-
1
-
-
37749047490
-
Sequence census methods for functional genomics
-
Wold B, Myers RM. Sequence census methods for functional genomics. Nat Meth 2008, 5:19-21.
-
(2008)
Nat Meth
, vol.5
, pp. 19-21
-
-
Wold, B.1
Myers, R.M.2
-
2
-
-
66149186985
-
Genomic location analysis by ChIP-Seq
-
10.1002/jcb.22077, 19173299
-
Barski A, Zhao K. Genomic location analysis by ChIP-Seq. Journal of Cellular Biochemistry 2009, 107:11-18. 10.1002/jcb.22077, 19173299.
-
(2009)
Journal of Cellular Biochemistry
, vol.107
, pp. 11-18
-
-
Barski, A.1
Zhao, K.2
-
3
-
-
70349312354
-
ChIP-seq: advantages and challenges of a maturing technology
-
10.1038/nrg2641, 19736561
-
Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10(10):669-680. 10.1038/nrg2641, 19736561.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.10
, pp. 669-680
-
-
Park, P.J.1
-
4
-
-
77955368935
-
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
-
10.1371/journal.pone.0011471, 2900203, 20628599
-
Wilbanks EG, Facciotti MT. Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS ONE 2010, 5(7):.. 10.1371/journal.pone.0011471, 2900203, 20628599.
-
(2010)
PLoS ONE
, vol.5
, Issue.7
-
-
Wilbanks, E.G.1
Facciotti, M.T.2
-
5
-
-
74549114755
-
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
-
10.1186/1471-2164-10-618, 2804666, 20017957
-
Laajala T, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo L. A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics 2009, 10:618. 10.1186/1471-2164-10-618, 2804666, 20017957., http://www.biomedcentral.com/1471-2164/10/618
-
(2009)
BMC Genomics
, vol.10
, pp. 618
-
-
Laajala, T.1
Raghav, S.2
Tuomela, S.3
Lahesmaa, R.4
Aittokallio, T.5
Elo, L.6
-
7
-
-
77955593047
-
Coverage statistics for sequence census methods
-
10.1186/1471-2105-11-430, 2940910, 20718980
-
Evans S, Hower V, Pachter L. Coverage statistics for sequence census methods. BMC Bioinformatics 2010, 11:430. 10.1186/1471-2105-11-430, 2940910, 20718980.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 430
-
-
Evans, S.1
Hower, V.2
Pachter, L.3
-
8
-
-
78649718643
-
Probability and real trees, Volume 1920 of Lecture Notes in Mathematics
-
Berlin: Springer, Lectures from the 35th Summer School on Probability Theory held in Saint Flour, July 6-23, 2005
-
Evans SN. Probability and real trees, Volume 1920 of Lecture Notes in Mathematics. 2008, Berlin: Springer, Lectures from the 35th Summer School on Probability Theory held in Saint Flour, July 6-23, 2005.
-
(2008)
-
-
Evans, S.N.1
-
10
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Meth 2009, 6(11s):S22-S32.
-
(2009)
Nat Meth
, vol.6
, Issue.11 S
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
12
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 1995, 57:289-300.
-
(1995)
J Roy Statist Soc Ser B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
13
-
-
0035733108
-
The control of the false discovery rate in multiple testing under dependency
-
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Statist 2001, 29(4):1165-1188.
-
(2001)
Ann Statist
, vol.29
, Issue.4
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
14
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-Seq experiments relative to controls
-
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-Seq experiments relative to controls. Nat Biotech 2009, 27:66-75.
-
(2009)
Nat Biotech
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
15
-
-
53849146020
-
Model-based Analysis of ChIP-Seq (MACS)
-
10.1186/gb-2008-9-9-r137, 2592715, 18798982
-
Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, Bernstein B, Nussbaum C, Myers R, Brown M, Li W, Liu XS. Model-based Analysis of ChIP-Seq (MACS). Genome Biology 2008, 9(9):R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982., http://genomebiology.com/2008/9/9/R137
-
(2008)
Genome Biology
, vol.9
, Issue.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.3
Eeckhoute, J.4
Johnson, D.5
Bernstein, B.6
Nussbaum, C.7
Myers, R.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
16
-
-
77950566643
-
Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species
-
10.1371/journal.pbio.1000343, 2843597, 20351773
-
Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species. PLoS Biol 2010, 8(3):e1000343. 10.1371/journal.pbio.1000343, 2843597, 20351773.
-
(2010)
PLoS Biol
, vol.8
, Issue.3
-
-
Bradley, R.K.1
Li, X.Y.2
Trapnell, C.3
Davidson, S.4
Pachter, L.5
Chu, H.C.6
Tonkin, L.A.7
Biggin, M.D.8
Eisen, M.B.9
-
17
-
-
58149182724
-
NCBI GEO: archive for high-throughput functional genomic data
-
10.1093/nar/gkn764, 2686538, 18940857
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucl Acids Res 2009, 37(suppl 1):D885-890. 10.1093/nar/gkn764, 2686538, 18940857., http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D885
-
(2009)
Nucl Acids Res
, vol.37
, Issue.SUPPL 1
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Marshall, K.A.10
Phillippy, K.H.11
Sherman, P.M.12
Muertter, R.N.13
Edgar, R.14
-
18
-
-
84888276133
-
-
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. Supplemental code and data for PeakSeq: scoring ChIP-seq experiments relative to controls , http://www.gersteinlab.org/proj/PeakSeq/
-
Supplemental code and data for PeakSeq: scoring ChIP-seq experiments relative to controls
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
19
-
-
84888278187
-
MACS Sample
-
MACS Sample. , http://liulab.dfci.harvard.edu/MACS/Sample.html
-
-
-
-
20
-
-
0036079158
-
The Human Genome Browser at UCSC
-
186604, 12045153
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The Human Genome Browser at UCSC. Genome Research 2002, 12(6):996-1006. 186604, 12045153., http://genome.cshlp.org/content/12/6/996.abstract
-
(2002)
Genome Research
, vol.12
, Issue.6
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
21
-
-
68849103482
-
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
-
10.1186/gb-2009-10-7-r80, 2728534, 19627575
-
MacArthur S, Li XY, Li J, Brown J, Chu HC, Zeng L, Grondona B, Hechmer A, Simirenko L, Keranen S, Knowles D, Stapleton M, Bickel P, Biggin M, Eisen M. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biology 2009, 10(7):R80. 10.1186/gb-2009-10-7-r80, 2728534, 19627575., http://genomebiology.com/2009/10/7/R80
-
(2009)
Genome Biology
, vol.10
, Issue.7
-
-
MacArthur, S.1
Li, X.Y.2
Li, J.3
Brown, J.4
Chu, H.C.5
Zeng, L.6
Grondona, B.7
Hechmer, A.8
Simirenko, L.9
Keranen, S.10
Knowles, D.11
Stapleton, M.12
Bickel, P.13
Biggin, M.14
Eisen, M.15
-
22
-
-
40849085514
-
FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription
-
10.1016/j.cell.2008.01.018, 2323438, 18358809
-
Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription. Cell 2008, 132(6):958-970. 10.1016/j.cell.2008.01.018, 2323438, 18358809.
-
(2008)
Cell
, vol.132
, Issue.6
, pp. 958-970
-
-
Lupien, M.1
Eeckhoute, J.2
Meyer, C.A.3
Wang, Q.4
Zhang, Y.5
Li, W.6
Carroll, J.S.7
Liu, X.S.8
Brown, M.9
-
23
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Meth 2007, 4(8):651-657.
-
(2007)
Nat Meth
, vol.4
, Issue.8
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
Thiessen, N.11
Griffith, O.L.12
He, A.13
Marra, M.14
Snyder, M.15
Jones, S.16
-
24
-
-
79951480123
-
-
R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], R Development Core Team
-
R Development Core Team R: A Language and Environment for Statistical Computing 2010, R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], R Development Core Team., http://www.R-project.org
-
(2010)
R: A Language and Environment for Statistical Computing
-
-
-
25
-
-
43349107222
-
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
-
10.1093/nar/gkn048, 2377422, 18332042
-
Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Research 2008, 36(8):2547-2560. 10.1093/nar/gkn048, 2377422, 18332042.
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.8
, pp. 2547-2560
-
-
Noyes, M.B.1
Meng, X.2
Wakabayashi, A.3
Sinha, S.4
Brodsky, M.H.5
Wolfe, S.A.6
-
26
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
10.1038/nature07509, 2593745, 18978772
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456(7221):470-476. 10.1038/nature07509, 2593745, 18978772.
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
27
-
-
34250370060
-
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
-
10.1101/gr.5574907, 1891349, 17568006
-
Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research 2007, 17(6):910-916. 10.1101/gr.5574907, 1891349, 17568006., http://genome.cshlp.org/content/17/6/910.abstract
-
(2007)
Genome Research
, vol.17
, Issue.6
, pp. 910-916
-
-
Bhinge, A.A.1
Kim, J.2
Euskirchen, G.M.3
Snyder, M.4
Iyer, V.R.5
|