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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...Francisco, San Francisco, California 94158, USA; 3Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: kpollard@gladstone.ucsf.eduAbstractChromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...defense systems on HGT is masked by their strong linkage with MGEs. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on plasticity.Gene exchange plays a key...
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ARTICLE: Extensive and breed-specific linkage disequilibrium in Canis familiaris
- Nathan B. Sutter,
- Michael A. Eberle,
- Heidi G. Parker,
- Barbara J. Pullar,
- Ewen F. Kirkness,
- Leonid Kruglyak,
- and Elaine A. Ostrander
Genome Res. December 2004 14: 2388-2396; Published in Advance November 15, 2004, doi:10.1101/gr.3147604
.... Biol. 68 : 171 -177. ↵ Hall, D., Wijsman, E.M., Roos, J.L., Gogos, J.A., and Karayiorgou, M. 2002 . Extended intermarker linkage disequilibrium in the Afrikaners. Genome Res. 12 : 956 -961. ↵ HapMap Consortium. 2003 . The International HapMap Project. Nature 426 : 789 -796. ↵ Hardy, R. and Stevens, J...
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Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits Olivia Corradin 1 , Alina Saiakhova 1 , Batool Akhtar-Zaidi 1 , Lois Myeroff 2 , Joseph...
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LETTER: Sequence features in regions of weak and strong linkage disequilibrium
- Albert V. Smith,
- Daryl J. Thomas,
- Heather M. Munro,
- and Gonçalo R. Abecasis
Genome Res. November 2005 15: 1519-1534; doi:10.1101/gr.4421405
...) The fitted disequilibrium coefficients for markers separated by 30 kb. Disequilibrium coefficients were calculated within 100-kb windows distributed throughout the . ( Bottom ) Intermarker intervals (in red), where linkage disequilibrium decays very rapidly, such that disequilibrium between spanning marker...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome Jessica Stapley 1 , Tim R. Birkhead , Terry Burke and Jon Slate Department of Animal and Plant Sciences, University of Sheffield...
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Methods: Genome-wide comparisons of variation in linkage disequilibrium
- Yik Y. Teo,
- Andrew E. Fry,
- Kanishka Bhattacharya,
- Kerrin S. Small,
- Dominic P. Kwiatkowski,
- and Taane G. Clark
Genome Res. October 2009 19: 1849-1860; Published in Advance June 18, 2009, doi:10.1101/gr.092189.109
...Genome-wide comparisons of variation in linkage disequilibrium Yik Y. Teo 1 , 3 , Andrew E. Fry 1 , Kanishka Bhattacharya 1 , Kerrin S. Small 1 , Dominic P. Kwiatkowski 1 , 2 and Taane G. Clark 1 , 2 1 Wellcome...
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LETTER: Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes
- Penelope E. Bonnen,
- Peggy J. Wang,
- Marek Kimmel,
- Ranajit Chakraborty,
- and David L. Nelson
Genome Res. December 1, 2002 12: 1846-1853; Published in Advance November 12, 2002, doi:10.1101/gr.483802
...Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes Penelope E. Bonnen 1 , Peggy J. Wang 1 , Marek Kimmel 2 , Ranajit Chakraborty 3 , and David L. Nelson 1 , 4 1Department of Molecular...
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METHODS: Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping
- Jun S. Liu,
- Chiara Sabatti,
- Jun Teng,
- Bronya J.B. Keats,
- and Neil Risch
Genome Res. October 1, 2001 11: 1716-1724; doi:10.1101/gr.194801
...Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping Jun S. Liu 1 , 6 , Chiara Sabatti 2 , Jun Teng 3 , Bronya J.B. Keats 4 , and Neil Risch 5 1Department of Statistics, Harvard University, Cambridge...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123

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