Searching journal content for articles similar to Kaplanis et al. 29 (7): 1047.

Displaying results 1-10 of 5624

For checked items

view abstracts
download to citation manager

Select this article
Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...regulation. (B) SynMall provides splice prediction scores for COL4A3 c.765G > A: (1) SpliceAI predicts the gain or loss of donor/acceptor sites caused by the mutation; (2) MMSplice evaluates the likelihood of the site being a functional donor or acceptor; (3) CADD-Splice assesses the pathogenicity...
Select this article
Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...integration, as the major mutation in HBV-related HCC tissues, occurs in the early stages of the disease. Once integrated into the human , HBV sequences may connect with other HBV sequences, leading to the expansion of dominant clones through positive selection during tumor development...
Select this article
Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...stem cell–derived SOD1E100G MNs and shows that dysregulation of VGF, INA, and PENK is a strong disease predictor across species and SOD1 mutations. Our study reveals MN population-specific gene expression and temporal disease-induced regulation that together provide a basis to explain ALS selective...
OPEN ACCESS ARTICLE
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
...this study, we aimed to deploy a well-established chimeric RNA prediction algorithm on publicly available and made-for-purpose RNA-seq data sets representing a range of conditions in which mtDNA deletion mutations are pathogenic. We further aimed to relate the chimeric mtRNAs to age, disease state, gene...
Select this article
Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...will be required to accurately assess the incremental diagnostic yield of long-read sequencing per genetic variant class, with a subset of the mutations detected by Steyaert et al. comprising single-nucleotide variants (SNVs) which could potentially be detected using short-read platforms in combination...
Select this article
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
..., and the mutation frequency varies among the subs. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale...
Select this article
Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...accumulate in the Huntington, Elongation Factor 3, PR65/A, TOR (HEAT) domain at its C terminus (Supplemental Fig. S1). The HEAT domain consists of 20 nonidentical HEAT repeats that form the RNA-binding interface (Cretu et al. 2016). These mutations are predicted to impact the N-terminal domain involved...
OPEN ACCESS ARTICLE
Select this article
Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...deaminate and are associated with elevated UV mutation ratesBecause previous biochemical studies have indicated that flanking DNA bases can significantly impact the rate of cytosine deamination in CPD lesions (Tu et al. 1998; Cannistraro and Taylor 2009), we used our dCPD-seq data to characterize the impact...
OPEN ACCESS ARTICLE
Select this article
Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...-read single-cell RNA sequencing (scRNA-seq) data reveals significant gene expression differences in SF3B1-mutated CLL cells, although it does not impact the sensitivity of the anticancer drug venetoclax. scRaCH-seq's capability to study long-read transcripts of multiple genes makes it a powerful tool...
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
.... However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kaplanis et al. 29 (7): 1047.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: