TY - JOUR AU - Ridgway, P. AU - Almouzni, G. PY - 2001 DA - 2001// TI - Chromatin assembly and organization JO - J Cell Sci VL - 114 ID - Ridgway2001 ER - TY - JOUR AU - Weiner, A. AU - Hughes, A. AU - Yassour, M. AU - Rando, O. J. AU - Friedman, N. PY - 2010 DA - 2010// TI - High-resolution nucleosome mapping reveals transcription-dependent promoter packaging JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.098509.109 DO - 10.1101/gr.098509.109 ID - Weiner2010 ER - TY - JOUR AU - Whitehouse, I. AU - Tsukiyama, T. PY - 2006 DA - 2006// TI - Antagonistic forces that position nucleosomes in vivo JO - Nat Struct Mol Biol VL - 13 UR - https://doi.org/10.1038/nsmb1111 DO - 10.1038/nsmb1111 ID - Whitehouse2006 ER - TY - JOUR AU - Cairns, B. R. PY - 2005 DA - 2005// TI - Chromatin remodeling complexes: strength in diversity, precision through specialization JO - Curr Opin Genet Dev VL - 15 UR - https://doi.org/10.1016/j.gde.2005.01.003 DO - 10.1016/j.gde.2005.01.003 ID - Cairns2005 ER - TY - JOUR AU - Sala, A. AU - Toto, M. AU - Pinello, L. AU - Gabriele, A. AU - Di Benedetto, V. AU - Ingrassia, A. M. R. AU - Lo Bosco, G. AU - Di Gesù, V. AU - Giancarlo, R. AU - Corona, D. F. V. PY - 2011 DA - 2011// TI - Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling atpase iswi JO - EMBO J VL - 30 UR - https://doi.org/10.1038/emboj.2011.98 DO - 10.1038/emboj.2011.98 ID - Sala2011 ER - TY - JOUR AU - Schnitzler, G. R. PY - 2008 DA - 2008// TI - Control of nucleosome positions by dna sequence and remodeling machines JO - Cell Biochem Biophys VL - 51 UR - https://doi.org/10.1007/s12013-008-9015-6 DO - 10.1007/s12013-008-9015-6 ID - Schnitzler2008 ER - TY - JOUR AU - Shahbazian, M. D. AU - Grunstein, M. PY - 2007 DA - 2007// TI - Functions of site-specific histone acetylation and deacetylation JO - Annu Rev Biochem VL - 76 UR - https://doi.org/10.1146/annurev.biochem.76.052705.162114 DO - 10.1146/annurev.biochem.76.052705.162114 ID - Shahbazian2007 ER - TY - STD TI - Nucleosome positioning In: Ranganathan S, Gribskov M, Nakai K, Schönbach C, editors. Encyclopedia of Bioinformatics and Computational Biology. Oxford: Academic Press: 2019. p. 308–17. ID - ref8 ER - TY - JOUR AU - Lu, Q. AU - Wallrath, L. L. AU - Elgin, S. C. PY - 1994 DA - 1994// TI - Nucleosome positioning and gene regulation JO - J Cell Biochem VL - 55 UR - https://doi.org/10.1002/jcb.240550110 DO - 10.1002/jcb.240550110 ID - Lu1994 ER - TY - JOUR AU - Svaren, J. AU - Horz, W. PY - 1997 DA - 1997// TI - Transcription factors vs. nucleosomes: Regulation of the pho5 promoter in yeast JO - Trends Biochem Sci VL - 22 UR - https://doi.org/10.1016/S0968-0004(97)01001-3 DO - 10.1016/S0968-0004(97)01001-3 ID - Svaren1997 ER - TY - JOUR AU - Liu, M. -. J. AU - Seddon, A. E. AU - Tsai, Z. T. -. Y. AU - Major, I. T. AU - Floer, M. AU - Howe, G. A. AU - Shiu, S. -. H. PY - 2015 DA - 2015// TI - Determinants of nucleosome positioning and their influence on plant gene expression JO - Genome Res VL - 25 UR - https://doi.org/10.1101/gr.188680.114 DO - 10.1101/gr.188680.114 ID - Liu2015 ER - TY - JOUR AU - Pulivarthy, S. R. AU - Lion, M. AU - Kuzu, G. AU - Matthews, A. G. AU - Borowsky, M. L. AU - Morris, J. AU - Kingston, R. E. AU - Dennis, J. H. AU - Tolstorukov, M. Y. AU - Oettinger, M. A. PY - 2016 DA - 2016// TI - Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with v (d) j recombination JO - Proc Natl Acad Sci VL - 113 UR - https://doi.org/10.1073/pnas.1605543113 DO - 10.1073/pnas.1605543113 ID - Pulivarthy2016 ER - TY - JOUR AU - Satchwell, S. C. AU - Drew, H. R. AU - Travers, A. A. PY - 1986 DA - 1986// TI - Sequence periodicities in chicken nucleosome core dna JO - J Mol Biol VL - 191 UR - https://doi.org/10.1016/0022-2836(86)90452-3 DO - 10.1016/0022-2836(86)90452-3 ID - Satchwell1986 ER - TY - JOUR AU - Drew, H. R. AU - Travers, A. A. PY - 1985 DA - 1985// TI - Dna bending and its relation to nucleosome positioning JO - J Mol Biol VL - 186 UR - https://doi.org/10.1016/0022-2836(85)90396-1 DO - 10.1016/0022-2836(85)90396-1 ID - Drew1985 ER - TY - STD TI - Lowman H, Bina M. Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite dna. Biopolymers. 1990; 30(9–10):861–76. https://doi.org/10.1002/bip.360300902. http://arxiv.org/abs/https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.360300902. ID - ref15 ER - TY - JOUR AU - Giancarlo, R. AU - Rombo, S. E. AU - Utro, F. PY - 2018 DA - 2018// TI - In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty799 DO - 10.1093/bioinformatics/bty799 ID - Giancarlo2018 ER - TY - JOUR AU - Kaplan, N. AU - K Moore, I. AU - Mittendorf, Y. AU - J Gossett, A. AU - Tillo, D. AU - Field, Y. AU - M LeProust, E. AU - R Hughes, T. AU - Lieb, J. AU - Widom, J. AU - Segal, E. PY - 2009 DA - 2009// TI - The dna-encoded nucleosome organization of a eukaryotic genome JO - Nature VL - 458 UR - https://doi.org/10.1038/nature07667 DO - 10.1038/nature07667 ID - Kaplan2009 ER - TY - CHAP AU - Lo Bosco, G. ED - Angelini, C. ED - Rancoita, P. M. ED - Rovetta, S. PY - 2016 DA - 2016// TI - Alignment free dissimilarities for nucleosome classification BT - Computational Intelligence Methods for Bioinformatics and Biostatistics PB - Springer CY - Cham ID - Lo Bosco2016 ER - TY - JOUR AU - Utro, F. AU - Di Benedetto, V. AU - Corona, D. F. V. AU - Giancarlo, R. PY - 2015 DA - 2015// TI - The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btv679 DO - 10.1093/bioinformatics/btv679 ID - Utro2015 ER - TY - JOUR AU - Giancarlo, R. AU - Rombo, S. E. AU - Utro, F. PY - 2019 DA - 2019// TI - Dna combinatorial messages and epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes JO - Theor Comput Sci VL - 792 UR - https://doi.org/10.1016/j.tcs.2018.06.047 DO - 10.1016/j.tcs.2018.06.047 ID - Giancarlo2019 ER - TY - JOUR AU - Chereji, R. V. AU - Clark, D. J. PY - 2018 DA - 2018// TI - Major determinants of nucleosome positioning JO - Biophys J VL - 114 UR - https://doi.org/10.1016/j.bpj.2018.03.015 DO - 10.1016/j.bpj.2018.03.015 ID - Chereji2018 ER - TY - JOUR AU - Zhao, Y. AU - Wang, J. AU - Liang, F. AU - Liu, Y. AU - Wang, Q. AU - Zhang, H. AU - Jiang, M. AU - Zhang, Z. AU - Zhao, W. AU - Bao, Y. AU - Zhang, Z. AU - Wu, J. AU - Asmann, Y. W. AU - Li, R. AU - Xiao, J. PY - 2018 DA - 2018// TI - NucMap: a database of genome-wide nucleosome positioning map across species JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky980 DO - 10.1093/nar/gky980 ID - Zhao2018 ER - TY - JOUR AU - Guo, S. -. H. AU - Deng, E. -. Z. AU - Xu, L. -. Q. AU - Ding, H. AU - Lin, H. AU - Chen, W. AU - Chou, K. -. C. PY - 2014 DA - 2014// TI - inuc-pseknc: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu083 DO - 10.1093/bioinformatics/btu083 ID - Guo2014 ER - TY - JOUR AU - Tahir, M. AU - Hayat, M. PY - 2016 DA - 2016// TI - inuc-stnc: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of saac and chou’s pseaac JO - Mol BioSyst VL - 12 UR - https://doi.org/10.1039/C6MB00221H DO - 10.1039/C6MB00221H ID - Tahir2016 ER - TY - JOUR AU - Zhang, J. AU - Peng, W. AU - Wang, L. PY - 2018 DA - 2018// TI - Lenup: learning nucleosome positioning from dna sequences with improved convolutional neural networks JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty003 DO - 10.1093/bioinformatics/bty003 ID - Zhang2018 ER - TY - JOUR AU - Di Gangi, M. AU - Lo Bosco, G. AU - Rizzo, R. PY - 2018 DA - 2018// TI - Deep learning architectures for prediction of nucleosome positioning from sequences data JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2386-9 DO - 10.1186/s12859-018-2386-9 ID - Di Gangi2018 ER - TY - STD TI - Lo Bosco G, Rizzo R, Fiannaca A, La Rosa M, Urso A. A deep learning model for epigenomic studies. In: 12th International Conference on Signal-Image Technology Internet-Based Systems (SITIS). IEEE: 2016. p. 688–92. https://doi.org/10.1109/sitis.2016.115. ID - ref27 ER - TY - CHAP AU - Di Gangi, M. A. AU - Gaglio, S. AU - La Bua, C. AU - Lo Bosco, G. AU - Rizzo, R. ED - Rojas, I. ED - Ortuño, F. PY - 2017 DA - 2017// TI - A deep learning network for exploiting positional information in nucleosome related sequences BT - Bioinformatics and Biomedical Engineering PB - Springer CY - Cham ID - Di Gangi2017 ER - TY - JOUR AU - Fiannaca, A. AU - La Paglia, L. AU - La Rosa, M. AU - Renda, G. AU - Rizzo, R. AU - Gaglio, S. AU - Urso, A. PY - 2018 DA - 2018// TI - Deep learning models for bacteria taxonomic classification of metagenomic data JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2182-6 DO - 10.1186/s12859-018-2182-6 ID - Fiannaca2018 ER - TY - STD TI - Amato D, Di Gangi MA, Lo Bosco G, Rizzo R. Recurrent deep neural networks for nucleosome classification In: Raposo M, Ribeiro P, Sério S, Staiano A, Ciaramella A, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. Cham: Springer: 2020. p. 118–27. ID - ref30 ER - TY - JOUR AU - Di Gesù, V. AU - Lo Bosco, G. AU - Pinello, L. AU - Yuan, G. -. C. AU - Corona, D. F. V. PY - 2009 DA - 2009// TI - A multi-layer method to study genome-scale positions of nucleosomes JO - Genomics VL - 93 UR - https://doi.org/10.1016/j.ygeno.2008.09.012 DO - 10.1016/j.ygeno.2008.09.012 ID - Di Gesù2009 ER - TY - JOUR AU - Pinello, L. AU - Lo Bosco, G. AU - Yuan, G. -. C. PY - 2014 DA - 2014// TI - Applications of alignment-free methods in epigenomics JO - Brief Bioinformatics VL - 15 UR - https://doi.org/10.1093/bib/bbt078 DO - 10.1093/bib/bbt078 ID - Pinello2014 ER - TY - STD TI - Szegedy C, Liu W, Jia Y, Sermanet P, Reed S, Anguelov D, Erhan D, Vanhoucke V, Rabinovich A. Going deeper with convolutions. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition: 2015. p. 1–9. https://doi.org/10.1109/cvpr.2015.7298594. ID - ref33 ER - TY - JOUR AU - Chen, W. AU - Feng, P. AU - Ding, H. AU - Lin, H. AU - Chou, K. -. C. PY - 2016 DA - 2016// TI - Using deformation energy to analyze nucleosome positioning in genomes JO - Genomics VL - 107 UR - https://doi.org/10.1016/j.ygeno.2015.12.005 DO - 10.1016/j.ygeno.2015.12.005 ID - Chen2016 ER - TY - STD TI - Liu H, Zhang R, Xiong W, Guan J, Zhuang Z, Zhou S. A comparative evaluation on prediction methods of nucleosome positioning. Brief Bioinforma. 2013; 15. https://doi.org/10.1093/bib/bbt062. ID - ref35 ER - TY - STD TI - Tensorflow. https://www.tensorflow.org/install. Accessed 07 April 2020. UR - https://www.tensorflow.org/install ID - ref36 ER - TY - STD TI - Kingma DP, Ba J. Adam: A method for stochastic optimization. In: 3rd International Conference on Learning Representations, ICLR 2015, San Diego, CA, USA, May 7-9, 2015, Conference Track Proceedings: 2015. http://arxiv.org/abs/1412.6980. ID - ref37 ER -