Searching journal content for articles similar to Eberle et al. 27 (1): 157.

Displaying results 1-10 of 15

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
...with detecting alterations in tandem repeats (TRs), and more generally, with variations found within repetitive sequences (e.g., segmental duplications, satellite sequences, transposable elements), leaving a large fraction of the inaccessible. Short-reads also have limited power to phase variants within the same...
OPEN ACCESS ARTICLE
Select this article
Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...-derived whole- sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. We identified 26 de novo MEIs in 437 births. The retrotransposition rate estimates for Alu elements, one in 40 births, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude...
OPEN ACCESS ARTICLE
Select this article
Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...of LRS technologies is that these events can be detected directly from the sequence of the reads or the assembly themselves. We assessed each method's ability to recover large variants using the HGSVC validation set from HG00733, including 63 deletions and 40 insertions. For HiFi reads, two trends emerge...
OPEN ACCESS ARTICLE
Select this article
Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...in plain sight. Genome Biol 20: 97. doi:10.1186/s13059-019-1707-2 ↵Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL, et al. 2017. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing...
Select this article
Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
- Xian Fan,
- Mark Chaisson,
- Luay Nakhleh,
- and Ken Chen
Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
..., Halpern AL, et al. 2016. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res 27: 157–164. English AC, Salerno WJ, Reid JG. 2014. PBHoney: identifying genomic variants via long-read discordance...
Select this article
Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang H-Y, Humphray SJ, Halpern AL, et al. 2017. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res 27: 157–164. doi:10.1101/gr.210500.116 ↵Edge...
Select this article
Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...wild canids, most of which were wolves. The final data set represents the largest single public release of high-coverage canine WGS data to date, consisting of more than 48 million single-nucleotide, indel, and structural variants.Other large-scale canine sequencing efforts include the Darwin's Ark...
OPEN ACCESS ARTICLE
Select this article
Method: Predicting genotype-specific gene regulatory networks
- Deborah Weighill,
- Marouen Ben Guebila,
- Kimberly Glass,
- John Quackenbush,
- and John Platig
Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
...-specific GRNs: an initial estimate of the binding locations of TFs in the form of a reference motif prior (Mij), the beta values of eQTL associations between “eSNPs” and “eGenes” (β), the genetic variants (s) harbored by the individual in question, PPI data as an estimate of TF–TF cooperativity (P), and gene...
OPEN ACCESS ARTICLE
Select this article
Method: Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
.... A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res 27: 157–164. doi:10.1101/gr.210500.116 ↵Findley AS, Monziani A, Richards AL, Rhodes K, Ward MC, Kalita CA, Alazizi A, Pazokitoroudi A, Sankararaman S...
OPEN ACCESS ARTICLE
Select this article
Research: Thousands of human mutation clusters are explained by short-range template switching
- Ari Löytynoja
Genome Res. August 2022 32: 1437-1447; Published in Advance June 27, 2022, doi:10.1101/gr.276478.121
...template switch. J Mol Biol 356: 300–311. doi:10.1016/j.jmb.2005.11.071 ↵Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang H-Y, Humphray SJ, Halpern AL, et al. 2017. A reference data set of 5.4 million phased human variants validated by genetic inheritance from...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Eberle et al. 27 (1): 157.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: