Searching journal content for articles similar to Smith et al. 19 (10): 1836.

Displaying results 1-10 of 103

For checked items

view abstracts
download to citation manager

Select this article
Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...-read sequencing technologies are enabling even larger population studies, enhancing our ability to associate genetic variations—particularly those previously undetectable—with human diversity, disease, and other phenotypes. For example, in 2021, the deCODE genetics initiative generated a major large-scale long...
OPEN ACCESS ARTICLE
Select this article
Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
..., Canada; 3Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA Corresponding authors: karine.choquet@usherbrooke.ca, churchman@genetics.med.harvard.eduAbstractQuantitative trait loci analyses have revealed an important role for genetic variants in regulating alternative...
Select this article
Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.In eukaryotes, gene transcription by RNA polymerase (Pol...
OPEN ACCESS ARTICLE
Select this article
Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...RNA.Such variations in the sequence present in mature RNA molecules—which we term “RNA variables” (Foord et al. 2023)—contribute to the complexity of isoform expression, which can broaden the diversity of phenotype across cells, cell types, tissues, organs, and individuals. For instance, a shift toward the more...
OPEN ACCESS ARTICLE
Select this article
Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...be explained by an allelic skew in X-Chromosome inactivation. Accurate measurement of X inactivation skew is crucial to understand and predict disease phenotype in carrier females, with prediction especially relevant for degenerative conditions. We propose a novel approach using nanopore sequencing to quantify...
Select this article
Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
- Jesper Eisfeldt,
- Adam Ameur,
- Felix Lenner,
- Esmee Ten Berk de Boer,
- Marlene Ek,
- Josephine Wincent,
- Raquel Vaz,
- Jesper Ottosson,
- Tord Jonson,
- Sofie Ivarsson,
- Sofia Thunström,
- Alexandra Topa,
- Simon Stenberg,
- Anna Rohlin,
- Anna Sandestig,
- Margareta Nordling,
- Pia Palmebäck,
- Magnus Burstedt,
- Frida Nordin,
- Eva-Lena Stattin,
- Maria Sobol,
- Panagiotis Baliakas,
- Marie-Louise Bondeson,
- Ida Höijer,
- Kristine Bilgrav Saether,
- Lovisa Lovmar,
- Hans Ehrencrona,
- Malin Melin,
- Lars Feuk,
- and Anna Lindstrand
Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
...in human blood using targeted amplification-free long-read sequencing. Hum Mutat 39: 1262–1272. doi:10.1002/humu.23580 ↵Johansson J, Lidéus S, Höijer I, Ameur A, Gudmundsson S, Annerén G, Bondeson ML, Wilbe M. 2023. A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore...
OPEN ACCESS ARTICLE
Select this article
Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...Ezequiel Calvo-Roitberg, Rachel F. Daniels and Athma A. Pai RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA Corresponding author: athma.pai@umassmed.eduAbstractLong-read sequencing (LRS) technologies have the potential...
OPEN ACCESS ARTICLE
Select this article
Method: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
- Yi Qiao,
- Xiaomeng Huang,
- Philip J. Moos,
- Jonathan M. Ahmann,
- Anthony D. Pomicter,
- Michael W. Deininger,
- John C. Byrd,
- Jennifer A. Woyach,
- Deborah M. Stephens,
- and Gabor T. Marth
Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
...to the problem this manuscript attempts to tackle, an alternative avenue exists to relate cellular genotype and phenotype via separately sequencing single-cell DNA and RNA followed by data integration (clonealign) (Campbell et al. 2019). Finally, a method (PhyloIEx [Jun et al. 2023]) has been developed very...
OPEN ACCESS ARTICLE
Select this article
Method: Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning
- Tian Tian,
- Cheng Zhong,
- Xiang Lin,
- Zhi Wei,
- and Hakon Hakonarson
Genome Res. February 2023 33: 232-246; Published in Advance February 27, 2023, doi:10.1101/gr.277068.122
...-cell sequencing techniques, numerous analytical methods have been developed for delineating cell development. However, most are based on Euclidean space, which would distort the complex hierarchical structure of cell differentiation. Recently, methods acting on hyperbolic space have been proposed to visualize...
Select this article
Method: A model-based constrained deep learning clustering approach for spatially resolved single-cell data
- Xiang Lin,
- Le Gao,
- Nathan Whitener,
- Ashley Ahmed,
- and Zhi Wei
Genome Res. October 2022 32: 1906-1917; Published in Advance October 5, 2022, doi:10.1101/gr.276477.121
...of application as it is primarily designed for decomposing the data with low resolution from sequencing-based technologies, such as 10x Visium. Some other methods, such as SpaGCN (Hu et al. 2021) and stLearn (Pham et al. 2020), use deep neural networks, such as CNN and GCN, to analyze the sp-scRNA-seq data...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Smith et al. 19 (10): 1836.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: