Searching journal content for articles similar to Murillo et al..

Displaying results 1-10 of 6186

For checked items

view abstracts
download to citation manager

Select this article
Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...-mRNA processing, or impair mt-mRNA degradation/turnover pathways. Effects of chimeric mtRNAs on protein translation could include the sequestration of ribosomes and tRNAs on these aberrant transcripts. Chimeric mtRNAs could also bind other mtRNA transcripts or even leak into the cytoplasm (Kim et al. 2017...
Select this article
Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...-mer in the Hamming ball and a k-mer in the outer orbits. Hence, we choose as the rough boundary.These transformations try to mitigate the intrinsic conflicts between Hamming distance and Euclidean distance. As shown in Figure 2A, all six k-mers have exactly one mutation from the consensus sequence, so we arrange...
OPEN ACCESS ARTICLE
Select this article
Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
.... Experimental overview of the CRX deep mutational scan. (A) Known CRX domains, sequence conservation, predicted disorder, and reported ClinVar missense variants. Per-residue conservation was computed using sequences from the UniProt UniRef50 cluster derived from human CRX. Disorder predicted with Metapredict...
OPEN ACCESS ARTICLE
Select this article
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
...genomics and phylogeny analyses identified regions of organismal s that show patterns of accelerated evolution (Ferris et al. 2018; Foley et al. 2023). The usage of mutation rate patterns, species sequence alignments, and the identification of highly conserved regions can provide insights into phenotypic...
OPEN ACCESS ARTICLE
Select this article
Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...is composed of GLC7, YER134C, GDI1, YER137C, and the transposon genes YER137C-A and YER138C. These genes are not significantly enriched in any functions. Unlike GAP1 CNVs, the GLC7-YER137C CNV is significantly enriched in tRNAs as it contains extra copies of tRNA-His, tRNA-Ile, tRNA-Lys, and tRNA...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...identifying a single consensus sequence might be more meaningful, EquiRep may have limited utility. For moderately long repeats (10–200 bp) found in telomeric or centromeric regions, as well as coding repeats like those in CEL or MUC1, a more defined repeat structure exists, and mutations within the repeat...
OPEN ACCESS ARTICLE
Select this article
Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets...
OPEN ACCESS ARTICLE
Select this article
Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...-induced misincorporation tRNA sequencing), an RNA-seq pipeline designed for tRNA analysis (Behrens et al. 2021), in our study of tsRNAs in Drosophila melanogaster. The library construction step of this pipeline includes necessary measures to minimize tRNA modifications that can hinder effective detection and quantitation...
Select this article
Research: Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription
- Mukund Patel,
- Jeremy M. Simon,
- Michael D. Iglesia,
- Sam B. Wu,
- Andrew W. McFadden,
- Jason D. Lieb,
- and Ian J. Davis
Genome Res. February 2012 22: 259-270; Published in Advance November 15, 2011, doi:10.1101/gr.125666.111
...the impact of chimerism on transcriptional output.Differentially targeted regions are marked by DNA sequence and regulatory variationSince EWS–FLI and FLI1 binding sites were mostly distinct, we hypothesized that additional factors might specify EWS–FLI or FLI1 targeting in a transcription factor– or cell...
Select this article
Method: Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
- Dalibor Miklík,
- Jiří Grim,
- Daniel Elleder,
- and Jiří Hejnar
Genome Res. August 2023 33: 1395-1408; Published in Advance July 18, 2023, doi:10.1101/gr.277694.123
...motif, which is preferentially located near the 3′ end of Alu repeats. The sequence hotspot is observed irrespective of the tethering of the HIV preintegration complex to chromatin and is an intrinsic feature of HIV IN. Under conditions not disrupting integration preference, about one in 175 HIV ISs...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Murillo et al..

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: