Nucleosome Dynamics Help - References

References Help

Buitrago, D., Codó, L., Illa, R., de Jorge, P., Battistini, F., Flores, O., Bayarri, G., Royo, R., Del Pino, M., Heath, S., Hospital, A., Gelpí, J.L., Heath, I.B., Orozco, M., 2019. “Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.” Nucleic Acids Research, gkz759. https://doi.org/10.1093/nar/gkz759

nucleR

Flores, O. and Orozco, M. (2011). “nucleR: a package for non-parametric nucleosome positioning.” Bioinformatics, 27, pp. 2149–2150. doi: 1093/bioinformatics/btr345.

Deniz, Ö., Flores, O., Aldea, M., Soler-López, M., Orozco, M. (2016). "Nucleosome architecture throughout the cell cycle." Scientific Reports, 6, doi: 1038/srep19729.

Flores, O., Deniz, O., Soler-Lopez, M., Orozco, M. (2014). "Fuzziness and noise in nucleosomal architecture." Nucleic Acids Research, 42, pp. 4934–4946. doi: 1093/nar/gku165.

Transcription Start Sites

Pelechano, V., Wei, W., Steinmetz, L.M. (2013). "Extensive transcriptional heterogeneity revealed by isoform profiling." Nature, 497, pp. 127–131. doi: 10.1038/nature12121

Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T. (2006). "A large-scale full-length cDNA analysis to explore the budding yeast transcriptome." Proc. Natl. Acad. Sci. U.S.A., 103, pp. 17846–17851. doi: 10.1073/pnas.0605645103

Yassour, M., Kaplan, T., Fraser, H.B., Levin, J.Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., Gnirke, A., Nusbaum, C., Thompson, D.-A., Friedman, N., Regev, A. (2009). "Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing." Proceedings of the National Academy of Sciences, 106, pp. 3264–3269. doi: 10.1073/pnas.0812841106

Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M. (2008). "The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing." Science, 320, pp. 1344–1349. doi: 10.1126/science.1158441

E-platform

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Grüning BA, et al. 2018. "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update." Nucleic Acids Research 46: W537–W544. doi: https://doi.org/10.1093/nar/gky379

Codó L, Bayarri G, Alvarez J, Conejero J, Hospital A, Royo R, Repchevsky D, Pasi M, Meletiou A, McDowall M, Reham F, Alcantara J.A, Jimenez-Garcia B, Walther J, Illa R, Serra F, Goodstadt M, Castillo D, Sati S, Buitrago D, Brun-Heath I, Fernandez-Recio J, Cavalli G, Marti-Renom M, Yates A, Laughton C.A, Badia R.M, Orozco M, Gelpí J.L. "MuGVRE. A virtual research environment for 3D/4D genomics." bioRxiv 602474; doi: https://doi.org/10.1101/602474