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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...’ nanopore sequencing (Jain et al. 2018b), made it possible to obtain long-read data. Besides their advantages in de novo assembly, structural variant analysis, and haplotype phasing, their abilities to analyze single molecules without GC bias allowed the discoveries of disease-causing stretches of GC...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...related species can provide additional context for accurate variant discovery.Assessing generalization across speciesRecommending a TrioTrain checkpoint for variant calling requires confirmation of accurate genotype predictions outside the training data, known as model testing. We assessed the 30 new...
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Method: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
- Jamie K. Teer,
- Lori L. Bonnycastle,
- Peter S. Chines,
- Nancy F. Hansen,
- Natsuyo Aoyama,
- Amy J. Swift,
- Hatice Ozel Abaan,
- Thomas J. Albert,
- NISC Comparative Sequencing Program,
- Elliott H. Margulies,
- Eric D. Green,
- Francis S. Collins,
- James C. Mullikin,
- and Leslie G. Biesecker
Genome Res. October 2010 20: 1420-1431; Published in Advance September 1, 2010, doi:10.1101/gr.106716.110
.... Additionally, the ability to apply variant discovery to other organisms with annotated s is also of great value. So-called next-generation DNA sequencing technologies that involve massively parallel clonal ensemble sequencing are creating new opportunities for comprehensive genomic interrogation, bypassing...
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Research: Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver
- Xia Yang,
- Bin Zhang,
- Cliona Molony,
- Eugene Chudin,
- Ke Hao,
- Jun Zhu,
- Andrea Gaedigk,
- Christine Suver,
- Hua Zhong,
- J. Steven Leeder,
- F. Peter Guengerich,
- Stephen C. Strom,
- Erin Schuetz,
- Thomas H. Rushmore,
- Roger G. Ulrich,
- J. Greg Slatter,
- Eric E. Schadt,
- Andrew Kasarskis,
- and Pek Yee Lum
Genome Res. August 2010 20: 1020-1036; Published in Advance June 10, 2010, doi:10.1101/gr.103341.109
...Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver Xia Yang 1 , 9 , 10 , 13 , Bin Zhang 1 , 9 , 10 , Cliona Molony 1 , Eugene Chudin 1 , Ke Hao 1 , Jun Zhu 1 , 10 , Andrea...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...). The G allele is predicted to result in a weaker motif match.To identify peaks that vary across individuals owing to genotype, we tested for caQTLs using genetic variants within 1 kb of the centers of autosomal peaks and identified 35,361 peaks with a significant caQTL (caPeaks; FDR < 5%) (Fig. 1B...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
...likelihoods are used to calculate the posterior probability of genotypes for each variant. Downstream filtering based on RD, read mapping quality, strand bias, and other indicators of error are applied to reject likely false-positive calls.Local assembly around candidate variants is efficient but inherently...
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
.... Haplotypes constructed in aneuploid regions by leveraging haplotype imbalanceIdentification and reconstruction of structural variants (SVs) from linked readsIn addition to phasing, another use for the linked-read sequencing data is to identify breakpoints of large-scale SVs by searching for the discordant...
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Research: Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
- Andreas Schlattl,
- Simon Anders,
- Sebastian M. Waszak,
- Wolfgang Huber,
- and Jan O. Korbel
Genome Res. December 2011 21: 2004-2013; Published in Advance August 23, 2011, doi:10.1101/gr.122614.111
...and these genes’ expression is explainable either by the CNVs frequently representing causative variants or by CNV genotypes displaying a slightly reduced genotyping error rate compared with SNP genotypes (which alsowould cause CNVs to bemore strongly associated). Strikingly, we found an abundance of gene...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...of heterozygous nucleotide variants. However, laboratory rat strains such as SHR have been inbred for more than 130 generations and are therefore homozygous at almost all loci across the . Lower depth of sequence coverage may therefore be required for such inbred s, because a single allele is present at almost...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...the fraction of loci with high levels of stutter (Fig. 2C; Supplemental Table S3), as measured by the fraction of reads supporting the called genotypes (variant allele fraction [VAF]; higher VAF = lower stutter). Across all technical replicates of both temperature conditions, an average of 432 (range: 429...

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