Introduction

This website contains:

• Supplementary data for our papers on chromatin structure prediction.
• Free software for predicting nucleosome formation energies, probabilities, and occupancies.
• An upload/download server for exchanging large (up to 4 GB) files. Enter File Exchange Server

People in the chromatin group

• Alexandre V. Morozov,    Denis Tolkunov (2009-12),   George Locke (2008-),   Rǎzvan V. Chereji (2010-)

References and Supplementary Data

1. Morozov, A.V., Fortney, K., Gaykalova, D.A., Studitsky, V.M., Widom, J. & Siggia, E.D. (2008). Extrinsic and intrinsic nucleosome positioning signals. arXiv:0805.4017   previous version of the Nucleosome Explorer website (DNA mechanics model)

2. Morozov, A.V., Fortney, K., Gaykalova, D.A., Studitsky, V.M., Widom, J. & Siggia, E.D. (2009). Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucl. Acids Res. 37, 4707-4722.   PDF   SI   previous version of the Nucleosome Explorer website (DNA mechanics model)

3. Zawadzki, K.A., Morozov, A.V. & Broach, J.R. (2009). Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae. Mol. Biol. Cell 20, 3503-3513.   PDF   SI   InCytes from MBC   online-only Supplementary Data

4. Tolkunov, D. & Morozov, A.V. (2010). Genomic studies and computational predictions of nucleosome positions and formation energies. Adv. Prot. Chem. Struc. Biol. 79, 1-57.   PDF

5. Bai, L. & Morozov, A.V. (2010). Gene regulation by nucleosome positioning. Trends Genet. 26, 476-483.   PDF

6. Locke, G., Tolkunov, D., Moqtaderi, Z., Struhl, K. & Morozov, A.V. (2010). High-throughput sequencing reveals a simple model of nucleosome energetics. Proc. Natl. Acad. Sci. USA 107, 20998-21003.   PDF  SI   SI Table 1 SI Table 2 online-only Supplementary Data and Software

7. Tolkunov, D., Zawadzki, K., Singer, C., Elfving, N., Morozov, A.V. & Broach, J.R. (2011). Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters. Mol. Biol. Cell 22, 2106-2118.   PDF  SI   online-only Supplementary Data

8. Chereji, R.V., Tolkunov, D., Locke, G. & Morozov, A.V. (2011). Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions. Phys. Rev. E Rapid Comm. 83, 050903.   PDF 

9. Chereji, R.V. & Morozov, A.V. (2011). Statistical mechanics of nucleosomes constrained by higher-order chromatin structure. J. Stat. Phys. 144, 379-404.   PDF 

10. Locke, G., Haberman, D., Johnson, S.M. & Morozov, A.V. (2013). Global remodeling of nucleosome positions in C. elegans.   submitted.  
    online-only Software online-only Supplementary Data