Searching journal content for articles similar to Tapper et al. 11 (7): 1290.

Displaying results 1-10 of 585

For checked items

view abstracts
download to citation manager

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
...for parental DNA to determine the origin of the variant and direction of the skew, and additional genetic testing to ascertain the deleterious variant. A sequencing-based version of this test has recently been proposed (Johansson et al. 2023), directly reading the methylation of the AR and RP2 CpG islands...
Select this article
Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...the SVM motif mutation score for ATF3 motif mutation SNPs. (G) Enrichment of SVM (blue) and PWM motif mutations scores (orange) in the STARR-seq-validated set.To test whether sequence-based genomic features differentiated validated from unvalidated variants, we evaluated the following metrics or test...
Select this article
Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...of such an event. Ragout 2 resolves this issue by integrating physical mappings from Thybert et al. (2018). Importantly, Ragout 2 did not generate any large inter-chromosomal rearrangements that were not expected from physical mappings or references. We also detected 36 adjacencies that do not appear in any...
OPEN ACCESS ARTICLE
Select this article
Method: Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren,
- Marjo de Ruiter,
- Taco Jesse,
- Hein van der Poel,
- Jifeng Tang,
- Feyruz Yalcin,
- Antoine Janssen,
- Hanne Volpin,
- Keith E. Stormo,
- Robert Bogden,
- Michiel J.T. van Eijk,
- and Marcel Prins
Genome Res. April 2011 21: 618-625; Published in Advance February 1, 2011, doi:10.1101/gr.112094.110
...whole genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. WGP leverages short read sequences derived from restriction fragments...
Select this article
Method: Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
- Severin Berger,
- Mikhail Pachkov,
- Phil Arnold,
- Saeed Omidi,
- Nicholas Kelley,
- Silvia Salatino,
- and Erik van Nimwegen
Genome Res. July 2019 29: 1164-1177; Published in Advance May 28, 2019, doi:10.1101/gr.239319.118
...ultimately be determined by local constellations of DNA-binding sites, current analysis is typically limited to identifying enriched motifs in ChIP-seq peaks. Here we present Crunch, a completely automated computational method that performs all ChIP-seq analysis from quality control through read mapping...
OPEN ACCESS ARTICLE
Select this article
Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...and middle; also missing one to two copies of Chr 19) were detected in a cellular fragment (bottom) from the same embryo. (B) Additional examples of individual, multiple, and/or partial chromosomes in fragments of rhesus embryos. (C) Heat map of maternal versus paternal SNP genotyping ratios showing...
Select this article
Method: Direct chromosome-length haplotyping by single-cell sequencing
- David Porubský,
- Ashley D. Sanders,
- Niek van Wietmarschen,
- Ester Falconer,
- Mark Hills,
- Diana C.J. Spierings,
- Marianna R. Bevova,
- Victor Guryev,
- and Peter M. Lansdorp
Genome Res. November 2016 26: 1565-1574; Published in Advance September 19, 2016, doi:10.1101/gr.209841.116
...structure in single cells. By avoiding preamplification, Strand-seq offers unmatched accuracy over other sequencing-based phasing techniques. Moreover, Strand-seq phasing can be combined with mapping of SVs, such as deletions and inversions, which is of major interest for clinical research. As single...
Select this article
Research: Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
- Cai Li,
- Boris Lenhard,
- and Nicholas M. Luscombe
Genome Res. May 2018 28: 676-688; Published in Advance April 4, 2018, doi:10.1101/gr.231449.117
...are given in Supplemental Methods.To analyze the distributions of TSSs along repeat elements, we calculated the relative distances of TSSs to the 5′ end of the corresponding consensus repeat sequences based on alignments provided by RepeatMasker.Evolutionary rate analysisTo study evolutionary rates, we...
OPEN ACCESS ARTICLE
Select this article
Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
.... This study reveals the diversity of TL in S. cerevisiae and highlights key factors shaping TL distributions both -wide and at individual chromosome extremities.Telomeres are repeated sequences found at chromosome extremities, which are essential for integrity and control of cell proliferation (Jain...
Select this article
Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
...of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Tapper et al. 11 (7): 1290.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: