Maintainer: Ji-Ping Wang, <jzwang@northwestern.edu>
References for methods:
- Wang, J.-P., Fondufe-Mittendorf, Y., Xi, L., Tsai, G.-F., Segal, E.,
and Widom, J. (2008). Preferentially quantized linker {DNA} lengths in
Saccharomyces cerevisiae. PLoS Computational Biology,
4(9):e1000175.
- Xi, L., Fondufe-Mittendorf, Y., Xia, L., Flatow, J., Widom, J., and
Wang, J.-P. (2010). Predicting nucleosome positioning using a duration
hidden markov model. BMC Bioinformatics, pages doi:10.1186/1471--2105--11--346.
- Xi, L., Brogaard,K., Zhang, Q., Lindsay, B.G., Widom, and Wang,
J.-P., A locally convoluted cluster model for nucleosome positioning
signals in chemical map, Journal of American Statistical
Association, 2013, 109(505) 48-62
References for chemical map data used:
- Brogaard, K., Xi, L., Wang, J.-P. and Widom, J. (2012), A base pair
resolution map of nucleosome positions in yeast, Nature, 2012,
486: 496–501
- Moyle-Heyrman, G., Zaichuk, T., Xi, L., Zhang, Q., Uhlenbeck, O.C.,
Holmgren, R., Widom, J. and Wang, J.-P., Chemical map of
Schizosaccharomyces pombe reveals species-specific features in
nucleosome positioning, PNAS , 2013,110(50),20158-20163
- Voong, L.N, Xi, L., Sebeson, A.C., Xiong, B., Wang, J.-P., Wang, X.
Insights into Nucleosome Organization in Mouse Embryonic Stem Cells
through Chemical Mapping , Cell, 2016,
167(6),1555-1570.e15
NuPoP versions hightlights
NuPoP V2.5 added adjustments of linker length
distribution.
NuPoP V2.0 added a funciton predNuPoP_chem for
prediction of nucleosomes using profiles trained based on chemical maps
of nucleosomes for yeast, pombe, mouse and human (profiles for other
species are extrapolated based on yeast profile). To show a clear
improvement, Figure: MNase_vs_Chemicale below compares the prediction
based on MNase profile vs chemical profile for yeast where the red curve
super-imposed is the occupancy from the chemical map for yeast
data.
A report of performance comparison of NuPoP (V2.0) vs
nuCpos (V1.14) can be found at https://github.com/jipingw/NuPoP_doc