-
1
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
10.1038/ng881, 11967538
-
Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 31:64-68. 10.1038/ng881, 11967538.
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
2
-
-
0037174670
-
Network motifs: simple building blocks of complex networks
-
10.1126/science.298.5594.824, 12399590
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827. 10.1126/science.298.5594.824, 12399590.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
3
-
-
34249079154
-
Network motifs: theory and experimental approaches
-
10.1038/nrg2102, 17510665
-
Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet 2007, 8:450-461. 10.1038/nrg2102, 17510665.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
4
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
10.1126/science.1089167, 15001784
-
Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. Superfamilies of evolved and designed networks. Science 2004, 303:1538-1542. 10.1126/science.1089167, 15001784.
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
Levitt, R.4
Shen-Orr, S.5
Ayzenshtat, I.6
Sheffer, M.7
Alon, U.8
-
5
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
10.1073/pnas.2133841100, 218699, 14530388
-
Mangan S, Alon U. Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 2003, 100:11980-11985. 10.1073/pnas.2133841100, 218699, 14530388.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
6
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
10.1126/science.1075090, 12399584
-
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 JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804. 10.1126/science.1075090, 12399584.
-
(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
Young, R.A.21
more..
-
7
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
10.1016/j.cell.2005.08.020, 3006442, 16153702
-
Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122:947-956. 10.1016/j.cell.2005.08.020, 3006442, 16153702.
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
Lee, T.I.2
Cole, M.F.3
Johnstone, S.E.4
Levine, S.S.5
Zucker, J.P.6
Guenther, M.G.7
Kumar, R.M.8
Murray, H.L.9
Jenner, R.G.10
Gifford, D.K.11
Melton, D.A.12
Jaenisch, R.13
Young, R.A.14
-
8
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
10.1126/science.1095486, 14988544
-
Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science 2004, 303:1311-1312. 10.1126/science.1095486, 14988544.
-
(2004)
Science
, vol.303
, pp. 1311-1312
-
-
Odom, D.T.1
Zizlsperger, N.2
Gordon, D.B.3
Bell, G.W.4
Rinaldi, N.J.5
Murray, H.L.6
Volkert, T.L.7
Schreiber, J.8
Rolfe, P.A.9
Gifford, D.K.10
Fraenkel, E.11
Bell, G.I.12
Young, R.A.13
-
9
-
-
32044462728
-
The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
-
Mangan S, Itzkovitz S, Zaslaver A, Alon U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 2005, 356:1073-1081.
-
(2005)
J Mol Biol
, vol.356
, pp. 1073-1081
-
-
Mangan, S.1
Itzkovitz, S.2
Zaslaver, A.3
Alon, U.4
-
10
-
-
33746428728
-
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
-
2005.0006
-
Kalir S, Mangan S, Alon U. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 2005, 1. 2005.0006.
-
(2005)
Mol Syst Biol
, vol.1
-
-
Kalir, S.1
Mangan, S.2
Alon, U.3
-
11
-
-
42749099345
-
Subgraphs in random networks
-
Itzkovitz S, Milo R, Kashtan N, Ziv G, Alon U. Subgraphs in random networks. Phys Rev E 2003, 68:026127.
-
(2003)
Phys Rev E
, vol.68
, pp. 026127
-
-
Itzkovitz, S.1
Milo, R.2
Kashtan, N.3
Ziv, G.4
Alon, U.5
-
12
-
-
34547555796
-
Global and local architecture of the mammalian microRNA-transcription factor regulatory network
-
10.1371/journal.pcbi.0030131, 1914371, 17630826
-
Shalgi R, Lieber D, Oren M, Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol 2007, 3:e131. 10.1371/journal.pcbi.0030131, 1914371, 17630826.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Shalgi, R.1
Lieber, D.2
Oren, M.3
Pilpel, Y.4
-
13
-
-
58149187893
-
The GOA database in 2009 - an integrated Gene Ontology Annotation resource
-
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Res 2009, (37 Database):D396-D403.
-
(2009)
Nucleic Acids Res
, Issue.37 DATABASE
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
14
-
-
0036428761
-
Negative autoregulation speeds the response times of transcription networks
-
10.1016/S0022-2836(02)00994-4, 12417193
-
Rosenfeld N, Elowitz MB, Alon U. Negative autoregulation speeds the response times of transcription networks. J Mol Biol 2002, 323:785-793. 10.1016/S0022-2836(02)00994-4, 12417193.
-
(2002)
J Mol Biol
, vol.323
, pp. 785-793
-
-
Rosenfeld, N.1
Elowitz, M.B.2
Alon, U.3
-
15
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
10.1038/35014651, 10850721
-
Becskei A, Serrano L. Engineering stability in gene networks by autoregulation. Nature 2000, 405:590-593. 10.1038/35014651, 10850721.
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
16
-
-
34047174559
-
A module of negative feedback regulators defines growth factor signaling
-
10.1038/ng1987, 17322878
-
Amit I, Citri A, Shay T, Lu Y, Katz M, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E, Yarden Y. A module of negative feedback regulators defines growth factor signaling. Nat Genet 2007, 39:503-512. 10.1038/ng1987, 17322878.
-
(2007)
Nat Genet
, vol.39
, pp. 503-512
-
-
Amit, I.1
Citri, A.2
Shay, T.3
Lu, Y.4
Katz, M.5
Zhang, F.6
Tarcic, G.7
Siwak, D.8
Lahad, J.9
Jacob-Hirsch, J.10
Amariglio, N.11
Vaisman, N.12
Segal, E.13
Rechavi, G.14
Alon, U.15
Mills, G.B.16
Domany, E.17
Yarden, Y.18
-
17
-
-
10344251533
-
Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network
-
10.1073/pnas.0407670101, 534610, 15572454
-
Iwama H, Gojobori T. Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network. Proc Natl Acad Sci USA 2004, 101:17156-17161. 10.1073/pnas.0407670101, 534610, 15572454.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 17156-17161
-
-
Iwama, H.1
Gojobori, T.2
-
18
-
-
40949117985
-
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences
-
Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T. ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. BMC Bioinform 2008, 9:112.
-
(2008)
BMC Bioinform
, vol.9
, pp. 112
-
-
Iwama, H.1
Hori, Y.2
Matsumoto, K.3
Murao, K.4
Ishida, T.5
-
19
-
-
79958827131
-
Alignments and conserved TFBSs for 5,169 human-mouse orthologs within 8-kb upstream sequences
-
Iwama H, Murao K, Imachi H, Ishida T. Alignments and conserved TFBSs for 5,169 human-mouse orthologs within 8-kb upstream sequences. , http://genet.med.kagawa-u.ac.jp/pub/HMO_5169/List.htm
-
-
-
Iwama, H.1
Murao, K.2
Imachi, H.3
Ishida, T.4
-
20
-
-
33846057724
-
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, (35 Database):D61-D65.
-
(2007)
Nucleic Acids Res
, Issue.35 DATABASE
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
21
-
-
46049087782
-
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
-
10.1093/bib/bbn016, 18436575
-
Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform 2008, 9:326-332. 10.1093/bib/bbn016, 18436575.
-
(2008)
Brief Bioinform
, vol.9
, pp. 326-332
-
-
Wingender, E.1
-
23
-
-
0041853625
-
MATCH: a tool for searching transcription factor binding sites in DNA sequences
-
10.1093/nar/gkg585, 169193, 12824369
-
Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31:3576-3579. 10.1093/nar/gkg585, 169193, 12824369.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3576-3579
-
-
Kel, A.E.1
Gössling, E.2
Reuter, I.3
Cheremushkin, E.4
Kel-Margoulis, O.V.5
Wingender, E.6
|