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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
.... The analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303. doi:10.1101/gr.107524.110 ↵Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, et al. 2013. Comparative analysis of tandem repeats from hundreds...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...ASM calls. Hence, we verified the genomic DNA sequences near the m6A modification sites using Sanger sequencing (Supplemental Table 5; Methods). In six selected ASM sites, we confirmed annotated SNPs (Nudt1, D site), and the absence of unannotated genetic variants. These results indicate...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...and reverse DUP of the adjacent sequences. (B) An example of HBV DNA integration resulting in a TRA (HCC13_T2). The Integrative Genomics Viewer (IGV; Robinson et al. 2011) plot below illustrates the alignment of long reads to Chr 22, HBV, and Chr 8. The plot above depicts the concordance of its breakpoint...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...these questions, we first analyzed two independent data sets comprising PCR-free whole- sequencing (WGS) and -wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using Hip...
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Research: Estimating genotype error rates from high-coverage next-generation sequence data
- Jeffrey D. Wall,
- Ling Fung Tang,
- Brandon Zerbe,
- Mark N. Kvale,
- Pui-Yan Kwok,
- Catherine Schaefer,
- and Neil Risch
Genome Res. November 2014 24: 1734-1739; Published in Advance October 10, 2014, doi:10.1101/gr.168393.113
...framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303. Meynert AM, Bicknell LS, Hurles ME, Jackson AP, Taylor MS. 2013. Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 14: 195. Nakamura K, Oshima T, Morimoto T, Ikeda S...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...sacrificed for this study. Total genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit and quantified on the Qubit DNA quantification system (Thermo Fisher Scientific) using Qubit broad range assay reagents, following the manufacturer's protocol. DNA concentration across all samples...
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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
.... The bin size is 100 kb. The color key indicates the number of mutations in each bin.Characterization of SNVs induced by tissue cultureSince SNV is the main type of DNA sequence variation, its characteristics were further analyzed. In general, C:G to T:A was the main type of transitions (Ts), and A:T to T...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...-019-0041-2 ↵McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303. doi:10.1101/gr.107524.110 ↵Miller ES, Kutter E...
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Method: High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics
- Maurizio Pellegrino,
- Adam Sciambi,
- Sebastian Treusch,
- Robert Durruthy-Durruthy,
- Kaustubh Gokhale,
- Jose Jacob,
- Tina X. Chen,
- Jennifer A. Geis,
- William Oldham,
- Jairo Matthews,
- Hagop Kantarjian,
- P. Andrew Futreal,
- Keyur Patel,
- Keith W. Jones,
- Koichi Takahashi,
- and Dennis J. Eastburn
Genome Res. September 2018 28: 1345-1352; Published in Advance August 7, 2018, doi:10.1101/gr.232272.117
...Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303. ↵Paguirigan AL, Smith J, Meshinchi S, Carroll M, Maley C, Radich JP. 2015. Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia. Sci Transl Med 7: 281re282...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
...authors: bpeters@completegenomics.com, rdrmanac@completegenomics.com, xuxun@genomics.cnAbstractHere, we describe single-tube long fragment read (stLFR), a technology that enables sequencing of data from long DNA molecules using economical second-generation sequencing technology. It is based on adding...
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