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Volumn 33, Issue 4, 2017, Pages 491-499

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CHROMATIN IMMUNOPRECIPITATION; DNA SEQUENCE; GENOMICS; HUMAN; PROCEDURES; SOFTWARE; SUPERVISED MACHINE LEARNING;

EID: 85028304189     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw672     Document Type: Article
Times cited : (30)

References (30)
  • 1
    • 84890027299 scopus 로고    scopus 로고
    • HMCan: A method for detecting chromatin modifications incancer samples using ChIP-seq data
    • Ashoor, H. et al. (2013) HMCan: a method for detecting chromatin modifications incancer samples using ChIP-seq data. Bioinformatics, 29, 2979-2986.
    • (2013) Bioinformatics , vol.29 , pp. 2979-2986
    • Ashoor, H.1
  • 2
    • 84888264156 scopus 로고    scopus 로고
    • Practical guidelines for the comprehensive analysis of ChIP-seq data
    • Bailey, T. et al. (2013) Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput. Biol., 9, 1-8.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. 1-8
    • Bailey, T.1
  • 3
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • Barski, A. et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1
  • 4
    • 84921690954 scopus 로고    scopus 로고
    • Epiviz: Interactive visual analytics for functional gen-omics data
    • Chelaru, F. et al. (2014) Epiviz: interactive visual analytics for functional gen-omics data. Nat. Methods, 11, 938-940.
    • (2014) Nat. Methods , vol.11 , pp. 938-940
    • Chelaru, F.1
  • 5
    • 77956507904 scopus 로고    scopus 로고
    • A varying threshold method for chip peak-calling using multiple sources of information
    • Chen, K.B. and Zhang, Y. (2010) A varying threshold method for chip peak-calling using multiple sources of information. Bioinformatics, 26, i504-i510.
    • (2010) Bioinformatics , vol.26 , pp. i504-i510
    • Chen, K.B.1    Zhang, Y.2
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Project, E.1
  • 7
    • 84868318661 scopus 로고    scopus 로고
    • Integration of chip-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
    • Gorkin, D.U. et al. (2012) Integration of chip-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res., 22, 2290-2301.
    • (2012) Genome Res. , vol.22 , pp. 2290-2301
    • Gorkin, D.U.1
  • 8
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors primecis-regulatory elements required for macrophage and B cell identities
    • Heinz, S. et al. (2010) Simple combinations of lineage-determining transcription factors primecis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1
  • 9
    • 84901362035 scopus 로고    scopus 로고
    • SegAnnDB: Interactive web-based genomic segmentation
    • Hocking, T.D. et al. (2014) SegAnnDB: interactive web-based genomic segmentation. Bioinformatics, 30, 1539-1546.
    • (2014) Bioinformatics , vol.30 , pp. 1539-1546
    • Hocking, T.D.1
  • 10
    • 84969528644 scopus 로고    scopus 로고
    • PeakSeg: Constrained optimal segmentation and supervised penalty learning for peak detection in count data
    • Hocking, T.D. et al. (2015) PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data. In: Proc. 32nd ICML pp. 324-332.
    • (2015) Proc. 32nd ICML , pp. 324-332
    • Hocking, T.D.1
  • 11
    • 84878010425 scopus 로고    scopus 로고
    • Learning smoothing models of copy number profiles using breakpoint annotations
    • Hocking, T.D. et al. (2013) Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinformatics, 14, 164.
    • (2013) BMC Bioinformatics , vol.14 , pp. 164
    • Hocking, T.D.1
  • 12
    • 84922390212 scopus 로고    scopus 로고
    • JAMM: A peak finder for joint analysis of NGS replicates
    • Ibrahim, M.M. et al. (2014) JAMM: a peak finder for joint analysis of NGS replicates. Bioinformatics, 31, 48-55.
    • (2014) Bioinformatics , vol.31 , pp. 48-55
    • Ibrahim, M.M.1
  • 13
    • 60549104030 scopus 로고    scopus 로고
    • Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
    • Jones, T.R. et al. (2009) Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc. Natl. Acad. Sci., 106, 1826-1831.
    • (2009) Proc. Natl. Acad. Sci. , vol.106 , pp. 1826-1831
    • Jones, T.R.1
  • 14
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent, W. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
    • (2002) Genome Res. , vol.12 , pp. 996-1006
    • Kent, W.1
  • 15
    • 77955895425 scopus 로고    scopus 로고
    • BigWig and BigBed: Enabling browsing of large distributed datasets
    • Kent, W.J. et al. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26, 2204-2207.
    • (2010) Bioinformatics , vol.26 , pp. 2204-2207
    • Kent, W.J.1
  • 16
    • 84867886980 scopus 로고    scopus 로고
    • The Triform algorithm: Improved sensitivity and specificity in ChIP-Seq peak finding
    • Kornacker, K. et al. (2012) The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. BMC Bioinformatics, 13, 176.
    • (2012) BMC Bioinformatics , vol.13 , pp. 176
    • Kornacker, K.1
  • 17
    • 84883204405 scopus 로고    scopus 로고
    • Web Apollo: A web-based genomic annotation editing platform
    • Lee, E. et al. (2013) Web Apollo: a web-based genomic annotation editing platform. Genome Biol., 14, R93.
    • (2013) Genome Biol. , vol.14 , pp. R93
    • Lee, E.1
  • 18
    • 84861397707 scopus 로고    scopus 로고
    • Picking chip-seq peak detectors for analyzing chro-matin modification experiments
    • Micsinai, M. et al. (2012) Picking chip-seq peak detectors for analyzing chro-matin modification experiments. Nucleic Acids Res., 40, e70.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e70
    • Micsinai, M.1
  • 19
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripo-tent and lineage-committed cells
    • Mikkelsen, T. et al. (2007) Genome-wide maps of chromatin state in pluripo-tent and lineage-committed cells. Nature, 448, 653-560.
    • (2007) Nature , vol.448 , pp. 653-660
    • Mikkelsen, T.1
  • 20
    • 84868328797 scopus 로고    scopus 로고
    • Spark: A navigational paradigm for genomic data exploration
    • Nielsen, C.B. et al. (2012) Spark: a navigational paradigm for genomic data exploration. Genome Res., 22, 2262-2269.
    • (2012) Genome Res. , vol.22 , pp. 2262-2269
    • Nielsen, C.B.1
  • 21
    • 84862254965 scopus 로고    scopus 로고
    • Improving chip-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information
    • Osmanbeyoglu, H.U. et al. (2012) Improving chip-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information. BMC Genomics, 13, S1.
    • (2012) BMC Genomics , vol.13 , pp. S1
    • Osmanbeyoglu, H.U.1
  • 22
    • 79952334870 scopus 로고    scopus 로고
    • A manually curated chip-seq benchmark demonstrates room for improvement in current peak-finder programs
    • Rye, M.B. et al. (2011) A manually curated chip-seq benchmark demonstrates room for improvement in current peak-finder programs. Nucleic Acids Res., 39, e25.
    • (2011) Nucleic Acids Res. , vol.39 , pp. e25
    • Rye, M.B.1
  • 23
    • 79952598545 scopus 로고    scopus 로고
    • Identifying dispersed epigenomic domains from chip-seq data
    • Song, Q. and Smith, A.D. (2011) Identifying dispersed epigenomic domains from chip-seq data. Bioinformatics, 27, 870-871.
    • (2011) Bioinformatics , vol.27 , pp. 870-871
    • Song, Q.1    Smith, A.D.2
  • 24
    • 82555193352 scopus 로고    scopus 로고
    • Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts
    • Szalkowski, A.M. and Schmid, C.D. (2011) Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. Brief. Bioinf., 12, 626-633.
    • (2011) Brief. Bioinf. , vol.12 , pp. 626-633
    • Szalkowski, A.M.1    Schmid, C.D.2
  • 25
    • 77952857912 scopus 로고    scopus 로고
    • A signal-noise model for significance analysis of ChIP-seq with negative control
    • Xu, H. et al. (2010) A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics, 26, 1199-1204.
    • (2010) Bioinformatics , vol.26 , pp. 1199-1204
    • Xu, H.1
  • 26
    • 84879834810 scopus 로고    scopus 로고
    • An interactive analysis and exploration tool for epi-genomic data
    • Younesy, H. et al. (2013) An interactive analysis and exploration tool for epi-genomic data. Comput. Graph. Forum, 32, 91-100.
    • (2013) Comput. Graph. Forum , vol.32 , pp. 91-100
    • Younesy, H.1
  • 27
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • Zang, C. et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics, 25, 1952-1958.
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1
  • 28
    • 84907502335 scopus 로고    scopus 로고
    • PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
    • Zhang, Y. et al. (2014) PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics, 30, 2568-2575.
    • (2014) Bioinformatics , vol.30 , pp. 2568-2575
    • Zhang, Y.1
  • 29
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 30
    • 77951610155 scopus 로고    scopus 로고
    • Genetic analysis of variation in transcription factor binding in yeast
    • Zheng, W. et al. (2010) Genetic analysis of variation in transcription factor binding in yeast. Nature, 464, 1187-1191.
    • (2010) Nature , vol.464 , pp. 1187-1191
    • Zheng, W.1


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