메뉴 건너뛰기




Volumn 3, Issue JAN, 2013, Pages

NSeq: A multithreaded Java application for finding positioned nucleosomes from sequencing data

Author keywords

Nucleosome; Nucleosome positioning

Indexed keywords


EID: 84876166912     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00320     Document Type: Article
Times cited : (10)

References (19)
  • 1
    • 80052966432 scopus 로고    scopus 로고
    • The dynamics of the nucleosome: thermal effects, external forces and ATP
    • Blossey, R., and Schiessel, H. (2011). The dynamics of the nucleosome: thermal effects, external forces and ATP. FEBSJ. 278, 3619-3632.
    • (2011) FEBS J , vol.278 , pp. 3619-3632
    • Blossey, R.1    Schiessel, H.2
  • 2
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • doi: 10.1371/journal.pcbi.1000216.
    • Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I., Sharon, E., Lubling, Y., et al. (2008). Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 4:e1000216. doi: 10.1371/journal.pcbi.1000216
    • (2008) PLoS Comput. Biol. , vol.4
    • Field, Y.1    Kaplan, N.2    Fondufe-Mittendorf, Y.3    Moore, I.4    Sharon, E.5    Lubling, Y.6
  • 3
    • 79960434317 scopus 로고    scopus 로고
    • nucleR: a package for non-parametric nucleosome positioning
    • Flores, O., and Orozco, M. (2011). nucleR: a package for non-parametric nucleosome positioning. Bioinformatics 27, 2149-2150.
    • (2011) Bioinformatics , vol.27 , pp. 2149-2150
    • Flores, O.1    Orozco, M.2
  • 5
    • 0002347322 scopus 로고
    • Median unbiased estimation for binary data
    • Hirji, K., Tsiatis, A., and Mehta, C. (1989). Median unbiased estimation for binary data. Am. Stat. 43, 7-11.
    • (1989) Am. Stat. , vol.43 , pp. 7-11
    • Hirji, K.1    Tsiatis, A.2    Mehta, C.3
  • 6
    • 0019888118 scopus 로고
    • Sequence specific cleavage of DNA by micrococcal nuclease
    • Horz, W., and Altenburger, W. (1981). Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res. 9, 2643-2658.
    • (1981) Nucleic Acids Res , vol.9 , pp. 2643-2658
    • Horz, W.1    Altenburger, W.2
  • 7
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
    • Nicol, J., Helt, G., Blanchard, S., Raja, A., and Loraine, A. (2009). The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730-2731.
    • (2009) Bioinformatics , vol.25 , pp. 2730-2731
    • Nicol, J.1    Helt, G.2    Blanchard, S.3    Raja, A.4    Loraine, A.5
  • 8
    • 33846862405 scopus 로고    scopus 로고
    • High-throughput mapping of the chromatin structure of human promoters
    • Ozsolak, F., Song, J., Liu, X., and Fisher, D. (2007). High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 25, 244-248.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 244-248
    • Ozsolak, F.1    Song, J.2    Liu, X.3    Fisher, D.4
  • 10
    • 84863535110 scopus 로고    scopus 로고
    • NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model
    • Polishko, A., Ponts, N., Le Roch, K., and Lonardi, S. (2012). NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model. Bioinformatics 28, i242-i249.
    • (2012) Bioinformatics , vol.28
    • Polishko, A.1    Ponts, N.2    Le Roch, K.3    Lonardi, S.4
  • 11
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • Schones, D., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., et al. (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887-898.
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.1    Cui, K.2    Cuddapah, S.3    Roh, T.4    Barski, A.5    Wang, Z.6
  • 12
    • 46449112609 scopus 로고    scopus 로고
    • A high-resolution map of nucleosome positioning on a fission yeast centromere
    • Song, J., Liu, X., Liu, X., and He, X. (2008). A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Res. 18, 1064-1072.
    • (2008) Genome Res , vol.18 , pp. 1064-1072
    • Song, J.1    Liu, X.2    Liu, X.3    He, X.4
  • 13
    • 77955045449 scopus 로고    scopus 로고
    • The role of nucleosome positioning in the evolution of gene regulation
    • doi: 10.1371/journal.pbio.1000414.
    • Tsankov, A., Thompson, D., Socha, A., Regev, A., and Rando, O. (2010). The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 8:e1000414. doi: 10.1371/journal.pbio.1000414
    • (2010) PLoS Biol , vol.8
    • Tsankov, A.1    Thompson, D.2    Socha, A.3    Regev, A.4    Rando, O.5
  • 14
    • 74949110964 scopus 로고    scopus 로고
    • High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
    • Weiner, A., Hughes, A., Yassour, M., Rando, O., and Friedman, N. (2010). High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 20, 90-100.
    • (2010) Genome Res , vol.20 , pp. 90-100
    • Weiner, A.1    Hughes, A.2    Yassour, M.3    Rando, O.4    Friedman, N.5
  • 15
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cere-visiae
    • Yuan, G., Liu, Y., Dion, M., Slack, M., Wu, L., Altschuler, S., et al. (2005). Genome-scale identification of nucleosome positions in S. cere-visiae. Science 309, 626-630.
    • (2005) Science , vol.309 , pp. 626-630
    • Yuan, G.1    Liu, Y.2    Dion, M.3    Slack, M.4    Wu, L.5    Altschuler, S.6
  • 16
    • 84863290812 scopus 로고    scopus 로고
    • Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data
    • doi: 10.1371/journal.pone.0032095
    • Zhang, X., Robertson, G., Woo, S., Hoffman, B., and Gottardo, R. (2012). Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. PLoS ONE 7:e32095. doi: 10.1371/journal.pone.0032095
    • (2012) PLoS ONE , vol.7
    • Zhang, X.1    Robertson, G.2    Woo, S.3    Hoffman, B.4    Gottardo, R.5
  • 17
    • 57249114511 scopus 로고    scopus 로고
    • Poisson approx imation for significance in genome-wide ChIP-chip tiling arrays
    • Zhang, Y (2008). Poisson approx imation for significance in genome-wide ChIP-chip tiling arrays. Bioinformatics 24, 2825-2831.
    • (2008) Bioinformatics , vol.24 , pp. 2825-2831
    • Zhang, Y.1
  • 18
    • 57449095143 scopus 로고    scopus 로고
    • Identifying positioned nucleosomes with epige-netic marks in human from ChIP-Seq
    • doi: 10.1186/1471-2164-9-537
    • Zhang, Y., Shin, H., Song, J., Lei, Y., and Liu, X. (2008a). Identifying positioned nucleosomes with epige-netic marks in human from ChIP-Seq. BMC Genomics 9:537. doi: 10.1186/1471-2164-9-537
    • (2008) BMC Genomics , vol.9 , pp. 537
    • Zhang, Y.1    Shin, H.2    Song, J.3    Lei, Y.4    Liu, X.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.