-
1
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
10.1038/nmeth.1226, 18516045
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
-
(2008)
Nat Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
2
-
-
77954041808
-
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
-
10.1186/1471-2105-11-369, 2912305, 20598134
-
Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics 2010, 11:369. 10.1186/1471-2105-11-369, 2912305, 20598134.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 369
-
-
Qin, Z.S.1
Yu, J.2
Shen, J.3
Maher, C.A.4
Hu, M.5
Kalyana-Sundaram, S.6
Yu, J.7
Chinnaiyan, A.M.8
-
3
-
-
48249140621
-
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
10.1093/bioinformatics/btn305, 2638869, 18599518
-
Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24(15):1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
-
(2008)
Bioinformatics
, vol.24
, Issue.15
, pp. 1729-1730
-
-
Fejes, A.P.1
Robertson, G.2
Bilenky, M.3
Varhol, R.4
Bainbridge, M.5
Jones, S.J.6
-
4
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
10.1038/nmeth.1371, 19844228
-
Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-S32. 10.1038/nmeth.1371, 19844228.
-
(2009)
Nat Methods
, vol.6
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
5
-
-
30444446362
-
Protein-structure prediction by recombination of fragments
-
Bujnicki JM. Protein-structure prediction by recombination of fragments. Chembiochem 2005, 7:19-27.
-
(2005)
Chembiochem
, vol.7
, pp. 19-27
-
-
Bujnicki, J.M.1
-
6
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
10.1186/gb-2008-9-9-r137, 2592715, 18798982
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
-
(2008)
Genome Biol
, vol.9
, Issue.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nussbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
7
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
10.1038/nbt.1505, 2596672, 18978777
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26(11):1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
-
(2008)
Nat Biotechnol
, vol.26
, Issue.11
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
8
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
10.1093/nar/gkn488, 2532738, 18684996
-
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008, 36(16):5221-5231. 10.1093/nar/gkn488, 2532738, 18684996.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.16
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
9
-
-
84870369023
-
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite
-
Wang X, Zhang X. Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol 2011, 5(Suppl 2):S3.
-
(2011)
BMC Syst Biol
, vol.5
, Issue.SUPPL 2
-
-
Wang, X.1
Zhang, X.2
-
10
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
10.1093/bioinformatics/btq033, 2832824, 20110278
-
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
-
(2010)
Bioinformatics
, vol.26
, Issue.6
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
11
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
10.1093/bioinformatics/btp352, 2723002, 19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
12
-
-
79952334870
-
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
-
10.1093/nar/gkq1187, 3045577, 21113027
-
Rye MB, Sætrom P, Drabløs F. A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. Nucleic Acids Res 2011, 39(4):e25-e25. 10.1093/nar/gkq1187, 3045577, 21113027.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.4
-
-
Rye, M.B.1
Sætrom, P.2
Drabløs, F.3
-
13
-
-
84866854032
-
A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells
-
10.1186/1471-2202-13-118, 3519639, 23031785
-
Polman JAE, Welten JE, Bosch DS, de Jonge RT, Balog J, van der Maarel SM, de Kloet ER, Datson NA. A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells. BMC Neurosci 2012, 13:118. 10.1186/1471-2202-13-118, 3519639, 23031785.
-
(2012)
BMC Neurosci
, vol.13
, pp. 118
-
-
Polman, J.A.E.1
Welten, J.E.2
Bosch, D.S.3
de Jonge, R.T.4
Balog, J.5
van der Maarel, S.M.6
de Kloet, E.R.7
Datson, N.A.8
|