Searching journal content for articles similar to McCaffrey et al. 27 (11): 1904.

Displaying results 1-10 of 67

For checked items

view abstracts
download to citation manager

Select this article
Method: Long-read single-molecule maps of the functional methylome
- Hila Sharim,
- Assaf Grunwald,
- Tslil Gabrieli,
- Yael Michaeli,
- Sapir Margalit,
- Dmitry Torchinsky,
- Rani Arielly,
- Gil Nifker,
- Matyas Juhasz,
- Felix Gularek,
- Miguel Almalvez,
- Brandon Dufault,
- Sreetama Sen Chandra,
- Alexander Liu,
- Surajit Bhattacharya,
- Yi-Wen Chen,
- Eric Vilain,
- Kathryn R. Wagner,
- Jonathan Pevsner,
- Jeff Reifenberger,
- Ernest T. Lam,
- Alex R. Hastie,
- Han Cao,
- Hayk Barseghyan,
- Elmar Weinhold,
- and Yuval Ebenstein
Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
...the at regions dense in CCGG sites. RRBS captures ∼60% of gene promoters, thus producing crucial regulatory information while requiring very little input sample (Gu et al. 2011). The low input implies that fewer reads are necessary for accurate sequencing, allowing for high-throughput, low-cost methylation...
OPEN ACCESS ARTICLE
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
...for rooting for 3 months and finally planted in soil for characterization.DNA extraction and high-throughput sequencingA total of 3 original plants (CK), 27 regenerated plants under different conditions (LS, LL, HS, HL, CA), and 12 “Beni hoppe” plants were used. For each sample, the young leaves were...
Select this article
Research: High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
- Houssam Hajjoul,
- Julien Mathon,
- Hubert Ranchon,
- Isabelle Goiffon,
- Julien Mozziconacci,
- Benjamin Albert,
- Pascal Carrivain,
- Jean-Marc Victor,
- Olivier Gadal,
- Kerstin Bystricky,
- and Aurélien Bancaud
Genome Res. November 2013 23: 1829-1838; Published in Advance September 27, 2013, doi:10.1101/gr.157008.113
...Research High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the Houssam Hajjoul,1,2,6 Julien Mathon,1,2,6 Hubert Ranchon,1,2 Isabelle Goiffon,2,3 Julien Mozziconacci,4,5 Benjamin Albert,2,3 Pascal Carrivain,4,5 Jean-Marc Victor,4,5 Olivier...
Select this article
Research: Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin
- Kez Cleal,
- Rhiannon E. Jones,
- Julia W. Grimstead,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2019 29: 737-749; Published in Advance March 14, 2019, doi:10.1101/gr.240705.118
...the accuracy of calling and assembly (Supplemental Figs. S20–S23). Additionally, we examined whether contig sequences were present within cell populations before transfection with DN-TERT and telomere crisis. Using a single-molecule assay to detect a contig present in LIG3−/−:NC3: sample 53 (DB53_1501), we...
OPEN ACCESS ARTICLE
Select this article
Research: Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4
- Kate Liddiard,
- Brian Ruis,
- Taylor Takasugi,
- Adam Harvey,
- Kevin E. Ashelford,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
...rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combination of high-throughput sequence analysis together with experimentally induced telomeric double-stranded DNA breaks. We show that a single...
OPEN ACCESS ARTICLE
Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., and the released DNA can be sequenced to identify all DNA sequences bound to the protein of interest using high-throughput platforms (Park 2009). Standard controls include comparing this immunoprecipitation to DNA binding by nonimmunized IgG raised in the same species as the protein targeting antibody, using q...
OPEN ACCESS ARTICLE
Select this article
Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...-read sequencing allows for high-throughput characterization of the locus, and efforts are underway to gather germline diversity across human populations (Rodriguez et al. 2020). However, although this strategy yields highly accurate reads, it does not contiguously resolve the entirety of the locus and may miss...
Select this article
Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. April 2026 36: 827-848; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...for FSHD1 fibroblasts from Cas9-targeted sequencing. Single-molecule and smoothed methylation plots for 4q and 10q D4Z4 alleles from the FSHD1 samples (A) 19,187, (B) 17,706, and (C) 12,566, generated using NanoMethViz (Su et al. 2021, 2025). The locations of DUX4 exons are shaded in gray on the smoothed...
OPEN ACCESS ARTICLE
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
...and disease diagnostics. DNA methylation signals directly obtained from long reads enhance the utility of single-molecule long-read sequencing technologies by enabling molecular phenotypes to be interpreted, and by allowing the identification of the parent of origin of de novo mutations. Despite this recent...
Select this article
Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
..., Spain; 10Gene Expression and mRNA Metabolism Laboratory, CIPF, 46012 Valencia, Spain ↵11 Joint first authorship. Corresponding author: aconesa@ufl.edu, aconesa@cipf.esAbstractHigh-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to McCaffrey et al. 27 (11): 1904.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: