Searching journal content for articles similar to Weckx et al. 15 (3): 436.

Displaying results 1-10 of 11

For checked items

view abstracts
download to citation manager

Select this article
Method: Copy number variation detection and genotyping from exome sequence data
- Niklas Krumm,
- Peter H. Sudmant,
- Arthur Ko,
- Brian J. O'Roak,
- Maika Malig,
- Bradley P. Coe,
- NHLBI Exome Sequencing Project,
- Aaron R. Quinlan,
- Deborah A. Nickerson,
- and Evan E. Eichler
Genome Res. August 2012 22: 1525-1532; Published in Advance May 14, 2012, doi:10.1101/gr.138115.112
..., USA Abstract While exome sequencing is readily amenable to single-nucleotide variant discovery, the sparse and nonuniform nature of the exome capture reaction has hindered exome-based detection and characterization of genic copy number variation. We developed a novel method using singular...
Select this article
Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...showed a strong separation between the Alpine and other sampling regions, with this differentiation explaining 14.48% of the variation on PC1 (Fig. 5). Further spatial differentiation between the Northwest region and the other Central European sampling locations explained 8.19% of the variation on PC2...
Select this article
Methods: A probabilistic approach for SNP discovery in high-throughput human resequencing data
- Rose Hoberman,
- Joana Dias,
- Bing Ge,
- Eef Harmsen,
- Michael Mayhew,
- Dominique J. Verlaan,
- Tony Kwan,
- Ken Dewar,
- Mathieu Blanchette,
- and Tomi Pastinen
Genome Res. September 2009 19: 1542-1552; Published in Advance July 15, 2009, doi:10.1101/gr.092072.109
...be identified with <7% FCR. De novo identification of polymorphic sites All the results presented above are based on the subset of sites with known genotypes listed in the HapMap database. However, these results cannot be extended directly to de novo SNP-calling because the fraction of heterozygous sites in our...
Select this article
Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...repeats (8% of the ) (Fig. 3A). We observed a significant correlation between the variation in mapped reads after depletion and the abundance of these repeat classes in terms of overall repeat length and occurrence in the (Fig. 3B,C; Supplemental Table S5). Given that the number of gRNAs targeting each...
OPEN ACCESS ARTICLE
Select this article
Research: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
- Vera B. Kaiser,
- Lana Talmane,
- Yatendra Kumar,
- Fiona Semple,
- Marie MacLennan,
- Deciphering Developmental Disorders Study,
- David R. FitzPatrick,
- Martin S. Taylor,
- and Colin A. Semple
Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
...and within the size range reliably detected by short-read sequencing). To speed up simulations and allow for easy comparison between categories of variants, all classes of indels and single nucleotide variants were down-sampled to 650,000 variants each.A total of 854,409 de novo SNPs and indels were compiled...
OPEN ACCESS ARTICLE
Select this article
Research: Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica
- Xu Wang,
- Kory C. Douglas,
- John L. VandeBerg,
- Andrew G. Clark,
- and Paul B. Samollow
Genome Res. January 2014 24: 70-83; Published in Advance September 24, 2013, doi:10.1101/gr.161919.113
...from the relative numbers of reads containing the reference and alternative alleles at highquality SNP positions (Supplemental Methods). Three hundred and twelve (312) X-linked gene models were covered in female fetal brain samples with sufficient expression levels to call de novo SNPs (Supplemental...
Select this article
RESOURCE: Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB)
- Jinghui Zhang,
- Richard P. Finney,
- William Rowe,
- Michael Edmonson,
- Sei Hoon Yang,
- Tatiana Dracheva,
- Jin Jen,
- Jeffery P. Struewing,
- and Kenneth H. Buetow
Genome Res. July 2007 17: 1111-1117; Published in Advance May 24, 2007, doi:10.1101/gr.5963407
...software ( Bhangale et al. 2006 ). The test data sets for the polymorphism analysis include: (1) the four-gene test data used by Bhangale et al. to compare the performance of polyphred with that of InSNP, MutationSurveyor, and novoSNP; and (2) the 16-gene test data used by Bhangale et al. to evaluate...
Select this article
Resource: SNP detection for massively parallel whole-genome resequencing
- Ruiqiang Li,
- Yingrui Li,
- Xiaodong Fang,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- and Jun Wang
Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108
...and filter low-quality mismatches according to their phred score, known as the “neighborhood quality standard” (NQS) ( Altshuler et al. 2000 ). With direct sequencing of PCR-amplified sequences from diploid samples, software, including SNPdetector ( Zhang et al. 2005 ), novoSNP ( Weckx et al. 2005 ), Poly...
Select this article
RESOURCE: Mapping short DNA sequencing reads and calling variants using mapping quality scores
- Heng Li,
- Jue Ruan,
- and Richard Durbin
Genome Res. November 2008 18: 1851-1858; Published in Advance August 19, 2008, doi:10.1101/gr.078212.108
...diploid samples. These algorithms directly examine chromatogram trace files and detect variants by extracting or comparing signals in the peaks of traces. The most widely used software includes PolyPhred ( Stephens et al. 2006 ), SNPdetector ( Zhang et al. 2005 ), and novoSNP ( Weckx et al. 2005 ), each...
OPEN ACCESS ARTICLE
Select this article
RESOURCE: PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
- Ken Chen,
- Michael D. McLellan,
- Li Ding,
- Michael C. Wendl,
- Yumi Kasai,
- Richard K. Wilson,
- and Elaine R. Mardis
Genome Res. May 2007 17: 659-666; Published in Advance April 6, 2007, doi:10.1101/gr.6151507
...signatures and their favorable prognostic significance . Blood 106 : 3747 – 3754 . ↵ Weckx, S. , Del-Favero, J. , Rademakers, R. , Claes, L. , Cruts, M. , De Jonghe, P. , Van Broeckhoven, C. , De Rijk, P. ( 2005 ) novoSNP, a novel computational tool for sequence variation discovery . Genome Res. 15 : 436...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Weckx et al. 15 (3): 436.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: