An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data
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DOI: 10.1515/sagmb-2020-0026
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- Bradley Efron, 2016. "Empirical Bayes deconvolution estimates," Biometrika, Biometrika Trust, vol. 103(1), pages 1-20.
- Fulai Jin & Yan Li & Jesse R. Dixon & Siddarth Selvaraj & Zhen Ye & Ah Young Lee & Chia-An Yen & Anthony D. Schmitt & Celso A. Espinoza & Bing Ren, 2013. "A high-resolution map of the three-dimensional chromatin interactome in human cells," Nature, Nature, vol. 503(7475), pages 290-294, November.
- Mark Carty & Lee Zamparo & Merve Sahin & Alvaro González & Raphael Pelossof & Olivier Elemento & Christina S. Leslie, 2017. "An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data," Nature Communications, Nature, vol. 8(1), pages 1-10, August.
- Jesse R. Dixon & Siddarth Selvaraj & Feng Yue & Audrey Kim & Yan Li & Yin Shen & Ming Hu & Jun S. Liu & Bing Ren, 2012. "Topological domains in mammalian genomes identified by analysis of chromatin interactions," Nature, Nature, vol. 485(7398), pages 376-380, May.
- Zhijun Duan & Mirela Andronescu & Kevin Schutz & Sean McIlwain & Yoo Jung Kim & Choli Lee & Jay Shendure & Stanley Fields & C. Anthony Blau & William S. Noble, 2010. "A three-dimensional model of the yeast genome," Nature, Nature, vol. 465(7296), pages 363-367, May.
- Efron B. & Tibshirani R. & Storey J.D. & Tusher V., 2001. "Empirical Bayes Analysis of a Microarray Experiment," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1151-1160, December.
- Jincheol Park & Shili Lin, 2017. "A random effect model for reconstruction of spatial chromatin structure," Biometrics, The International Biometric Society, vol. 73(1), pages 52-62, March.
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Keywords
empirical Bayes; epigenetics; Hi–C; peak identification;All these keywords.
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