The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Abstract
We trained Segway, a dynamic Bayesian network method, simultaneously on chromatin data from multiple experiments, including positions of histone modifications, transcription-factor binding and open chromatin, all derived from a human chronic myeloid leukemia cell line. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, transcriptional regulator CTCF-binding regions and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/proj/segway/.
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Maximum Likelihood from Incomplete Data Via the EM Algorithm
Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1977.tb01600.x · Cited by 50,444
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
Research works printed but not linked: 30
- ENCODE Project Consortium. PLoS Biol. 9, e1001046 (2011). · DOI · Paper page
- Day, N., Hemmaplardh, A., Thurman, R.E., Stamatoyannopoulos, J.A. & Noble, W.S. Bioinformatics 23, 1424–1426 (2007). · DOI
- Erdman, C. & Emerson, J.W. Bioinformatics 24, 2143–2148 (2008). · DOI
- Jaschek, R. & Tanay, A. in Research in Computational Molecular Biology, Lecture Notes in Computer Science Vol. 5541 (ed. Batzoglou, S.) 170–183 (Springer, Berlin, 2009). · DOI
- Ernst, J. & Kellis, M. Nat. Biotechnol. 28, 817–825 (2010). · DOI · Paper page
- Filion, G.J. et al. Cell 143, 212–224 (2010). · DOI · Paper page
- Kharchenko, P.V. et al. Nature 471, 480–485 (2011). · DOI · Paper page
- Bilmes, J. & Bartels, C. IEEE Signal Process. Mag. 22, 89–100 (2005). · DOI
- Reynolds, S.M., Käll, L., Riffle, M.E., Bilmes, J.A. & Noble, W.S. PLOS Comput. Biol. 4, e1000213 (2008). · DOI · Paper page
- Wang, Z., Schones, D.E. & Zhao, K. Curr. Opin. Genet. Dev. 19, 127–134 (2009). · DOI
- Hon, G., Ren, B. & Wang, W. PLOS Comput. Biol. 4, e1000201 (2008). · DOI
- Raney, B.J. et al. Nucleic Acids Res. 39, D871–D875 (2011). · DOI · Paper page
- Hoffman, M.M., Buske, O.J. & Noble, W.S. Bioinformatics 26, 1458–1459 (2010). · DOI
- Johnson, N.L. Biometrika 36, 149–176 (1949). · DOI · Paper page
- Bilmes, J. in UAI '00: Proceedings of the 16th Conference on Uncertainty in Artificial Intelligence (eds. Boutilier, C. & Goldszmidt, M.) 38–45 (Morgan Kaufmann, San Francisco, 2000).
- Grundy, W.N., Bailey, T.L., Elkan, C.P. & Baker, M.E. Comput. Appl. Biosci. 13, 397–406 (1997).
- Bilmes, J. & Bartels, C. in UAI '03, Proceedings of the 19th Conference in Uncertainty in Artificial Intelligence (eds. Meek, C. & Kjærulff, U.) 47–56 (Morgan Kaufmann Publishers, San Francisco, 2003).
- Viterbi, A.J. IEEE Trans. Inf. Theory 13, 260–269 (1967). · DOI · Paper page
- Fujita, P.A. et al. Nucleic Acids Res. 39, D876–D882 (2011). · DOI · Paper page
- Harrow, J. et al. Genome Biol. 7, S4.1–S4.9 (2006). · DOI · Paper page
- Takahashi, H., Kato, S., Murata, M. & Carninci, P. Methods Mol. Biol. 786, 181–200 (2012). · DOI
- Buske, O.J., Hoffman, M.M., Ponts, N., Roch, K.G.L. & Noble, W.S. BMC Bioinformatics 12, 415 (2011). · DOI
- Davis, J. & Goadrich, M. in Proceedings of the 23rd International Conference on Machine Learning 233–240 (ACM, New York, 2006). · DOI · Paper page
- Flicek, P. et al. Nucleic Acids Res. 39, D800–D806 (2011). · DOI · Paper page
- UniProt Consortium. Nucleic Acids Res. 39, D214–D219 (2011). · DOI · Paper page
- Berriz, G.F., Beaver, J.E., Cenik, C., Tasan, M. & Roth, F.P. Bioinformatics 25, 3043–3044 (2009). · DOI · Paper page
- Wingender, E. et al. Nucleic Acids Res. 28, 316–319 (2000). · DOI · Paper page
- Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W. & Lenhard, B. Nucleic Acids Res. 32, D91–D94 (2004). · DOI · Paper page
- Grant, C.E., Bailey, T.L. & Noble, W.S. Bioinformatics 27, 1017–1018 (2011). · DOI · Paper page
- Bickel, P.J., Boley, N., Brown, J.B., Huang, H. & Zhang, N.R. Ann. Appl. Stat. 4, 1660–1697 (2010). · DOI
Cited by
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550
Cunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1010 · Cited by 1,115
Parker, S. C. J., Stitzel, M. L., Taylor, D. L., Orozco, J. M., Erdos, M. R., Akiyama, J. A., van Bueren, K. L., Chines, P. S., Narisu, N., Program, N. C. S., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317023110 · Cited by 665
Metadata
- Authors
- Hoffman, M. M., Buske, O. J., Wang, J., Weng, Z., Bilmes, J. A., & Noble, W. S.
- Venue
- Nature Methods
- Published
- 2012-03-18
- Volume
- 9
- Issue
- 5
- Pages
- 473-476
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W4230875896
- Cited by
- 565
- References
- 2
- FWCI
- 15.68
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
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