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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
...Fig. S25). We show this as an example for MAP3K7, a frequently described gene with an ASE in SF3B1mut/wt (DeBoever et al. 2015; Wang et al. 2016; Shiozawa et al. 2018).The effect of SF3B1 mutations depends on the distance and sequence context of 3′ASsWhen we plotted the fraction of differential 3′AS...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...-mers and their potential influence on sequencing efficacy. A key advantage of the VAE (Doersch 2016) model lies in its ability to capture and represent subtle structural nuances of k-mers through its latent dimensions. This capability is anticipated to surpass that of traditional methods, potentially enabling a more...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...of our findings, we analyzed an existing AlkAniline-Seq data set (Schöller et al. 2021), which selectively sequences m3C-modified RNAs as well as RNAs modified with m7G and dihydrouridine. Among 4566 candidate cleavage sites with sufficient coverage, 790 C-base sites were identified as potential m3C...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS data sets grow allowing for better variant-frequency annotation, the additional lrGS-only rare disease yield will grow over time.Although and exome sequencing (GS/ES) are increasingly used to identify molecular...
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Research: A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations
- Adam Yongxin Ye,
- Yanmei Dou,
- Xiaoxu Yang,
- Sheng Wang,
- August Yue Huang,
- and Liping Wei
Genome Res. July 2018 28: 943-951; Published in Advance June 6, 2018, doi:10.1101/gr.230003.117
...cleavage steps.We then estimated the average mutation rate per cell division from de novo heterozygous mutations and compared it with the mutation rate we estimated from pSNMs. Based on the trio sequencing data from the WES data set of 1301 children, a list of 1571 single-nucleotide de novo mutations...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
..., and genetic disease, including cancers. Sequencing of mutation accumulation (MA) lines has provided estimates of rates and spectra of single-nucleotide and indel mutations in many species, yet the rate of new SMs is largely unknown. Here, we use long-read sequencing to determine the full mutation spectrum...
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Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...regions and set a cut-off value to 0.25, in which 20% of the insertion ratio of coding regions fell below the intergenic distribution, which was similar to the kernel density estimates of known S. cerevisiae essential genes. The kernel density estimates were computed in R and visualized using ggplot2...
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Method: Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
- Yi-Fei Huang and
- Adam Siepel
Genome Res. August 2019 29: 1310-1321; Published in Advance June 27, 2019, doi:10.1101/gr.245522.118
...protein-coding sequences in the human . This map is generally consistent with previous inferences of the bulk distribution of fitness effects but reveals pervasive weak negative selection against synonymous mutations. In addition, the estimated selection coefficients are highly predictive of inherited...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
...-of-the-art methods. Of the 98 events predicted from the data set simulating fusions at fivefold expression, only 10 were false positives, which is the smallest fraction of incorrect predictions among all tested methods. At higher simulated expression levels, Arriba achieves average specificity. The number of false...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...-graph structure to present a more accurate representation of the mutated cancer s. We find hundreds of variants within known cancer-related genes detectable only through long-read sequencing. These findings highlight the need for long-read sequencing of cancer s for the precise analysis of their genetic...

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