the sampled laboratory...
Select this article
Method: LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq
- Danny A. Bitton,
- Charalampos Rallis,
- Daniel C. Jeffares,
- Graeme C. Smith,
- Yuan Y.C. Chen,
- Sandra Codlin,
- Samuel Marguerat,
- and Jürg Bähler
Genome Res. July 2014 24: 1169-1179; Published in Advance April 7, 2014, doi:10.1101/gr.166819.113
...for organisms like human, which generally have much larger introns, although the shortest human introns may still be affected (‘‘minimal’’ introns) (Yu et al. 2002). Another issue was the aggregation of branch points next to the primary branch point that was most likely introduced by reverse...
OPEN ACCESS ARTICLE
Select this article
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
...evident functional effects. These include three of six intronic STR expansions we found to be associated with intron retention. Coding STRs were depleted of variation relative to noncoding STRs, and we detected a total of 56 coding STRs (11%) showing low variation consistent with the action of purifying...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Yu et al. 12 (8): 1185.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: