-
1
-
-
43549101608
-
Text-mining assisted regulatory annotation
-
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM. (2008). Text-mining assisted regulatory annotation. Genome Biol. 9: R31
-
(2008)
Genome Biol
, vol.9
, pp. R31
-
-
Aerts, S.1
Haeussler, M.2
Van Vooren, S.3
Griffith, O.L.4
Hulpiau, P.5
Jones, S.J.6
Montgomery, S.B.7
Bergman, C.M.8
-
2
-
-
34249079154
-
Networkmotifs: Theory and experimental approaches
-
Alon U. (2007). Networkmotifs: theory and experimental approaches. Nat Rev Genet. 8: 450-461
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
3
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. (2007). Divergence of transcription factor binding sites across related yeast species. Science 317: 815-819
-
(2007)
Science
, vol.317
, pp. 815-819
-
-
Borneman, A.R.1
Gianoulis, T.A.2
Zhang, Z.D.3
Yu, H.4
Rozowsky, J.5
Seringhaus, M.R.6
Wang, L.Y.7
Gerstein, M.8
Snyder, M.9
-
4
-
-
0025753467
-
Genetic interactions among floral homeotic genes of Arabidopsis
-
Bowman JL, Smyth DR, Meyerowitz EM. (1991). Genetic interactions among floral homeotic genes of Arabidopsis. Development 112: 1-20
-
(1991)
Development
, vol.112
, pp. 1-20
-
-
Bowman, J.L.1
Smyth, D.R.2
Meyerowitz, E.M.3
-
5
-
-
84907263788
-
Comparative analysis of regulatory information and circuits across distant species
-
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, et al. (2014). Comparative analysis of regulatory information and circuits across distant species. Nature 512: 453-456
-
(2014)
Nature
, vol.512
, pp. 453-456
-
-
Boyle, A.P.1
Araya, C.L.2
Brdlik, C.3
Cayting, P.4
Cheng, C.5
Cheng, Y.6
Gardner, K.7
Hillier, L.W.8
Janette, J.9
Jiang, L.10
-
6
-
-
0031015315
-
Inflorescence commitment and architecture in arabidopsis
-
Bradley D, Ratcliffe O, Vincent C, Carpenter R, Coen E. (1997). Inflorescence commitment and architecture in Arabidopsis. Science 275: 80-83
-
(1997)
Science
, vol.275
, pp. 80-83
-
-
Bradley, D.1
Ratcliffe, O.2
Vincent, C.3
Carpenter, R.4
Coen, E.5
-
7
-
-
84882340111
-
New genes as drivers of phenotypic evolution
-
Chen S, Krinsky BH, Long M. (2013). New genes as drivers of phenotypic evolution. Nat Rev Genet. 14: 645-660
-
(2013)
Nat Rev Genet
, vol.14
, pp. 645-660
-
-
Chen, S.1
Krinsky, B.H.2
Long, M.3
-
8
-
-
78650385315
-
New genes in drosophila quickly become essential
-
Chen S, Zhang YE, Long M. (2010). New genes in drosophila quickly become essential. Science 330: 1682-1685
-
(2010)
Science
, vol.330
, pp. 1682-1685
-
-
Chen, S.1
Zhang, Y.E.2
Long, M.3
-
9
-
-
74049087026
-
Community detection in graphs
-
Fortunato S. (2010). Community detection in graphs. Phys Rep. 486: 75-174
-
(2010)
Phys Rep
, vol.486
, pp. 75-174
-
-
Fortunato, S.1
-
10
-
-
84865739425
-
Architecture of the human regulatory network derived from encode data
-
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, et al. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature 489: 91-100
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
Kundaje, A.2
Hariharan, M.3
Landt, S.G.4
Yan, K.K.5
Cheng, C.6
Mu, X.J.7
Khurana, E.8
Rozowsky, J.9
Alexander, R.10
-
11
-
-
84899494165
-
Plant and animal stem cells: Similar yet different
-
Heidstra R, Sabatini S. (2014). Plant and animal stem cells: similar yet different. Nat Rev Mol Cell Biol. 15: 301-312
-
(2014)
Nat Rev Mol Cell Biol
, vol.15
, pp. 301-312
-
-
Heidstra, R.1
Sabatini, S.2
-
12
-
-
77950454617
-
The flowering of Arabidopsis flower development
-
Irish VF. (2010). The flowering of Arabidopsis flower development. Plant J. 61: 1014-1028
-
(2010)
Plant J.
, vol.61
, pp. 1014-1028
-
-
Irish, V.F.1
-
13
-
-
84891810676
-
Planttfdb 3.0: A portal for the functional and evolutionary study of plant transcription factors
-
Jin J, Zhang H, Kong L, Gao G, Luo J. (2014). PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 42: D1182-D1187
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D1182-D1187
-
-
Jin, J.1
Zhang, H.2
Kong, L.3
Gao, G.4
Luo, J.5
-
14
-
-
84872540994
-
DNA-binding specificities of human transcription factors
-
Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, et al. (2013). DNA-binding specificities of human transcription factors. Cell 152: 327-339
-
(2013)
Cell
, vol.152
, pp. 327-339
-
-
Jolma, A.1
Yan, J.2
Whitington, T.3
Toivonen, J.4
Nitta, K.R.5
Rastas, P.6
Morgunova, E.7
Enge, M.8
Taipale, M.9
Wei, G.10
-
15
-
-
69249127529
-
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
-
Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, Babu MM. (2009). Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol. 5: 294
-
(2009)
Mol Syst Biol
, vol.5
, pp. 294
-
-
Jothi, R.1
Balaji, S.2
Wuster, A.3
Grochow, J.A.4
Gsponer, J.5
Przytycka, T.M.6
Aravind, L.7
Babu, M.M.8
-
16
-
-
77958506746
-
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: A timeline of loss, gain, expansion, and correlation with complexit
-
Lang D, Weiche B, Timmerhaus G, Richardt S, Riaño-Pachón DM, Correa LGG, Reski R, Mueller-Roeber B, Rensing SA. (2010). Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503
-
(2010)
Genome Biol Evol
, vol.2
, pp. 488-503
-
-
Lang, D.1
Weiche, B.2
Timmerhaus, G.3
Richardt, S.4
Riaño-Pachón, D.M.5
Correa, L.G.G.6
Reski, R.7
Mueller-Roeber, B.8
Rensing, S.A.9
-
17
-
-
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, 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
-
18
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
19
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan S, Alon U. (2003). Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA. 100: 11980-11985
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
20
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. (2002). Network motifs: simple building blocks of complex networks. Science 298: 824-827
-
(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
-
21
-
-
84866361701
-
Circuitry and dynamics of human transcription factor regulatory networks
-
Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. (2012). Circuitry and dynamics of human transcription factor regulatory networks. Cell 150: 1274-1286
-
(2012)
Cell
, vol.150
, pp. 1274-1286
-
-
Neph, S.1
Stergachis, A.B.2
Reynolds, A.3
Sandstrom, R.4
Borenstein, E.5
Stamatoyannopoulos, J.A.6
-
22
-
-
67650601963
-
Evolution of transcriptional regulatory circuits in bacteria
-
Perez JC, Groisman EA. (2009). Evolution of transcriptional regulatory circuits in bacteria. Cell 138: 233-244
-
(2009)
Cell
, vol.138
, pp. 233-244
-
-
Perez, J.C.1
Groisman, E.A.2
-
23
-
-
40149098889
-
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
-
Price MN, Dehal PS, Arkin AP. (2008). Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol. 9: R4
-
(2008)
Genome Biol
, vol.9
, pp. R4
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
24
-
-
0036180002
-
The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons
-
Rajewsky N, Socci ND, Zapotocky M, Siggia ED. (2002). The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res. 12: 298-308
-
(2002)
Genome Res
, vol.12
, pp. 298-308
-
-
Rajewsky, N.1
Socci, N.D.2
Zapotocky, M.3
Siggia, E.D.4
-
25
-
-
0034671865
-
Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes
-
Riechmann JL, Heard J, Martin G, Reuber L. (2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105-2110
-
(2000)
Science
, vol.290
, pp. 2105-2110
-
-
Riechmann, J.L.1
Heard, J.2
Martin, G.3
Reuber, L.4
-
26
-
-
77953062527
-
Fivevertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S. (2010). Fivevertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: 1036-1040
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
MacKay, S.10
-
27
-
-
0036578795
-
Network motifs in the transcriptional regulation network of escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U. (2002). Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 31: 64-68
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
28
-
-
79551521494
-
Measuring the evolutionary rewiring of biological networks
-
Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. (2011). Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol. 7: e1001050
-
(2011)
Plos Comput Biol
, vol.7
, pp. e1001050
-
-
Shou, C.1
Bhardwaj, N.2
Lam, H.Y.3
Yan, K.K.4
Kim, P.M.5
Snyder, M.6
Gerstein, M.B.7
-
29
-
-
84863010950
-
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
-
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. (2012). Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol. 30: 159-164
-
(2012)
Nat Biotechnol
, vol.30
, pp. 159-164
-
-
Wang, X.1
Wei, X.2
Thijssen, B.3
Das, J.4
Lipkin, S.M.5
Yu, H.6
-
30
-
-
0028142020
-
The ABCs of floral homeotic genes
-
Weigel D, Meyerowitz EM. (1994). The ABCs of floral homeotic genes. Cell 78: 203-209
-
(1994)
Cell
, vol.78
, pp. 203-209
-
-
Weigel, D.1
Meyerowitz, E.M.2
-
31
-
-
84907413210
-
Determination and inference of eukaryotic transcription factor sequence specificity
-
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, et al. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158: 1431-1443
-
(2014)
Cell
, vol.158
, pp. 1431-1443
-
-
Weirauch, M.T.1
Yang, A.2
Albu, M.3
Cote, A.G.4
Montenegro-Montero, A.5
Drewe, P.6
Najafabadi, H.S.7
Lambert, S.A.8
Mann, I.9
Cook, K.10
-
32
-
-
78651339097
-
Agris: The arabidopsis gene regulatory information server, an updat
-
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E. (2011). AGRIS: the Arabidopsis gene regulatory information server, an update. Nucleic Acids Res. 39: D1118-D1122
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D1118-D1122
-
-
Yilmaz, A.1
Mejia-Guerra, M.K.2
Kurz, K.3
Liang, X.4
Welch, L.5
Grotewold, E.6
-
33
-
-
78651337578
-
PlantTFDB 2.0: Update and improvement of the comprehensive plant transcription factor database
-
Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J. (2011). PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res. 39: D1114-D1117
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D1114-D1117
-
-
Zhang, H.1
Jin, J.2
Tang, L.3
Zhao, Y.4
Gu, X.5
Gao, G.6
Luo, J.7
-
34
-
-
80055025720
-
Accelerated recruitment of new brain development genes into the human genome
-
Zhang YE, Landback P, Vibranovski MD, Long M. (2011). Accelerated recruitment of new brain development genes into the human genome. PLoS Biol. 9: e1001179
-
(2011)
Plos Biol
, vol.9
, pp. e1001179
-
-
Zhang, Y.E.1
Landback, P.2
Vibranovski, M.D.3
Long, M.4
|