-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402
-
(1997)
Nucl Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK (2003) Computational discovery of gene modules and regulatory networks. Nat Biotech 21:1337-1342
-
(2003)
Nat Biotech
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaakkola, T.S.9
Young, R.A.10
Gifford, D.K.11
-
3
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117:185-198
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
4
-
-
0030979616
-
Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism
-
Blaiseau PL, Isnard AD, Surdin-Kerjan Y, Thomas D (1997) Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism. Mol Cell Biol 17:3640-3648
-
(1997)
Mol Cell Biol
, vol.17
, pp. 3640-3648
-
-
Blaiseau, P.L.1
Isnard, A.D.2
Surdin-Kerjan, Y.3
Thomas, D.4
-
5
-
-
0003516147
-
-
Cambridge, UK: Cambridge University Press
-
Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press
-
(1998)
Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
6
-
-
33846521053
-
Reconstructing dynamic regulatory maps
-
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3:74
-
(2007)
Mol Syst Biol
, vol.3
, pp. 74
-
-
Ernst, J.1
Vainas, O.2
Harbison, C.T.3
Simon, I.4
Bar-Joseph, Z.5
-
7
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucl Acids Res 34: D247-D251
-
(2006)
Nucl Acids Res
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.L.12
Bateman, A.13
-
8
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao F, Foat B, Bussemaker H (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5: 31
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.2
Bussemaker, H.3
-
9
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne J-B, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104
-
(2004)
Nature
, vol.431
, 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
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gifford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
10
-
-
0035883741
-
Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: Implications for regulating the cell cycle and differentiation
-
Hollenhorst PC, Pietz G, Fox CA (2001) Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation. Genes Dev 15:2445-2456
-
(2001)
Genes Dev
, vol.15
, pp. 2445-2456
-
-
Hollenhorst, P.C.1
Pietz, G.2
Fox, C.A.3
-
11
-
-
0036894656
-
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
-
Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16: 3017-3033
-
(2002)
Genes Dev
, vol.16
, pp. 3017-3033
-
-
Horak, C.E.1
Luscombe, N.M.2
Qian, J.3
Bertone, P.4
Piccirrillo, S.5
Gerstein, M.6
Snyder, M.7
-
12
-
-
34247629588
-
Genetic reconstruction of a functional transcriptional regulatory network
-
Hu Z, Killion PJ, Iyer VR (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687
-
(2007)
Nat Genet
, vol.39
, pp. 683-687
-
-
Hu, Z.1
Killion, P.J.2
Iyer, V.R.3
-
13
-
-
15044353444
-
Transcription control reprogramming in genetic backup circuits
-
Kafri R, Bar-Even A, Pilpel Y (2005) Transcription control reprogramming in genetic backup circuits. Nat Genet 37: 295-299
-
(2005)
Nat Genet
, vol.37
, pp. 295-299
-
-
Kafri, R.1
Bar-Even, A.2
Pilpel, Y.3
-
14
-
-
33846659953
-
Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters
-
Kwon Y-S, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan J-B, Duan L, Glass CK, Rosenfeld MG, Fu X-D (2007) Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci 104: 4852-4857
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 4852-4857
-
-
Kwon, Y.-S.1
Garcia-Bassets, I.2
Hutt, K.R.3
Cheng, C.S.4
Jin, M.5
Liu, D.6
Benner, C.7
Wang, D.8
Ye, Z.9
Bibikova, M.10
Fan, J.-B.11
Duan, L.12
Glass, C.K.13
Rosenfeld, M.G.14
Fu, X.-D.15
-
15
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne J-B, Volkert TL, Fraenkel E, Gifford DK et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.-B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
more..
-
16
-
-
0345824737
-
Network component analysis: Reconstruction of regulatory signals in biological systems
-
Liao JC, Boscolo R, Yang Y-L, Tran LM, Sabatti C, Roychowdhury VP (2003) Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 100: 15522-15527
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15522-15527
-
-
Liao, J.C.1
Boscolo, R.2
Yang, Y.-L.3
Tran, L.M.4
Sabatti, C.5
Roychowdhury, V.P.6
-
17
-
-
47249142028
-
Glucocorticoid receptor-dependent gene regulatory networks
-
Phuc Le P, Friedman JR, Schug J, Brestelli JE, Parker JB, Bochkis IM, Kaestner KH (2005) Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet 1: e16
-
(2005)
PLoS Genet
, vol.1
-
-
Phuc, L.P.1
Friedman, J.R.2
Schug, J.3
Brestelli, J.E.4
Parker, J.B.5
Bochkis, I.M.6
Kaestner, K.H.7
-
18
-
-
33847064282
-
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
-
Reguly T, Breitkreutz A, Boucher L, Breitkreutz B-J, Hon G, Myers C, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya O, Ideker T, Dolinski K, Batada N, Tyers M (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 5: 11
-
(2006)
J Biol
, vol.5
, pp. 11
-
-
Reguly, T.1
Breitkreutz, A.2
Boucher, L.3
Breitkreutz, B.-J.4
Hon, G.5
Myers, C.6
Parsons, A.7
Friesen, H.8
Oughtred, R.9
Tong, A.10
Stark, C.11
Ho, Y.12
Botstein, D.13
Andrews, B.14
Boone, C.15
Troyanskya, O.16
Ideker, T.17
Dolinski, K.18
Batada, N.19
Tyers, M.20
more..
-
19
-
-
37049010139
-
Membrane-active compounds activate the transcription factors Pdr1 and Pdr3 connecting pleiotropic drug resistance and membrane lipid homeostasis in Saccharomyces cerevisiae
-
Schuller C, Mamnun YM, Wolfger H, Rockwell N, Thorner J, Kuchler K (2007) Membrane-active compounds activate the transcription factors Pdr1 and Pdr3 connecting pleiotropic drug resistance and membrane lipid homeostasis in Saccharomyces cerevisiae. Mol Biol Cell 18: 4932-4944
-
(2007)
Mol Biol Cell
, vol.18
, pp. 4932-4944
-
-
Schuller, C.1
Mamnun, Y.M.2
Wolfger, H.3
Rockwell, N.4
Thorner, J.5
Kuchler, K.6
-
20
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucl Acids Res 34: D535-D539
-
(2006)
Nucl Acids Res
, vol.34
-
-
Stark, C.1
Breitkreutz, B.-J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
21
-
-
33646748283
-
A systems approach to mapping DNA damage response pathways
-
Workman CT, Mak HC, McCuine S, Tagne J-B, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T (2006) A systems approach to mapping DNA damage response pathways. Science 312: 1054-1059
-
(2006)
Science
, vol.312
, pp. 1054-1059
-
-
Workman, C.T.1
Mak, H.C.2
McCuine, S.3
Tagne, J.-B.4
Agarwal, M.5
Ozier, O.6
Begley, T.J.7
Samson, L.D.8
Ideker, T.9
-
22
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434: 338-345
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
23
-
-
33847057887
-
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells
-
Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell 24: 593-602
-
(2006)
Mol Cell
, vol.24
, pp. 593-602
-
-
Yang, A.1
Zhu, Z.2
Kapranov, P.3
McKeon, F.4
Church, G.M.5
Gingeras, T.R.6
Struhl, K.7
-
24
-
-
27744521520
-
Validation and refinement of gene-regulatory pathways on a network of physical interactions
-
Yeang C-H, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T (2005) Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol 6: R62
-
(2005)
Genome Biol
, vol.6
-
-
Yeang, C.-H.1
Mak, H.C.2
McCuine, S.3
Workman, C.4
Jaakkola, T.5
Ideker, T.6
|