Searching journal content for articles similar to Ovchinnikov et al. 11 (12): 2050.

Displaying results 1-10 of 155

For checked items

view abstracts
download to citation manager

Select this article
Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...(Fig. 4B). Again, processed and unprocessed pseudogenes show different patterns, reporting the highest overlap with LINEs and SINEs, respectively. Because pseudogenes originate from a non-random subset of protein-coding genes, we next asked whether enrichment of TEs in pseudogene promoters could...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...lost by random mutations (McLaughlin et al. 2014). This hypothetical model was also proposed in the viral restriction factors derived from ERVs (Johnson 2019). Nonetheless, a recent reporter-based assay showed that the human L1TD1 protein is not capable of suppressing human L1 activity (Jin et al. 2024...
Select this article
Research: Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control
- Miguel L. Soares,
- Carol A. Edwards,
- Frances L. Dearden,
- Sacri R. Ferrón,
- Scott Curran,
- Jennifer A. Corish,
- Rebecca C. Rancourt,
- Sarah E. Allen,
- Marika Charalambous,
- Malcolm A. Ferguson-Smith,
- Willem Rens,
- David J. Adams,
- and Anne C. Ferguson-Smith
Genome Res. March 2018 28: 345-356; Published in Advance January 24, 2018, doi:10.1101/gr.221366.117
...genes (seven and eight regions, respectively; P < 0.01 when compared with 500 randomly generated genomic regions by binomial test). High LINE repeat content has previously been shown to be associated with random monoallelic genes such as the olfactory and vomeronasal receptors (Allen et al. 2003...
OPEN ACCESS ARTICLE
Select this article
Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...shown as a number on the right of the bar. The black transparent bars represent the expected number of peaks following a random distribution. The FDR of the enrichment is shown with stars (FDR > 0.0001 = ****, >0.001 = ***, >0.01 = **, >0.05 = *, ≥0.05 = n.s.). Rows are ordered by FDR. The number next...
OPEN ACCESS ARTICLE
Select this article
Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...observed fractions (left bars) and fractions based on random shuffling of TE insertion identities across the , keeping locations fixed (right bars, color desaturated). P-values calculated using binomial tests. (E) Median, per family, distance of insertions from nearest genes. Top halves indicate distance...
OPEN ACCESS ARTICLE
Select this article
Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
- Adam D. Ewing and
- Haig H. Kazazian, Jr.
Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
...Fig. S3). Based on this random distribution, we might expect to see atmost two insertions specific to any possible grouping of three populations from this data set. Taken together, these results suggest a significant level of retrotransposition-induced interpopulation variation, although the majority...
Select this article
Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Keyi Geng,
- Lara G. Merino,
- Linda Wedemann,
- Aniek Martens,
- Małgorzata Sobota,
- Yerma P. Sanchez,
- Jonas Nørskov Søndergaard,
- Robert J. White,
- and Claudia Kutter
Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
...and then configured in a random order (Stephens et al. 2011; Ly et al. 2017), matching the molecular signatures of clustered interchromosomal rearrangements found in the HepG2 Δt8 deletion clone.In the deletion clone HepG2 Δi50, we postulate that the detected large genomic deletion resided on one allele whereas...
Select this article
Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
...of the nascent transcriptome using allele-specific Precision nuclear Run-On sequencing (PRO-seq). We have developed a Random Forest machine-learning model that can predict the measured silencing dynamics based on a large set of epigenetic and genomic features and tested its predictive power experimentally...
OPEN ACCESS ARTICLE
Select this article
Method: Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
- David J. Witherspoon,
- Yuhua Zhang,
- Jinchuan Xing,
- W. Scott Watkins,
- Hongseok Ha,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2013 23: 1170-1181; Published in Advance April 18, 2013, doi:10.1101/gr.148973.112
...trios) (Table S2 of Stewart et al. 2011). The long sequencing reads were particularly useful due to the difficulty of identifying repetitive insertions using random short reads. Naturally, high-coverage whole- sequencing yields more total information than a targeted approach. The two main limitations...
Select this article
Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...the publishedmethods to the identification of insertions polymorphic among taxa could be both more and less difficult. Obviously, there are likely to be multiple polymorphisms when comparing two species that diverged multiple millions of years ago. Thus, finding random differential insertions could be a trivial task...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ovchinnikov et al. 11 (12): 2050.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: