-
1
-
-
0037154982
-
A unified theory of gene expression
-
Orphanides G, Reinberg D. A unified theory of gene expression. Cell. 2002 108 : 439 51.
-
(2002)
Cell.
, vol.108
, pp. 439-51
-
-
Orphanides, G.1
Reinberg, D.2
-
2
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
International Human Genome Sequencing Consortium.
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang HM, Yu J, Wang J, Huang GY, Gu J, Hood L, Rowen L, Madan A, Qin SZ, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan HQ, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JGR, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang WH, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz JR, Slater G, Smit AFA, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 409 : 860 921.
-
(2001)
Nature.
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
Fitzhugh, W.10
Funke, R.11
Gage, D.12
Harris, K.13
Heaford, A.14
Howland, J.15
Kann, L.16
Lehoczky, J.17
Levine, R.18
McEwan, P.19
McKernan, K.20
Meldrim, J.21
Mesirov, J.P.22
Miranda, C.23
Morris, W.24
Naylor, J.25
Raymond, C.26
Rosetti, M.27
Santos, R.28
Sheridan, A.29
Sougnez, C.30
Stange-Thomann, N.31
Stojanovic, N.32
Subramanian, A.33
Wyman, D.34
Rogers, J.35
Sulston, J.36
Ainscough, R.37
Beck, S.38
Bentley, D.39
Burton, J.40
Clee, C.41
Carter, N.42
Coulson, A.43
Deadman, R.44
Deloukas, P.45
Dunham, A.46
Dunham, I.47
Durbin, R.48
French, L.49
Grafham, D.50
Gregory, S.51
Hubbard, T.52
Humphray, S.53
Hunt, A.54
Jones, M.55
Lloyd, C.56
McMurray, A.57
Matthews, L.58
Mercer, S.59
Milne, S.60
Mullikin, J.C.61
Mungall, A.62
Plumb, R.63
Ross, M.64
Shownkeen, R.65
Sims, S.66
Waterston, R.H.67
Wilson, R.K.68
Hillier, L.W.69
McPherson, J.D.70
Marra, M.A.71
Mardis, E.R.72
Fulton, L.A.73
Chinwalla, A.T.74
Pepin, K.H.75
Gish, W.R.76
Chissoe, S.L.77
Wendl, M.C.78
Delehaunty, K.D.79
Miner, T.L.80
Delehaunty, A.81
Kramer, J.B.82
Cook, L.L.83
Fulton, R.S.84
Johnson, D.L.85
Minx, P.J.86
Clifton, S.W.87
Hawkins, T.88
Branscomb, E.89
Predki, P.90
Richardson, P.91
Wenning, S.92
Slezak, T.93
Doggett, N.94
Cheng, J.F.95
Olsen, A.96
Lucas, S.97
Elkin, C.98
Uberbacher, E.99
more..
-
3
-
-
0035895505
-
The sequence of the human genome
-
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XQH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang JH, Miklos GLG, Nelson C, Broder S, Clark AG, Nadeau C, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng ZM, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge WM, Gong FC, Gu ZP, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke ZX, Ketchum KA, Lai ZW, Lei YD, Li ZY, Li JY, Liang Y, Lin XY, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue BX, Sun JT, Wang ZY, Wang AH, Wang X, Wang J, Wei MH, Wides R, Xiao CL, Yan CH, Yao A, Ye J, Zhan M, Zhang WQ, Zhang HY, Zhao Q, Zheng LS, Zhong F, Zhong WY, Zhu SPC, Zhao SY, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An HJ, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi HY, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays AD, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu XJ, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen MY, Wu D, Wu M, Xia A, Zandieh A, Zhu XH. The sequence of the human genome. Science. 2001 291 : 1304 51.
-
(2001)
Science.
, vol.291
, pp. 1304-51
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
Sutton, G.G.6
Smith, H.O.7
Yandell, M.8
Evans, C.A.9
Holt, R.A.10
Gocayne, J.D.11
Amanatides, P.12
Ballew, R.M.13
Huson, D.H.14
Wortman, J.R.15
Zhang, Q.16
Kodira, C.D.17
Zheng, X.Q.H.18
Chen, L.19
Skupski, M.20
Subramanian, G.21
Thomas, P.D.22
Zhang, J.H.23
Miklos, G.L.G.24
Nelson, C.25
Broder, S.26
Clark, A.G.27
Nadeau, C.28
McKusick, V.A.29
Zinder, N.30
Levine, A.J.31
Roberts, R.J.32
Simon, M.33
Slayman, C.34
Hunkapiller, M.35
Bolanos, R.36
Delcher, A.37
Dew, I.38
Fasulo, D.39
Flanigan, M.40
Florea, L.41
Halpern, A.42
Hannenhalli, S.43
Kravitz, S.44
Levy, S.45
Mobarry, C.46
Reinert, K.47
Remington, K.48
Abu-Threideh, J.49
Beasley, E.50
Biddick, K.51
Bonazzi, V.52
Brandon, R.53
Cargill, M.54
Chandramouliswaran, I.55
Charlab, R.56
Chaturvedi, K.57
Deng, Z.M.58
Di Francesco, V.59
Dunn, P.60
Eilbeck, K.61
Evangelista, C.62
Gabrielian, A.E.63
Gan, W.64
Ge, W.M.65
Gong, F.C.66
Gu, Z.P.67
Guan, P.68
Heiman, T.J.69
Higgins, M.E.70
Ji, R.R.71
Ke, Z.X.72
Ketchum, K.A.73
Lai, Z.W.74
Lei, Y.D.75
Li, Z.Y.76
Li, J.Y.77
Liang, Y.78
Lin, X.Y.79
Lu, F.80
Merkulov, G.V.81
Milshina, N.82
Moore, H.M.83
Naik, A.K.84
Narayan, V.A.85
Neelam, B.86
Nusskern, D.87
Rusch, D.B.88
Salzberg, S.89
Shao, W.90
Shue, B.X.91
Sun, J.T.92
Wang, Z.Y.93
Wang, A.H.94
Wang, X.95
Wang, J.96
Wei, M.H.97
Wides, R.98
Xiao, C.L.99
more..
-
4
-
-
33644844520
-
Microarray technology: Beyond transcript profiling and genotype analysis
-
Hoheisel JD. Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet. 2006 7 : 200 10.
-
(2006)
Nat Rev Genet.
, vol.7
, pp. 200-10
-
-
Hoheisel, J.D.1
-
5
-
-
0037464973
-
Functional genomics and gene microar-rays - The use in research and clinical medicine
-
Joos L, Eryüksel E, Brutsche MH. Functional genomics and gene microar-rays - the use in research and clinical medicine. Swiss Med Wkly. 2003 133 : 31 8.
-
(2003)
Swiss Med Wkly.
, vol.133
, pp. 31-8
-
-
Joos, L.1
Eryüksel, E.2
Brutsche, M.H.3
-
6
-
-
8844232706
-
Functional genomics to new drug targets
-
Kramer R, Cohen D. Functional genomics to new drug targets. Nat Rev Drug Discov. 2004 3 : 965 72.
-
(2004)
Nat Rev Drug Discov.
, vol.3
, pp. 965-72
-
-
Kramer, R.1
Cohen, D.2
-
7
-
-
27144548985
-
Towards quantitative biology: Integration of biological information to elucidate disease pathways and to guide drug discovery
-
Fischer HP. Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery. Biotechnol Annu Rev. 2005 11 : 1 68.
-
(2005)
Biotechnol Annu Rev.
, vol.11
, pp. 1-68
-
-
Fischer, H.P.1
-
8
-
-
33751099342
-
The application of genomic and proteomic technologies in predictive, preventive and personalized medicine
-
Collins CD, Purohit S, Podolsky RH, Zhao HS, Schatz D, Eckenrode SE, Yang P, Hopkins D, Muir A, Hoffman M, McIndoe RA, Rewers M, She JX. The application of genomic and proteomic technologies in predictive, preventive and personalized medicine. Vascul Pharmacol. 2006 45 : 258 67.
-
(2006)
Vascul Pharmacol.
, vol.45
, pp. 258-67
-
-
Collins, C.D.1
Purohit, S.2
Podolsky, R.H.3
Zhao, H.S.4
Schatz, D.5
Eckenrode, S.E.6
Yang, P.7
Hopkins, D.8
Muir, A.9
Hoffman, M.10
McIndoe, R.A.11
Rewers, M.12
She, J.X.13
-
9
-
-
33745956888
-
Joining high-throughput technology with in silico modelling advances genome-wide screening towards targeted discovery
-
Werner T, Nelson PJ. Joining high-throughput technology with in silico modelling advances genome-wide screening towards targeted discovery. Brief Funct Genomic Proteomic. 2006 5 : 32 6.
-
(2006)
Brief Funct Genomic Proteomic.
, vol.5
, pp. 32-6
-
-
Werner, T.1
Nelson, P.J.2
-
10
-
-
22344449669
-
Constructing transcriptional regulatory networks
-
Blais A, Dynlacht BD. Constructing transcriptional regulatory networks. Genes Dev. 2005 19 : 1499 511.
-
(2005)
Genes Dev.
, vol.19
, pp. 1499-511
-
-
Blais, A.1
Dynlacht, B.D.2
-
11
-
-
33947521882
-
Integrative content-driven concepts for bioinformatics "beyond the cell"
-
Wingender E, Crass T, Hogan JD, Kel AE, Kel-Margoulis OV, Potapov AP. Integrative content-driven concepts for bioinformatics "beyond the cell". J Biosci. 2006 32 : 169 80.
-
(2006)
J Biosci.
, vol.32
, pp. 169-80
-
-
Wingender, E.1
Crass, T.2
Hogan, J.D.3
Kel, A.E.4
Kel-Margoulis, O.V.5
Potapov, A.P.6
-
12
-
-
34249853738
-
Computational and experimental approaches for modeling gene regulatory networks
-
Goutsias J, Lee NH. Computational and experimental approaches for modeling gene regulatory networks. Curr Pharm Des. 2007 13 : 1415 36.
-
(2007)
Curr Pharm Des.
, vol.13
, pp. 1415-36
-
-
Goutsias, J.1
Lee, N.H.2
-
13
-
-
0035477896
-
Core promoters: Active contributors to combinatorial gene regulation
-
Smale ST. Core promoters: active contributors to combinatorial gene regulation. Gene Dev. 2001 15 : 2503 8.
-
(2001)
Gene Dev.
, vol.15
, pp. 2503-8
-
-
Smale, S.T.1
-
14
-
-
0037108159
-
The RNA poly-merase II core promoter: A key component in the regulation of gene expression
-
Butler JEF, Kadonaga JT. The RNA poly-merase II core promoter: a key component in the regulation of gene expression. Gene Dev. 2002 16 : 2583 92.
-
(2002)
Gene Dev.
, vol.16
, pp. 2583-92
-
-
Butler, J.E.F.1
Kadonaga, J.T.2
-
15
-
-
0037948267
-
Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression
-
Hochheimer A, Tjian R. Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Gene Dev. 2003 17 : 1309 20.
-
(2003)
Gene Dev.
, vol.17
, pp. 1309-20
-
-
Hochheimer, A.1
Tjian, R.2
-
16
-
-
0037212661
-
Promoters can contribute to the elucidation of protein function
-
Werner T. Promoters can contribute to the elucidation of protein function. Trends Biotechnol. 2003 21 : 9 13.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 9-13
-
-
Werner, T.1
-
17
-
-
33846515642
-
Tissue-specific regulatory elements in mammalian promoters
-
Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol. 2007 3 : 73.
-
(2007)
Mol Syst Biol.
, vol.3
, pp. 73
-
-
Smith, A.D.1
Sumazin, P.2
Zhang, M.Q.3
-
18
-
-
33847298964
-
The gateway to transcription: Identifying, characterizing and understanding promoters in the eukaryotic genome
-
Heintzman ND, Ren B. The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome. Cell Mol Life Sci. 2007 64 : 386 400.
-
(2007)
Cell Mol Life Sci.
, vol.64
, pp. 386-400
-
-
Heintzman, N.D.1
Ren, B.2
-
19
-
-
0035146351
-
Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity
-
Gailus-Durner V, Scherf M, Werner T. Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity. Mamm Genome. 2001 12 : 67 72.
-
(2001)
Mamm Genome.
, vol.12
, pp. 67-72
-
-
Gailus-Durner, V.1
Scherf, M.2
Werner, T.3
-
20
-
-
0036468869
-
Regulatory context is a crucial part of gene function
-
Fessele S, Maier H, Zischek C, Nelson PJ, Werner T. Regulatory context is a crucial part of gene function. Trends Genet. 2002 18 : 60 3.
-
(2002)
Trends Genet.
, vol.18
, pp. 60-3
-
-
Fessele, S.1
Maier, H.2
Zischek, C.3
Nelson, P.J.4
Werner, T.5
-
21
-
-
0037785111
-
Computer modeling of promoter organization as a tool to study transcriptional coregulation
-
Werner T, Fessele S, Maier H, Nelson PJ. Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J. 2003 17 : 1228 37.
-
(2003)
FASEB J.
, vol.17
, pp. 1228-37
-
-
Werner, T.1
Fessele, S.2
Maier, H.3
Nelson, P.J.4
-
22
-
-
13944266038
-
Linking disease-associated genes to regulatory networks via promoter organization
-
Döhr S, Klingenhoff A, Maier H, Hrabé de Angelis M, Werner T, Schneider R. Linking disease-associated genes to regulatory networks via promoter organization. Nucleic Acids Res. 2005 33 : 864 72.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 864-72
-
-
Döhr, S.1
Klingenhoff, A.2
Maier, H.3
Hrabé De Angelis, M.4
Werner, T.5
Schneider, R.6
-
23
-
-
27144527504
-
Pharmacologic profiling of transcriptional targets deciphers promoter logic
-
Freebern WJ, Haggerty CM, Montano I, McNutt MC, Collins I, Graham A, Chandramouli GV, Stewart DH, Biebuyck HA, Taub DD, Gardner K. Pharmacologic profiling of transcriptional targets deciphers promoter logic. Pharmacogenomics J. 2005 5 : 305 23.
-
(2005)
Pharmacogenomics J.
, vol.5
, pp. 305-23
-
-
Freebern, W.J.1
Haggerty, C.M.2
Montano, I.3
McNutt, M.C.4
Collins, I.5
Graham, A.6
Chandramouli, G.V.7
Stewart, D.H.8
Biebuyck, H.A.9
Taub, D.D.10
Gardner, K.11
-
24
-
-
14744304798
-
Transcription factor therapeutics: Long-shot or lodestone
-
Ghosh D, Papavassiliou AG. Transcription factor therapeutics: long-shot or lodestone. Curr Med Chem. 2005 12 : 691 701.
-
(2005)
Curr Med Chem.
, vol.12
, pp. 691-701
-
-
Ghosh, D.1
Papavassiliou, A.G.2
-
25
-
-
34347237542
-
Predictive modeling of genomewide mRNA expression: From modules to molecules
-
Bussemaker HJ, Foat BC, Ward LD. Predictive modeling of genomewide mRNA expression: from modules to molecules. Annu Rev Biophys Biomol Struct. 2007 36 : 329 47.
-
(2007)
Annu Rev Biophys Biomol Struct.
, vol.36
, pp. 329-47
-
-
Bussemaker, H.J.1
Foat, B.C.2
Ward, L.D.3
-
26
-
-
16644364007
-
In silico representation and discovery of transcription factor binding sites
-
Pavesi G, Mauri G, Pesole G. In silico representation and discovery of transcription factor binding sites. Brief Bioinform. 2004 5 : 217 36.
-
(2004)
Brief Bioinform.
, vol.5
, pp. 217-36
-
-
Pavesi, G.1
Mauri, G.2
Pesole, G.3
-
27
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004 5 : 276 87.
-
(2004)
Nat Rev Genet.
, vol.5
, pp. 276-87
-
-
Wasserman, W.W.1
Sandelin, A.2
-
28
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa M, Li N, Bailey TL, Church GM, de Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 23 : 137 44.
-
(2005)
Nat Biotechnol.
, vol.23
, pp. 137-44
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
Makeev, V.J.11
Mironov, A.A.12
Noble, W.S.13
Pavesi, G.14
Pesole, G.15
Régnier, M.16
Simonis, N.17
Sinha, S.18
Thijs, G.19
Van Helden, J.20
Vandenbogaert, M.21
Weng, Z.22
Workman, C.23
Ye, C.24
Zhu, Z.25
more..
-
29
-
-
33845341455
-
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
-
Elnitski L, Jin VX, Farnham PJ, Jones SJM. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 2006 16 : 1455 64.
-
(2006)
Genome Res.
, vol.16
, pp. 1455-64
-
-
Elnitski, L.1
Jin, V.X.2
Farnham, P.J.3
Jones, S.J.M.4
-
30
-
-
33747044757
-
Analysis of computational approaches for motif discovery
-
Li N, Tompa M. Analysis of computational approaches for motif discovery. Algorithms Mol Biol. 2006 1 : 8.
-
(2006)
Algorithms Mol Biol.
, vol.1
, pp. 8
-
-
Li, N.1
Tompa, M.2
-
31
-
-
34548295841
-
Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes
-
Kolchanov NA, Merkulova TI, Ignatieva EV, Ananko EA, Oshchepkov DY, Levitsky VG, Vasiliev GV, Klimova NV, Merkulov VM, Hodgman TC. Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. Brief Bioinform. 2007 8 : 266 74.
-
(2007)
Brief Bioinform.
, vol.8
, pp. 266-74
-
-
Kolchanov, N.A.1
Merkulova, T.I.2
Ignatieva, E.V.3
Ananko, E.A.4
Oshchepkov, D.Y.5
Levitsky, V.G.6
Vasiliev, G.V.7
Klimova, N.V.8
Merkulov, V.M.9
Hodgman, T.C.10
-
32
-
-
0002759539
-
Unsupervised learning of multiple motifs in biopolymers using Expectation Maximization
-
Bailey TL, Elkan C. Unsupervised learning of multiple motifs in biopolymers using Expectation Maximization. Mach. Learn. 1995 21 : 51 80.
-
(1995)
Mach. Learn.
, vol.21
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
-
33
-
-
0027912333
-
Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
-
Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AN, Wootton J. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993 262 : 208 14.
-
(1993)
Science.
, vol.262
, pp. 208-14
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.N.5
Wootton, J.6
-
34
-
-
0036105591
-
RVista for comparative sequence-based discovery of functional transcription factor binding sites
-
Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 2002 12 : 832 9.
-
(2002)
Genome Res.
, vol.12
, pp. 832-9
-
-
Loots, G.G.1
Ovcharenko, I.2
Pachter, L.3
Dubchak, I.4
Rubin, E.M.5
-
35
-
-
0034284481
-
Conserved noncoding sequences are reliable guides to regulatory elements
-
Hardison RC. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 2000 16 : 369 72.
-
(2000)
Trends Genet.
, vol.16
, pp. 369-72
-
-
Hardison, R.C.1
-
36
-
-
0033976586
-
TRANSFAC: An integrated system for gene expression regulation
-
Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüß M, Reuter I, Schacherer F. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 2000 28 : 316 9.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 316-9
-
-
Wingender, E.1
Chen, X.2
Hehl, R.3
Karas, H.4
Liebich, I.5
Matys, V.6
Meinhardt, T.7
Prüß, M.8
Reuter, I.9
Schacherer, F.10
-
37
-
-
0347125328
-
JASPAR: An open-access database for eukaryotic transcription factor binding profiles
-
Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004 32 : D91 4.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Sandelin, A.1
Alkema, W.2
Engström, P.3
Wasserman, W.W.4
Lenhard, B.5
-
38
-
-
0034941211
-
Cluster analysis and promoter modelling as bioinformatics tools for the identification of target genes from expression array data
-
Werner T. Cluster analysis and promoter modelling as bioinformatics tools for the identification of target genes from expression array data. Pharmacogenomics. 2001 2 : 25 36.
-
(2001)
Pharmacogenomics.
, vol.2
, pp. 25-36
-
-
Werner, T.1
-
39
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001 29 : 153 9.
-
(2001)
Nat Genet.
, vol.29
, pp. 153-9
-
-
Pilpel, Y.1
Sudarsanam, P.2
Church, G.M.3
-
40
-
-
1942453302
-
Predicting Gene Expression from Sequence
-
Beer MA, Tavazoie S. Predicting Gene Expression from Sequence. Cell. 2004 117 : 185 98.
-
(2004)
Cell.
, vol.117
, pp. 185-98
-
-
Beer, M.A.1
Tavazoie, S.2
-
41
-
-
32844455250
-
A bottom-up approach to gene regulation
-
Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC, Collins JJ. A bottom-up approach to gene regulation. Nature. 2006 439 : 856 60.
-
(2006)
Nature.
, vol.439
, pp. 856-60
-
-
Guido, N.J.1
Wang, X.2
Adalsteinsson, D.3
McMillen, D.4
Hasty, J.5
Cantor, C.R.6
Elston, T.C.7
Collins, J.J.8
-
42
-
-
33751360783
-
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
-
Pierstorff N, Bergman CM, Wiehe T. Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics. 2006 22 : 2858 64.
-
(2006)
Bioinformatics.
, vol.22
, pp. 2858-64
-
-
Pierstorff, N.1
Bergman, C.M.2
Wiehe, T.3
-
43
-
-
33644674789
-
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles
-
Chang LW, Nagarajan R, Magee JA, Milbrandt J, Stormo GD. A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. Genome Res. 2006 16 : 405 13.
-
(2006)
Genome Res.
, vol.16
, pp. 405-13
-
-
Chang, L.W.1
Nagarajan, R.2
Magee, J.A.3
Milbrandt, J.4
Stormo, G.D.5
-
44
-
-
34447299123
-
Identification of polymorphic antioxidant response elements in the human genome
-
Wang X, Tomso DJ, Chorley BN, Cho H-Y, Cheung VG, Kleeberger SR, Bell DA. Identification of polymorphic antioxidant response elements in the human genome. Hum Mol Genet. 2007 16 : 1188 1200.
-
(2007)
Hum Mol Genet.
, vol.16
, pp. 1188-1200
-
-
Wang, X.1
Tomso, D.J.2
Chorley, B.N.3
Cho, H.-Y.4
Cheung, V.G.5
Kleeberger, S.R.6
Bell, D.A.7
-
45
-
-
33646580422
-
DNA motifs in human and mouse proximal promoters predict tissue-specific expression
-
Smith AD, Sumazin P, Xuan Z, Zhang MQ. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Nat Acad Sci USA. 2006 103 : 6275 80.
-
(2006)
Proc Nat Acad Sci USA.
, vol.103
, pp. 6275-80
-
-
Smith, A.D.1
Sumazin, P.2
Xuan, Z.3
Zhang, M.Q.4
-
46
-
-
33845880374
-
Computational prediction of novel components of lung transcriptional networks
-
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. Computational prediction of novel components of lung transcriptional networks. Bioinformatics. 2007 23 : 21 9.
-
(2007)
Bioinformatics.
, vol.23
, pp. 21-9
-
-
Martinez, M.J.1
Smith, A.D.2
Li, B.3
Zhang, M.Q.4
Harrod, K.S.5
-
47
-
-
34247402972
-
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes
-
van Deursen D, Botma GJ, Jansen H, Verhoeven AJM. Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes. BMC Genomics. 2007 8 : 99.
-
(2007)
BMC Genomics.
, vol.8
, pp. 99
-
-
Van Deursen, D.1
Botma, G.J.2
Jansen, H.3
Verhoeven, A.J.M.4
-
48
-
-
29944437635
-
Genes induced by Reovirus infection have a distinct modular cis-regulatory architecture
-
Lapadat R, DeBiasi RL, Johnson GL, Tyler KL, Shah I. Genes induced by Reovirus infection have a distinct modular cis-regulatory architecture. Curr Genomics. 2005 6 : 501 13.
-
(2005)
Curr Genomics.
, vol.6
, pp. 501-13
-
-
Lapadat, R.1
Debiasi, R.L.2
Johnson, G.L.3
Tyler, K.L.4
Shah, I.5
-
49
-
-
26844493084
-
Androgen receptor binding sites identified by a GREF-GATA model
-
Masuda K, Werner T, Maheshwari S, Frisch M, Oh S, Petrovics G, May K, Srikantan V, Srivastava S, Dobi A. Androgen receptor binding sites identified by a GREF-GATA model. J Mol Biol. 2005 353 : 763 71.
-
(2005)
J Mol Biol.
, vol.353
, pp. 763-71
-
-
Masuda, K.1
Werner, T.2
Maheshwari, S.3
Frisch, M.4
Oh, S.5
Petrovics, G.6
May, K.7
Srikantan, V.8
Srivastava, S.9
Dobi, A.10
-
50
-
-
15444366250
-
Construction of predictive promoter models on the example of antibacterial response of human epithelial cells
-
Shelest E, Wingender E. Construction of predictive promoter models on the example of antibacterial response of human epithelial cells. Theor Biol Med Model. 2005 2 : 2.
-
(2005)
Theor Biol Med Model.
, vol.2
, pp. 2
-
-
Shelest, E.1
Wingender, E.2
-
51
-
-
33947174458
-
Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation
-
Stegmann A, Hansen M, Wang Y, Larsen JB, Lund LR, Ritie L, Nicholson JK, Quistorff B, Simon-Assmann P, Troelsen JT, Olsen J. Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation. Physiol Genomics. 2006 27 : 141 55.
-
(2006)
Physiol Genomics.
, vol.27
, pp. 141-55
-
-
Stegmann, A.1
Hansen, M.2
Wang, Y.3
Larsen, J.B.4
Lund, L.R.5
Ritie, L.6
Nicholson, J.K.7
Quistorff, B.8
Simon-Assmann, P.9
Troelsen, J.T.10
Olsen, J.11
-
52
-
-
34248187723
-
Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators
-
Keller MA, Addya S, Vadigepalli R, Banini B, Delgrosso K, Huang H, Surrey S. Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators. Physiol Genomics. 2006 28 : 114 28.
-
(2006)
Physiol Genomics.
, vol.28
, pp. 114-28
-
-
Keller, M.A.1
Addya, S.2
Vadigepalli, R.3
Banini, B.4
Delgrosso, K.5
Huang, H.6
Surrey, S.7
-
53
-
-
33646598690
-
Cis-Regulatory sequences of the genes involved in apoptosis, cell growth, and proliferation may provide a target for some of the effects of acute ethanol exposure
-
Uddin RK, Singh SM. cis-Regulatory sequences of the genes involved in apoptosis, cell growth, and proliferation may provide a target for some of the effects of acute ethanol exposure. Brain Res. 2006 1088 : 31 44.
-
(2006)
Brain Res.
, vol.1088
, pp. 31-44
-
-
Uddin, R.K.1
Singh, S.M.2
-
54
-
-
34248546744
-
In silico mining identifies IGFBP3 as a novel target of methylation in prostate cancer
-
Perry AS, Loftus B, Moroose R, Lynch TH, Hollywood D, Watson RWG, Woodson K, Lawler M. In silico mining identifies IGFBP3 as a novel target of methylation in prostate cancer. Br J Cancer. 2007 96 : 1587 94.
-
(2007)
Br J Cancer.
, vol.96
, pp. 1587-94
-
-
Perry, A.S.1
Loftus, B.2
Moroose, R.3
Lynch, T.H.4
Hollywood, D.5
Watson, R.W.G.6
Woodson, K.7
Lawler, M.8
-
55
-
-
2942572926
-
Quantifying the relationship between co-expression, co-regulation and gene function
-
Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2007 5 : 18.
-
(2007)
BMC Bioinformatics.
, vol.5
, pp. 18
-
-
Allocco, D.J.1
Kohane, I.S.2
Butte, A.J.3
-
56
-
-
33846076975
-
EMBL Nucleotide Sequence Database in 2006
-
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MPG, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R. EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res. 2007 35 : D16 D20.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Kulikova, T.1
Akhtar, R.2
Aldebert, P.3
Althorpe, N.4
Andersson, M.5
Baldwin, A.6
Bates, K.7
Bhattacharyya, S.8
Bower, L.9
Browne, P.10
Castro, M.11
Cochrane, G.12
Duggan, K.13
Eberhardt, R.14
Faruque, N.15
Hoad, G.16
Kanz, C.17
Lee, C.18
Leinonen, R.19
Lin, Q.20
Lombard, V.21
Lopez, R.22
Lorenc, D.23
McWilliam, H.24
Mukherjee, G.25
Nardone, F.26
Pastor, M.P.G.27
Plaister, S.28
Sobhany, S.29
Stoehr, P.30
Vaughan, R.31
Wu, D.32
Zhu, W.33
Apweiler, R.34
more..
-
57
-
-
33645807621
-
Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins
-
Cohen CD, Klingenhoff A, Boucherot A, Nitsche A, Henger A, Brunner B, Schmid H, Merkle M, Saleem MA, Koller K-P, Werner T, Gröne H-J, Nelson PJ, Kretzler M. Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Nat Acad Sci USA. 2006 103 : 5682 7.
-
(2006)
Proc Nat Acad Sci USA.
, vol.103
, pp. 5682-7
-
-
Cohen, C.D.1
Klingenhoff, A.2
Boucherot, A.3
Nitsche, A.4
Henger, A.5
Brunner, B.6
Schmid, H.7
Merkle, M.8
Saleem, M.A.9
Koller, K.-P.10
Werner, T.11
Gröne, H.-J.12
Nelson, P.J.13
Kretzler, M.14
-
58
-
-
34548525518
-
In silico promoter analysis can predict genes of functional relevance in cell proliferation: Validation in a colon cancer model
-
Moss AC, Doran PP, MacMathuna P. In silico promoter analysis can predict genes of functional relevance in cell proliferation: validation in a colon cancer model. Translational Oncogenomics 2007 2 : 1 16.
-
(2007)
Translational Oncogenomics
, vol.2
, pp. 1-16
-
-
Moss, A.C.1
Doran, P.P.2
MacMathuna, P.3
|