-
1
-
-
70450265377
-
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
-
10.1186/1471-2105-10-345, 2771022, 19857274
-
Wang J. BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. BMC bioinformatics 2009, 10:345. 10.1186/1471-2105-10-345, 2771022, 19857274.
-
(2009)
BMC bioinformatics
, vol.10
, pp. 345
-
-
Wang, J.1
-
2
-
-
0003611509
-
Bayesian Learning for Neural Networks
-
University of Toronto
-
Neal RM. Bayesian Learning for Neural Networks. PhD thesis 1994, University of Toronto.
-
(1994)
PhD thesis
-
-
Neal, R.M.1
-
3
-
-
0000673452
-
Bayesian Regularization and Pruning Using a Laplace Prior
-
Williams PM. Bayesian Regularization and Pruning Using a Laplace Prior. Neural Computation 1995, 7(1):117-143.
-
(1995)
Neural Computation
, vol.7
, Issue.1
, pp. 117-143
-
-
Williams, P.M.1
-
4
-
-
0003748256
-
Bayesian Methods for Adaptive Models
-
California Institute of Technology
-
Mackay D. Bayesian Methods for Adaptive Models. PhD thesis 1991, California Institute of Technology.
-
(1991)
PhD thesis
-
-
Mackay, D.1
-
5
-
-
0000597408
-
Comparison of Approximate Methods for Handling Hyperparameters
-
Mackay DJC. Comparison of Approximate Methods for Handling Hyperparameters. Neural Computation 1999, 11(5):1035-1068.
-
(1999)
Neural Computation
, vol.11
, Issue.5
, pp. 1035-1068
-
-
Mackay, D.J.C.1
-
6
-
-
40649107189
-
Discovering gapped binding sites of yeast transcription factors
-
10.1073/pnas.0712188105, 2268170, 18272477
-
Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH. Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci USA 2008, 105(7):2527-2532. 10.1073/pnas.0712188105, 2268170, 18272477.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.7
, pp. 2527-2532
-
-
Chen, C.Y.1
Tsai, H.K.2
Hsu, C.M.3
May Chen, M.J.4
Hung, H.G.5
Huang, G.T.6
Li, W.H.7
-
7
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
10.1038/nature02800, 15343339
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431(7004):99-104. 10.1038/nature02800, 15343339.
-
(2004)
Nature
, vol.431
, Issue.7004
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
-
8
-
-
33748191291
-
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
-
10.1093/bioinformatics/btl223, 16873464
-
Foat BC, Morozov AV, Bussemaker HJ. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 2006, 22(14):e141-149. 10.1093/bioinformatics/btl223, 16873464.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Foat, B.C.1
Morozov, A.V.2
Bussemaker, H.J.3
-
9
-
-
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
-
10
-
-
39449088572
-
Genome-wide approaches to studying chromatin modifications
-
10.1038/nrg2270, 18250624
-
Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nature reviews 2008, 9(3):179-191. 10.1038/nrg2270, 18250624.
-
(2008)
Nature reviews
, vol.9
, Issue.3
, pp. 179-191
-
-
Schones, D.E.1
Zhao, K.2
-
11
-
-
1242316281
-
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
10.1016/j.ygeno.2003.11.004, 14986705
-
Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
-
(2004)
Genomics
, vol.83
, Issue.3
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
12
-
-
33747069931
-
High-resolution computational models of genome binding events
-
10.1038/nbt1233, 16900145
-
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, et al. High-resolution computational models of genome binding events. Nature biotechnology 2006, 24(8):963-970. 10.1038/nbt1233, 16900145.
-
(2006)
Nature biotechnology
, vol.24
, Issue.8
, pp. 963-970
-
-
Qi, Y.1
Rolfe, A.2
MacIsaac, K.D.3
Gerber, G.K.4
Pokholok, D.5
Zeitlinger, J.6
Danford, T.7
Dowell, R.D.8
Fraenkel, E.9
Jaakkola, T.S.10
-
13
-
-
34250658998
-
Bayesian methods in bioinformatics and computational systems biology
-
10.1093/bib/bbm007, 17430978
-
Wilkinson DJ. Bayesian methods in bioinformatics and computational systems biology. Briefings in bioinformatics 2007, 8(2):109-116. 10.1093/bib/bbm007, 17430978.
-
(2007)
Briefings in bioinformatics
, vol.8
, Issue.2
, pp. 109-116
-
-
Wilkinson, D.J.1
-
14
-
-
0000255539
-
Fast exact multiplication by the Hessian
-
Pearlmutter BA. Fast exact multiplication by the Hessian. Neural Computation 1994, 6(1).
-
(1994)
Neural Computation
, vol.6
, Issue.1
-
-
Pearlmutter, B.A.1
-
15
-
-
33747871502
-
Method for identifying transcription factor binding sites in yeast
-
10.1093/bioinformatics/btl160, 16644789
-
Tsai HK, Huang GT, Chou MY, Lu HH, Li WH. Method for identifying transcription factor binding sites in yeast. Bioinformatics 2006, 22(14):1675-1681. 10.1093/bioinformatics/btl160, 16644789.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
, pp. 1675-1681
-
-
Tsai, H.K.1
Huang, G.T.2
Chou, M.Y.3
Lu, H.H.4
Li, W.H.5
-
16
-
-
0031858914
-
SGD: Saccharomyces Genome Database
-
10.1093/nar/26.1.73, 147204, 9399804
-
Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, et al. SGD: Saccharomyces Genome Database. Nucleic Acids Res 1998, 26(1):73-79. 10.1093/nar/26.1.73, 147204, 9399804.
-
(1998)
Nucleic Acids Res
, vol.26
, Issue.1
, pp. 73-79
-
-
Cherry, J.M.1
Adler, C.2
Ball, C.3
Chervitz, S.A.4
Dwight, S.S.5
Hester, E.T.6
Jia, Y.7
Juvik, G.8
Roe, T.9
Schroeder, M.10
-
17
-
-
0032518996
-
Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity
-
10.1101/gad.12.4.586, 316529, 9472026
-
Gorner W, Durchschlag E, Martinez-Pastor MT, Estruch F, Ammerer G, Hamilton B, Ruis H, Schuller C. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev 1998, 12(4):586-597. 10.1101/gad.12.4.586, 316529, 9472026.
-
(1998)
Genes Dev
, vol.12
, Issue.4
, pp. 586-597
-
-
Gorner, W.1
Durchschlag, E.2
Martinez-Pastor, M.T.3
Estruch, F.4
Ammerer, G.5
Hamilton, B.6
Ruis, H.7
Schuller, C.8
-
18
-
-
0033523113
-
Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast
-
10.1074/jbc.274.23.16040, 10347154
-
Lee J, Godon C, Lagniel G, Spector D, Garin J, Labarre J, Toledano MB. Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. J Biol Chem 1999, 274(23):16040-16046. 10.1074/jbc.274.23.16040, 10347154.
-
(1999)
J Biol Chem
, vol.274
, Issue.23
, pp. 16040-16046
-
-
Lee, J.1
Godon, C.2
Lagniel, G.3
Spector, D.4
Garin, J.5
Labarre, J.6
Toledano, M.B.7
-
19
-
-
0033916138
-
The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress
-
14923, 10888672
-
Raitt DC, Johnson AL, Erkine AM, Makino K, Morgan B, Gross DS, Johnston LH. The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Mol Biol Cell 2000, 11(7):2335-2347. 14923, 10888672.
-
(2000)
Mol Biol Cell
, vol.11
, Issue.7
, pp. 2335-2347
-
-
Raitt, D.C.1
Johnson, A.L.2
Erkine, A.M.3
Makino, K.4
Morgan, B.5
Gross, D.S.6
Johnston, L.H.7
-
20
-
-
0028898763
-
Multiple elements and auto-repression regulate Rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae
-
1206446, 7768429
-
Deckert J, Perini R, Balasubramanian B, Zitomer RS. Multiple elements and auto-repression regulate Rox1, a repressor of hypoxic genes in Saccharomyces cerevisiae. Genetics 1995, 139(3):1149-1158. 1206446, 7768429.
-
(1995)
Genetics
, vol.139
, Issue.3
, pp. 1149-1158
-
-
Deckert, J.1
Perini, R.2
Balasubramanian, B.3
Zitomer, R.S.4
-
21
-
-
0030868697
-
Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family
-
232502, 9343412
-
Mai B, Breeden L. Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family. Mol Cell Biol 1997, 17(11):6491-6501. 232502, 9343412.
-
(1997)
Mol Cell Biol
, vol.17
, Issue.11
, pp. 6491-6501
-
-
Mai, B.1
Breeden, L.2
|