-
1
-
-
84890027299
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|