-
1
-
-
78651339097
-
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
-
3013708, 21059685
-
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E. AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Research 2011, 39(suppl 1):D1118-D1122. 3013708, 21059685.
-
(2011)
Nucleic Acids Research
, vol.39
, Issue.SUPPL. 1
-
-
Yilmaz, A.1
Mejia-Guerra, M.K.2
Kurz, K.3
Liang, X.4
Welch, L.5
Grotewold, E.6
-
2
-
-
78651335916
-
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
-
3013816, 20965965
-
Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Research 2010, 39(suppl 1):D118-D123. 3013816, 20965965.
-
(2010)
Nucleic Acids Research
, vol.39
, Issue.SUPPL. 1
-
-
Gallo, S.M.1
Gerrard, D.T.2
Miner, D.3
Simich, M.4
Des Soye, B.5
Bergman, C.M.6
Halfon, M.S.7
-
3
-
-
38549087902
-
ORegAnno: an open-access community-driven resource for regulatory annotation
-
2239002, 18006570
-
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJM, Consortium TORA. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research 2008, 36(suppl 1):D107-D113. 2239002, 18006570.
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Griffith, O.L.1
Montgomery, S.B.2
Bernier, B.3
Chu, B.4
Kasaian, K.5
Aerts, S.6
Mahony, S.7
Sleumer, M.C.8
Bilenky, M.9
Haeussler, M.10
Griffith, M.11
Gallo, S.M.12
Giardine, B.13
Hooghe, B.14
Van Loo, P.15
Blanco, E.16
Ticoll, A.17
Lithwick, S.18
Portales-Casamar, E.19
Donaldson, I.J.20
Robertson, G.21
Wadelius, C.22
De Bleser, P.23
Vlieghe, D.24
Halfon, M.S.25
Wasserman, W.26
Hardison, R.27
Bergman, C.M.28
Jones, S.J.M.29
Consortium, T.O.R.A.30
more..
-
4
-
-
18444387984
-
Transcription Regulatory Regions Database (TRRD): its status in 2002
-
10.1093/nar/30.1.312, 99088, 11752324
-
Kolchanov NA, Ignatieva EV, Ananko EA, Podkolodnaya OA, Stepanenko IL, Merkulova TI, Pozdnyakov MA, Podkolodny NL, Naumochkin AN, Romashchenko AG. Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic acids research 2002, 30:312-317. 10.1093/nar/30.1.312, 99088, 11752324., http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99088/
-
(2002)
Nucleic acids research
, vol.30
, pp. 312-317
-
-
Kolchanov, N.A.1
Ignatieva, E.V.2
Ananko, E.A.3
Podkolodnaya, O.A.4
Stepanenko, I.L.5
Merkulova, T.I.6
Pozdnyakov, M.A.7
Podkolodny, N.L.8
Naumochkin, A.N.9
Romashchenko, A.G.10
-
5
-
-
58349110961
-
MotifMap: a human genome-wide map of candidate regulatory motif sites
-
10.1093/bioinformatics/btn605, 2732295, 19017655
-
Xie X, Rigor P, Baldi P. MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 2009, 25(2):167-174. 10.1093/bioinformatics/btn605, 2732295, 19017655.
-
(2009)
Bioinformatics
, vol.25
, Issue.2
, pp. 167-174
-
-
Xie, X.1
Rigor, P.2
Baldi, P.3
-
6
-
-
75549083247
-
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
-
Database
-
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic acids research 2010, (38 Database):D105-110., http://dx.doi.org/10.1093/nar/gkp950
-
(2010)
Nucleic acids research
, Issue.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
7
-
-
0037208166
-
TRANSFAC: transcriptional regulation, from patterns to profiles
-
10.1093/nar/gkg108, 165555, 12520026
-
Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DUU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic acids research 2003, 31:374-378. 10.1093/nar/gkg108, 165555, 12520026., http://dx.doi.org/10.1093/nar/gkg108
-
(2003)
Nucleic acids research
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gössling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.U.U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Münch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
8
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
10.1101/gr.3715005, 1182216, 16024819
-
Siepel A, Bejerano G, Pedersen J, Hinrichs A, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier L, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome research 2005, 15(8):1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
-
(2005)
Genome research
, vol.15
, Issue.8
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.3
Hinrichs, A.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.9
Richards, S.10
-
9
-
-
74949092081
-
Detection of nonneutral substitution rates on mammalian phylogenies
-
10.1101/gr.097857.109, 2798823, 19858363
-
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Research 2010, 20:110-121. 10.1101/gr.097857.109, 2798823, 19858363., http://dx.doi.org/10.1101/gr.097857.109
-
(2010)
Genome Research
, vol.20
, pp. 110-121
-
-
Pollard, K.S.1
Hubisz, M.J.2
Rosenbloom, K.R.3
Siepel, A.4
-
10
-
-
33744507263
-
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
-
10.1186/gb-2005-6-12-r104, 1414082, 16356267
-
Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biology 2005, 6(12):R104. 10.1186/gb-2005-6-12-r104, 1414082, 16356267.
-
(2005)
Genome Biology
, vol.6
, Issue.12
-
-
Ettwiller, L.1
Paten, B.2
Souren, M.3
Loosli, F.4
Wittbrodt, J.5
Birney, E.6
-
11
-
-
22344437987
-
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach
-
10.1186/gb-2005-6-2-r18, 551538, 15693947
-
Elemento O, Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome biology 2005, 6(2):R18. 10.1186/gb-2005-6-2-r18, 551538, 15693947.
-
(2005)
Genome biology
, vol.6
, Issue.2
-
-
Elemento, O.1
Tavazoie, S.2
-
12
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
10.1038/nature03441, 2923337, 15735639
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 2005, 434(7031):338-345. 10.1038/nature03441, 2923337, 15735639.
-
(2005)
Nature
, vol.434
, Issue.7031
, 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
-
13
-
-
36049018312
-
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
-
10.1038/nature06340, 2474711, 17994088, Harvard FlyBase curators, Berkeley Drosophila Genome Project
-
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby GG, Brennecke J, , , Hodges E, Hinrichs AS, Caspi A, Paten B, Park SWW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent JJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Harvard FlyBase curators, Berkeley Drosophila Genome Project Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450(7167):219-232. 10.1038/nature06340, 2474711, 17994088, Harvard FlyBase curators, Berkeley Drosophila Genome Project.
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 219-232
-
-
Stark, A.1
Lin, M.F.2
Kheradpour, P.3
Pedersen, J.S.4
Parts, L.5
Carlson, J.W.6
Crosby, M.A.7
Rasmussen, M.D.8
Roy, S.9
Deoras, A.N.10
Ruby, G.G.11
Brennecke, J.12
Hodges, E.13
Hinrichs, A.S.14
Caspi, A.15
Paten, B.16
Park, S.W.W.17
Han, M.V.18
Maeder, M.L.19
Polansky, B.J.20
Robson, B.E.21
Aerts, S.22
van Helden, J.23
Hassan, B.24
Gilbert, D.G.25
Eastman, D.A.26
Rice, M.27
Weir, M.28
Hahn, M.W.29
Park, Y.30
Dewey, C.N.31
Pachter, L.32
Kent, J.J.33
Haussler, D.34
Lai, E.C.35
Bartel, D.P.36
Hannon, G.J.37
Kaufman, T.C.38
Eisen, M.B.39
Clark, A.G.40
Smith, D.41
Celniker, S.E.42
Gelbart, W.M.43
Kellis, M.44
more..
-
14
-
-
34249848791
-
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
-
Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proceedings of the National Academy of Sciences 2007, 104(17):7145-7150.
-
(2007)
Proceedings of the National Academy of Sciences
, vol.104
, Issue.17
, pp. 7145-7150
-
-
Xie, X.1
Mikkelsen, T.S.2
Gnirke, A.3
Lindblad-Toh, K.4
Kellis, M.5
Lander, E.S.6
-
15
-
-
75549089967
-
The UCSC Genome Browser database: update 2010
-
Database
-
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic acids research 2010, (38 Database):D613-619., http://dx.doi.org/10.1093/nar/gkp939
-
(2010)
Nucleic acids research
, Issue.38
-
-
Rhead, B.1
Karolchik, D.2
Kuhn, R.M.3
Hinrichs, A.S.4
Zweig, A.S.5
Fujita, P.A.6
Diekhans, M.7
Smith, K.E.8
Rosenbloom, K.R.9
Raney, B.J.10
Pohl, A.11
Pheasant, M.12
Meyer, L.R.13
Learned, K.14
Hsu, F.15
Hillman-Jackson, J.16
Harte, R.A.17
Giardine, B.18
Dreszer, T.R.19
Clawson, H.20
Barber, G.P.21
Haussler, D.22
Kent, W.J.23
more..
-
16
-
-
1542748076
-
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
-
10.1101/gr.1933104, 383317, 15060014
-
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner. Genome Research 2004, 14(4):708-715. 10.1101/gr.1933104, 383317, 15060014.
-
(2004)
Genome Research
, vol.14
, Issue.4
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
Elnitski, L.4
Smit, A.F.A.5
Roskin, K.M.6
Baertsch, R.7
Rosenbloom, K.8
Clawson, H.9
Green, E.D.10
Haussler, D.11
Miller, W.12
-
17
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
10.1126/science.1141319, 17540862
-
Johnson D, Mortazavi A, Myers R, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316(5830):1497. 10.1126/science.1141319, 17540862.
-
(2007)
Science
, vol.316
, Issue.5830
, pp. 1497
-
-
Johnson, D.1
Mortazavi, A.2
Myers, R.3
Wold, B.4
-
18
-
-
30344478870
-
A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome
-
10.1016/j.cell.2005.10.043, 16413492
-
Wei C, Wu Q, Vega V, Chiu K, Ng P, Zhang T, Shahab A, Yong H, Fu Y, Weng Z. A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome. Cell 2006, 124:207-219. 10.1016/j.cell.2005.10.043, 16413492., http://dx.doi.org/10.1016/j.cell.2005.10.043
-
(2006)
Cell
, vol.124
, pp. 207-219
-
-
Wei, C.1
Wu, Q.2
Vega, V.3
Chiu, K.4
Ng, P.5
Zhang, T.6
Shahab, A.7
Yong, H.8
Fu, Y.9
Weng, Z.10
-
19
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
10.1038/nmeth1068, 17558387
-
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature methods 2007, 4(8):651-658. 10.1038/nmeth1068, 17558387.
-
(2007)
Nature methods
, vol.4
, Issue.8
, pp. 651-658
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
-
20
-
-
33845187907
-
Global mapping of c-Myc binding sites and target gene networks in human B cells
-
Zeller KI, Zhao X, Lee CWH, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proceedings of the National Academy of Sciences 2006, 103(47):17834-17839.
-
(2006)
Proceedings of the National Academy of Sciences
, vol.103
, Issue.47
, pp. 17834-17839
-
-
Zeller, K.I.1
Zhao, X.2
Lee, C.W.H.3
Chiu, K.P.4
Yao, F.5
Yustein, J.T.6
Ooi, H.S.7
Orlov, Y.L.8
Shahab, A.9
Yong, H.C.10
Fu, Y.11
Weng, Z.12
Kuznetsov, V.A.13
Sung, W.K.14
Ruan, Y.15
Dang, C.V.16
Wei, C.L.17
-
21
-
-
34547838179
-
Genome-wide mapping of RELA (p65) binding identifies E2F1 as a transcriptional activator recruited by NF-κB upon TLR4 activation
-
10.1016/j.molcel.2007.06.038, 17707233
-
Lim C, Yao F, Wong J, George J, Xu H, Chiu K, Sung W, Lipovich L, Vega V, Chen J, et al. Genome-wide mapping of RELA (p65) binding identifies E2F1 as a transcriptional activator recruited by NF-κB upon TLR4 activation. Molecular cell 2007, 27(4):622-635. 10.1016/j.molcel.2007.06.038, 17707233.
-
(2007)
Molecular cell
, vol.27
, Issue.4
, pp. 622-635
-
-
Lim, C.1
Yao, F.2
Wong, J.3
George, J.4
Xu, H.5
Chiu, K.6
Sung, W.7
Lipovich, L.8
Vega, V.9
Chen, J.10
-
22
-
-
33947201809
-
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
-
10.1016/j.cell.2006.12.048, 2572726, 17382889
-
Kim T, Abdullaev Z, Smith A, Ching K, Loukinov D, Green R, Zhang M, Lobanenkov V, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128(6):1231-1245. 10.1016/j.cell.2006.12.048, 2572726, 17382889.
-
(2007)
Cell
, vol.128
, Issue.6
, pp. 1231-1245
-
-
Kim, T.1
Abdullaev, Z.2
Smith, A.3
Ching, K.4
Loukinov, D.5
Green, R.6
Zhang, M.7
Lobanenkov, V.8
Ren, B.9
-
23
-
-
58149178579
-
NCBI Reference Sequences: current status, policy and new initiatives
-
2686572, 18927115
-
Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Research 2009, 37(suppl 1):D32-D36. 2686572, 18927115.
-
(2009)
Nucleic Acids Research
, vol.37
, Issue.SUPPL. 1
-
-
Pruitt, K.D.1
Tatusova, T.2
Klimke, W.3
Maglott, D.R.4
-
24
-
-
78651289449
-
Ensembl 2011
-
3013672, 21045057
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Vogel J, Searle SMJ. Ensembl 2011. Nucleic Acids Research 2011, 39(suppl 1):D800-D806. 3013672, 21045057.
-
(2011)
Nucleic Acids Research
, vol.39
, Issue.SUPPL. 1
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Chen, Y.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
Gordon, L.11
Hendrix, M.12
Hourlier, T.13
Johnson, N.14
Kähäri, A.15
Keefe, D.16
Keenan, S.17
Kinsella, R.18
Kokocinski, F.19
Kulesha, E.20
Larsson, P.21
Longden, I.22
McLaren, W.23
Overduin, B.24
Pritchard, B.25
Riat, H.S.26
Rios, D.27
Ritchie, G.R.S.28
Ruffier, M.29
Schuster, M.30
Sobral, D.31
Spudich, G.32
Tang, Y.A.33
Trevanion, S.34
Vandrovcova, J.35
Vilella, A.J.36
White, S.37
Wilder, S.P.38
Zadissa, A.39
Zamora, J.40
Aken, B.L.41
Birney, E.42
Cunningham, F.43
Dunham, I.44
Durbin, R.45
Fernández-Suarez, X.M.46
Herrero, J.47
Hubbard, T.J.P.48
Parker, A.49
Proctor, G.50
Vogel, J.51
Searle, S.M.J.52
more..
-
25
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 2000, 25:25-29. 10.1038/75556, 3037419, 10802651., http://dx.doi.org/10.1038/75556
-
(2000)
Nature genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
26
-
-
49649116149
-
FlyBase Drosophila
-
Totowa, NJ: Humana Press, Dahmann C, Walker JM, Walker JM
-
Drysdale R, t FC. FlyBase Drosophila. Methods in molecular biology (Clifton, N.J.), Volume 420 of Methods in Molecular Biology 2008, 45-59. Totowa, NJ: Humana Press, Dahmann C, Walker JM, Walker JM., http://dx.doi.org/10.1007/978-1-59745-583-1/_3
-
(2008)
Methods in molecular biology (Clifton, N.J.), Volume 420 of Methods in Molecular Biology
, pp. 45-59
-
-
Drysdale, R.1
t, F.C.2
-
27
-
-
49549122021
-
Saccharomyces Genome Database
-
project S. Saccharomyces Genome Database. Saccharomyces Genome Database 2011, , http://downloads.yeastgenome.org/
-
(2011)
Saccharomyces Genome Database
-
-
project, S.1
-
28
-
-
30044442790
-
Functional polymorphisms in dopamine and serotonin pathway genes
-
10.1002/humu.20278, 16320307
-
D'Souza UM, Craig IW. Functional polymorphisms in dopamine and serotonin pathway genes. Human Mutation 2006, 27:1-13. 10.1002/humu.20278, 16320307., http://dx.doi.org/10.1002/humu.20278
-
(2006)
Human Mutation
, vol.27
, pp. 1-13
-
-
D'Souza, U.M.1
Craig, I.W.2
-
29
-
-
79959503826
-
The International HapMap Project
-
10.1038/nature02168, 14685227, International HapMap Consortium
-
International HapMap Consortium The International HapMap Project. Nature 2003, 426(6968):789-796. 10.1038/nature02168, 14685227, International HapMap Consortium.
-
(2003)
Nature
, vol.426
, Issue.6968
, pp. 789-796
-
-
-
30
-
-
0035173378
-
DbSNP: the NCBI database of genetic variation
-
10.1093/nar/29.1.308, 29783, 11125122
-
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucl Acids Res 2001, 29:308-311. 10.1093/nar/29.1.308, 29783, 11125122., http://dx.doi.org/10.1093/nar/29.1.308
-
(2001)
Nucl Acids Res
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
Smigielski, E.M.6
Sirotkin, K.7
-
31
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
10.1093/nar/28.1.27, 102409, 10592173
-
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173., http://dx.doi.org/10.1093/nar/28.1.27
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
32
-
-
0036863624
-
REDD1, a Developmentally Regulated Transcriptional Target of p63 and p53, Links p63 to Regulation of Reactive Oxygen Species
-
10.1016/S1097-2765(02)00706-2, 12453409
-
Ellisen LW, Ramsayer KD, Johannessen CM, Yang A, Beppu H, Minda K, Oliner JD, McKeon F, Haber DA. REDD1, a Developmentally Regulated Transcriptional Target of p63 and p53, Links p63 to Regulation of Reactive Oxygen Species. Molecular Cell 2002, 10(5):995-1005. 10.1016/S1097-2765(02)00706-2, 12453409., http://www.sciencedirect.com/science/article/pii/S1097276502007062
-
(2002)
Molecular Cell
, vol.10
, Issue.5
, pp. 995-1005
-
-
Ellisen, L.W.1
Ramsayer, K.D.2
Johannessen, C.M.3
Yang, A.4
Beppu, H.5
Minda, K.6
Oliner, J.D.7
McKeon, F.8
Haber, D.A.9
-
33
-
-
59049083119
-
PH Domain-Only Protein PHLDA3 Is a p53-Regulated Repressor of Akt
-
10.1016/j.cell.2008.12.002, 19203586
-
Kawase T, Ohki R, Shibata T, Tsutsumi S, Kamimura N, Inazawa J, Ohta T, Ichikawa H, Aburatani H, Tashiro F, Taya Y. PH Domain-Only Protein PHLDA3 Is a p53-Regulated Repressor of Akt. Cell 2009, 136(3):535-550. 10.1016/j.cell.2008.12.002, 19203586., http://www.sciencedirect.com/science/article/pii/S0092867408015638
-
(2009)
Cell
, vol.136
, Issue.3
, pp. 535-550
-
-
Kawase, T.1
Ohki, R.2
Shibata, T.3
Tsutsumi, S.4
Kamimura, N.5
Inazawa, J.6
Ohta, T.7
Ichikawa, H.8
Aburatani, H.9
Tashiro, F.10
Taya, Y.11
-
34
-
-
0033590144
-
Gli genes in development and cancer
-
Matise MP, Joyner AL. Gli genes in development and cancer. Oncogene 1999, 18(55):7852-7859.
-
(1999)
Oncogene
, vol.18
, Issue.55
, pp. 7852-7859
-
-
Matise, M.P.1
Joyner, A.L.2
-
35
-
-
0035873922
-
Wnt signals are targets and mediators of Gli function
-
10.1016/S0960-9822(01)00229-9, 11378387
-
Mullor JL, Dahmane N, Sun T, Ruiz i Altaba A. Wnt signals are targets and mediators of Gli function. Current biology: CB 2001, 11(10):769-773. 10.1016/S0960-9822(01)00229-9, 11378387., http://view.ncbi.nlm.nih.gov/pubmed/11378387
-
(2001)
Current biology: CB
, vol.11
, Issue.10
, pp. 769-773
-
-
Mullor, J.L.1
Dahmane, N.2
Sun, T.3
Ruiz i Altaba, A.4
-
36
-
-
33846107777
-
TRED: a transcriptional regulatory element database, new entries and other development
-
Database
-
Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic acids research 2007, (35 Database):D137-D140., http://dx.doi.org/10.1093/nar/gkl1041
-
(2007)
Nucleic acids research
, Issue.35
-
-
Jiang, C.1
Xuan, Z.2
Zhao, F.3
Zhang, M.Q.4
-
37
-
-
0037112420
-
Induction of Medulloblastomas in Mice by Sonic Hedgehog, Independent of Gli1
-
Weiner HL, Bakst R, Hurlbert MS, Ruggiero J, Ahn E, Lee WS, Stephen D, Zagzag D, Joyner AL, Turnbull DH. Induction of Medulloblastomas in Mice by Sonic Hedgehog, Independent of Gli1. Cancer Research 2002, 62(22):6385-6389., http://cancerres.aacrjournals.org/content/62/22/6385.abstract
-
(2002)
Cancer Research
, vol.62
, Issue.22
, pp. 6385-6389
-
-
Weiner, H.L.1
Bakst, R.2
Hurlbert, M.S.3
Ruggiero, J.4
Ahn, E.5
Lee, W.S.6
Stephen, D.7
Zagzag, D.8
Joyner, A.L.9
Turnbull, D.H.10
-
38
-
-
33244463281
-
GLI3-dependent transcriptional repression of Gli1, Gli2 and kidney patterning genes disrupts renal morphogenesis
-
10.1242/dev.02220, 16396903
-
Hu MC, Mo R, Bhella S, Wilson CW, Chuang PT, Hui C, Rosenblum ND. GLI3-dependent transcriptional repression of Gli1, Gli2 and kidney patterning genes disrupts renal morphogenesis. Development 2006, 133(3):569-578. 10.1242/dev.02220, 16396903.
-
(2006)
Development
, vol.133
, Issue.3
, pp. 569-578
-
-
Hu, M.C.1
Mo, R.2
Bhella, S.3
Wilson, C.W.4
Chuang, P.T.5
Hui, C.6
Rosenblum, N.D.7
-
39
-
-
34250612602
-
Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning
-
10.1242/dev.001966, 17442700
-
Vokes SA, Ji H, McCuine S, Tenzen T, Giles S, Zhong S, Longabaugh WJR, Davidson EH, Wong WH, McMahon AP. Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development 2007, 134(10):1977-1989. 10.1242/dev.001966, 17442700.
-
(2007)
Development
, vol.134
, Issue.10
, pp. 1977-1989
-
-
Vokes, S.A.1
Ji, H.2
McCuine, S.3
Tenzen, T.4
Giles, S.5
Zhong, S.6
Longabaugh, W.J.R.7
Davidson, E.H.8
Wong, W.H.9
McMahon, A.P.10
-
40
-
-
0141790017
-
Identification of Cis-regulatory Elements in the Mouse Pax9/Nkx2-9 Genomic Region: Implication for Evolutionary Conserved Synteny
-
1462746, 14504231
-
Santagati F, Abe K, Schmidt V, Schmitt-John T, Suzuki M, Yamamura K, Imai K. Identification of Cis-regulatory Elements in the Mouse Pax9/Nkx2-9 Genomic Region: Implication for Evolutionary Conserved Synteny. Genetics 2003, 165:235-242. 1462746, 14504231., http://www.genetics.org/content/165/1/235.abstract
-
(2003)
Genetics
, vol.165
, pp. 235-242
-
-
Santagati, F.1
Abe, K.2
Schmidt, V.3
Schmitt-John, T.4
Suzuki, M.5
Yamamura, K.6
Imai, K.7
-
41
-
-
58149193222
-
Human Protein Reference Database-2009 update
-
2686490, 18988627
-
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database-2009 update. Nucl Acids Res 2009, 37(suppl_1):D767-772. 2686490, 18988627.
-
(2009)
Nucl Acids Res
, vol.37
, Issue.SUPPL. 1
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
Kumar, S.5
Mathivanan, S.6
Telikicherla, D.7
Raju, R.8
Shafreen, B.9
Venugopal, A.10
Balakrishnan, L.11
Marimuthu, A.12
Banerjee, S.13
Somanathan, D.S.14
Sebastian, A.15
Rani, S.16
Ray, S.17
Harrys Kishore, C.J.18
Kanth, S.19
Ahmed, M.20
Kashyap, M.K.21
Mohmood, R.22
Ramachandra, Y.L.23
Krishna, V.24
Rahiman, B.A.25
Mohan, S.26
Ranganathan, P.27
Ramabadran, S.28
Chaerkady, R.29
Pandey, A.30
more..
-
42
-
-
33644873184
-
BioGRID: a general repository for interaction datasets
-
1347471, 16381927
-
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucl Acids Res 2006, 34(suppl_1):D535-539. 1347471, 16381927.
-
(2006)
Nucl Acids Res
, vol.34
, Issue.SUPPL. 1
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
43
-
-
3042767202
-
MicroRNAs: small RNAs with a big role in gene regulation
-
10.1038/nrg1379, 15211354
-
He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nature Reviews Genetics 2004, 5(7):522-531. 10.1038/nrg1379, 15211354.
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.7
, pp. 522-531
-
-
He, L.1
Hannon, G.J.2
-
44
-
-
58149182724
-
NCBI GEO: archive for high-throughput functional genomic data
-
2686538, 18940857
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucl Acids Res 2009, 37(suppl_1):D885-890. 2686538, 18940857.
-
(2009)
Nucl Acids Res
, vol.37
, Issue.SUPPL. 1
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Marshall, K.A.10
Phillippy, K.H.11
Sherman, P.M.12
Muertter, R.N.13
Edgar, R.14
-
45
-
-
79955550445
-
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
-
3079585, 21526222
-
Consortium TEP. A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 2011, 9(4):e1001046+. 3079585, 21526222., http://dx.doi.org/10.1371/journal.pbio.1001046
-
(2011)
PLoS Biol
, vol.9
, Issue.4
-
-
Consortium, T.E.P.1
-
46
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
-
10.1038/ng1896, 17033623
-
Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genetics 2006, 38(11):1348-1354. 10.1038/ng1896, 17033623.
-
(2006)
Nature Genetics
, vol.38
, Issue.11
, pp. 1348-1354
-
-
Simonis, M.1
Klous, P.2
Splinter, E.3
Moshkin, Y.4
Willemsen, R.5
de Wit, E.6
van Steensel, B.7
de Laat, W.8
-
47
-
-
70349873824
-
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
-
10.1126/science.1181369, 2858594, 19815776
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 2009, 326(5950):289-293. 10.1126/science.1181369, 2858594, 19815776.
-
(2009)
Science
, vol.326
, Issue.5950
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
Sandstrom, R.11
Bernstein, B.12
Bender, M.A.13
Groudine, M.14
Gnirke, A.15
Stamatoyannopoulos, J.16
Mirny, L.A.17
Lander, E.S.18
Dekker, J.19
-
48
-
-
63849091245
-
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
-
10.1101/gr.074906.107, 19339662
-
Fullwood MJ, Wei CL, Liu ET, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Research 2009, 19(4):521-532. 10.1101/gr.074906.107, 19339662.
-
(2009)
Genome Research
, vol.19
, Issue.4
, pp. 521-532
-
-
Fullwood, M.J.1
Wei, C.L.2
Liu, E.T.3
Ruan, Y.4
-
49
-
-
79955569948
-
Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements
-
10.1101/gr.111153.110, 3083086, 21471403
-
Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Research 2011, 21(5):697-706. 10.1101/gr.111153.110, 3083086, 21471403.
-
(2011)
Genome Research
, vol.21
, Issue.5
, pp. 697-706
-
-
Hakim, O.1
Sung, M.H.2
Voss, T.C.3
Splinter, E.4
John, S.5
Sabo, P.J.6
Thurman, R.E.7
Stamatoyannopoulos, J.A.8
de Laat, W.9
Hager, G.L.10
-
50
-
-
79959510516
-
Build Watson: an overview of DeepQA for the Jeopardy! challenge
-
PACT '10, New York, NY, USA: ACM
-
Ferrucci D. Build Watson: an overview of DeepQA for the Jeopardy! challenge. Proceedings of the 19th international conference on Parallel architectures and compilation techniques 2010, 1-2. PACT '10, New York, NY, USA: ACM., http://doi.acm.org/10.1145/1854273.1854275
-
(2010)
Proceedings of the 19th international conference on Parallel architectures and compilation techniques
, pp. 1-2
-
-
Ferrucci, D.1
-
51
-
-
77953062527
-
Five-vertebrate 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, Talianidis I, Flicek P, Odom DT. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (New York, NY) 2010, 328(5981):1036-1040.
-
(2010)
Science (New York, NY)
, vol.328
, Issue.5981
, 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
Talianidis, I.11
Flicek, P.12
Odom, D.T.13
-
52
-
-
34250358295
-
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
-
10.1101/gr.5592107, 1891337, 17567996, groups for Transcriptional Regulation E
-
King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, , Analysis MS, Chiaromonte F, Miller W, Hardison RC. groups for Transcriptional Regulation E Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data. Genome Research 2007, 17(6):775-786. 10.1101/gr.5592107, 1891337, 17567996, groups for Transcriptional Regulation E.
-
(2007)
Genome Research
, vol.17
, Issue.6
, pp. 775-786
-
-
King, D.C.1
Taylor, J.2
Zhang, Y.3
Cheng, Y.4
Lawson, H.A.5
Martin, J.6
Analysis, M.S.7
Chiaromonte, F.8
Miller, W.9
Hardison, R.C.10
|