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METHODS: DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays
- Magnus Jobs,
- W. Mathias Howell,
- Linda Strömqvist,
- Torsten Mayr,
- and Anthony J. Brookes
Genome Res. May 1, 2003 13: 916-924; doi:10.1101/gr.801103
...by dynamic allele-specific hybridization (DASH): Design criteria and assay validation. Genome Res. 11 : 152 – 162 . ↵ Shuber A.P. , Michalowsky L.A. , Nass G.S. , Skoletsky J. , Hire L.M. , Kotsopoulos S.K. , Phipps M.F. , Barberio D.M. , Klinger K.W. ( 1997 ) High-throughput parallel analysis of hundreds...
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Method: The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism
- Maximilian P.A. Salm,
- Stuart D. Horswell,
- Claire E. Hutchison,
- Helen E. Speedy,
- Xia Yang,
- Liming Liang,
- Eric E. Schadt,
- William O. Cookson,
- Anthony S. Wierzbicki,
- Rossi P. Naoumova,
- and Carol C. Shoulders
Genome Res. June 2012 22: 1144-1153; Published in Advance March 7, 2012, doi:10.1101/gr.126037.111
...of phased SNP genotypes was used to predict inversion-type (Deng et al. 2008), but as discussed by Antonacci et al. (2009), these predictions differed considerably from FISH genotype data. Herein we present a novel, robust high-throughput method to genotype 8p23-inv. By use of this tool, we define...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...) linked to allelic imbalances in gene expression in these hybrid pigs. It should be noted that although relatively stringent criteria and rigorous analyses were used to screen differential A/B compartmentalization, shifts in TAD boundaries, and rewired PEIs, the advanced statistical methods used...
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METHODS: iFRET: An Improved Fluorescence System for DNA-Melting Analysis
- W. Mathias Howell,
- Magnus Jobs,
- and Anthony J. Brookes
Genome Res. September 1, 2002 12: 1401-1407; doi:10.1101/gr.297202
.... A new method for scoring single nucleotide polymorphisms. Nat. Biotechnol. 17 : 87 – 88 . ↵ Prince J.A. , Feuk L. , Howell W.M. , Jobs M. , Emahazion T. , Blennow K. , Brookes A.J. ( 2001 ) Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...accuracy models.IG transcript–enriched transcriptome sequencing10x cDNA was reamplified as described above. To increase IG heavy and light chain transcript coverage, an xGen Custom Hybridization Panel (Integrated DNA Technologies) was designed targeting IG and TCR exons. The hybridization panel consisted...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...providing acceptably accurate estimations. (F) Ages and autosomal CNA percentages of each sample. The dashed line indicates a weak linear relationship between age and CNA ratios.With a shallow sequencing depth (∼ 0.1×; i.e., 0.3 Gb per cell), we obtained an average 3.50% ± 1.50% (CI = 95%) coverage...
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Methods: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
- Daisuke Komura,
- Fan Shen,
- Shumpei Ishikawa,
- Karen R. Fitch,
- Wenwei Chen,
- Jane Zhang,
- Guoying Liu,
- Sigeo Ihara,
- Hiroshi Nakamura,
- Matthew E. Hurles,
- Charles Lee,
- Stephen W. Scherer,
- Keith W. Jones,
- Michael H. Shapero,
- Jing Huang,
- and Hiroyuki Aburatani
Genome Res. December 2006 16: 1575-1584; Published in Advance November 22, 2006, doi:10.1101/gr.5629106
...good resolving power to identify CNVs &lt;100 kb in size, CNVs spanning segmental duplications are underrepresented because of the difficulty in developing robust SNP assays in these regions ( Fredman et al. 2004 ). Future generations of oligonucleotide-based copy number arrays can be designed...

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