Statistical Applications in Genetics and Molecular Biology
Editor-in-Chief: Stumpf, Michael P.H.
6 Issues per year
Increased IMPACT FACTOR 2012: 1.717
Rank 18 out of 117 in category Statistics & Probability in the 2012 Thomson Reuters Journal Citation Report/Science Edition
Mathematical Citation Quotient 2012: 0.07
Volume 12 (0)
Volume 11 (2012)
Volume 10 (2011)
Volume 9 (2010)
Volume 8 (2009)
Volume 6 (2007)
Volume 5 (2006)
Volume 4 (2005)
Volume 3 (2004)
Volume 2 (2003)
Volume 1 (2002)
Most Downloaded Articles
- A General Framework for Weighted Gene Co-Expression Network Analysis by Zhang, Bin and Horvath, Steve
- Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments by Smyth, Gordon K
- Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates by Lund, Steven P./ Nettleton, Dan/ McCarthy, Davis J. and Smyth, Gordon K.
- A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics by Schäfer, Juliane and Strimmer, Korbinian
- Normalization, bias correction, and peak calling for ChIP-seq by Diaz, Aaron/ Park, Kiyoub/ Lim, Daniel A. and Song, Jun S.
A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning
Citation Information: Statistical Applications in Genetics and Molecular Biology. Volume 11, Issue 2, Pages –, ISSN (Online) 1544-6115, DOI: 10.2202/1544-6115.1707, January 2012
- Published Online:
Chromatin structure, in terms of positioning of nucleosomes and nucleosome-free regions in the DNA, has been found to have an immense impact on various cell functions and processes, ranging from transcriptional regulation to growth and development. In spite of numerous experimental and computational approaches being developed in the past few years to determine the intrinsic relationship between chromatin structure (nucleosome positioning) and DNA sequence features, there is yet no universally accurate approach to predict nucleosome positioning from the underlying DNA sequence alone. We here propose an alternative approach to predicting nucleosome positioning from sequence, making use of characteristic sequence differences, and inherent dependencies in overlapping sequence features. Our nucleosomal positioning prediction algorithm, based on the idea of generalized hierarchical hidden Markov models (HGHMMs), was used to predict nucleosomal state based on the DNA sequence in yeast chromosome III, and compared with two other existing methods. The HGHMM method performed favorably among the three models in terms of specificity and sensitivity, and provided estimates that were largely consistent with predictions from the method of Yuan and Liu (2008). However, all the methods still give higher than desirable misclassification rates, indicating that sequence-based features may provide only limited information towards understanding positioning of nucleosomes. The method is implemented in the open-source statistical software R, and is freely available from the authors website.