- About this Journal ·
- Abstracting and Indexing ·
- Advance Access ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 617545, 7 pages
Exploring the Cooccurrence Patterns of Multiple Sets of Genomic Intervals
1Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
2Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
3Center for Comprehensive Informative, Emory University, Atlanta, GA, USA
Received 27 March 2013; Accepted 4 May 2013
Academic Editor: Zhongming Zhao
Copyright © 2013 Hao Wu and Zhaohui S. Qin. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- A. P. Bird, “CpG-rich islands and the function of DNA methylation,” Nature, vol. 321, no. 6067, pp. 209–213, 1986.
- D. S. Johnson, A. Mortazavi, R. M. Myers, and B. Wold, “Genome-wide mapping of in vivo protein-DNA interactions,” Science, vol. 316, no. 5830, pp. 1497–1502, 2007.
- X. Chen, H. Xu, P. Yuan et al., “Integration of external signaling pathways with the core transcriptional network in embryonic stem cells,” Cell, vol. 133, no. 6, pp. 1106–1117, 2008.
- A. Favorov, L. Mularoni, L. Cope et al., “Exploring massive, genome scale datasets with the genometricorr package,” PLoS Computational Biology, vol. 8, no. 5, Article ID e1002529, 2012.
- M. Chikina and O. Troyanskaya, “An effective statistical evaluation of ChIPseq dataset similarity,” Bioinformatics, vol. 28, no. 5, pp. 607–613, 2012.
- A. Q. Fu and B. Adryan, “Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays,” Molecular BioSystems, vol. 5, no. 12, pp. 1429–1438, 2009.
- J. Ernst and M. Kellis, “ChromHMM: automating chromatin-state discovery and characterization,” Nature Methods, vol. 9, no. 3, pp. 215–216, 2012.
- X. Zeng, R. Sanalkumar, E. Bresnick, H. Li, Q. Change, and S. Keles, “jMOSAiCS: joint analysis of multiple ChIP-seq datasets,” Genome Biology, vol. 14, article R38, 2013.
- A. Doi, I. H. Park, B. Wen et al., “Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts,” Nature Genetics, vol. 41, no. 12, pp. 1350–1353, 2009.
- A. Dempster, N. Laird, and D. Rubin, “Maximum likelihood from incomplete data via the EM algorithm,” Journal of the Royal Statistical Society Series B, pp. 1–38, 1977.
- G. Schwarz, “Estimating the dimension of a model,” The Annals of Statistics, pp. 461–464, 1978.
- R. Giancarlo and F. Utro, “Stability-based model selection for high throughput genomic data: an algorithmic paradigm,” Artificial Immune Systems, pp. 260–270, 2012.
- J. Ernst and M. Kellis, “Discovery and characterization of chromatin states for systematic annotation of the human genome,” Nature Biotechnology, vol. 28, no. 8, pp. 817–825, 2010.
- T. Hastie, R. Tibshirani, J. Friedman, and J. Franklin, “The elements of statistical learning: data mining, inference and prediction,” The Mathematical Intelligencer, vol. 27, no. 2, pp. 83–85, 2005.
- T. Barrett, D. B. Troup, S. E. Wilhite et al., “NCBI GEO: archive for high-throughput functional genomic data,” Nucleic Acids Research, vol. 37, no. 1, pp. D885–D890, 2009.
- H. Wu and H. Ji, “JAMIE: joint analysis of multiple ChIP-chip experiments,” Bioinformatics, vol. 26, no. 15, pp. 1864–1870, 2010.
- Z. S. Qin, “Clustering microarray gene expression data using weighted Chinese restaurant process,” Bioinformatics, vol. 22, no. 16, pp. 1988–1997, 2006.