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Items: 1 to 20 of 36

1.

Thermodynamic state ensemble models of cis-regulation.

Sherman MS, Cohen BA.

PLoS Comput Biol. 2012;8(3):e1002407. doi: 10.1371/journal.pcbi.1002407.

2.

Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube.

Balaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V.

Cell. 2012 Jan 20;148(1-2):273-84. doi: 10.1016/j.cell.2011.10.047.

3.

Morphogen gradients: from generation to interpretation.

Rogers KW, Schier AF.

Annu Rev Cell Dev Biol. 2011;27:377-407. doi: 10.1146/annurev-cellbio-092910-154148. Review.

PMID:
21801015
4.

The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity.

Parker DS, White MA, Ramos AI, Cohen BA, Barolo S.

Sci Signal. 2011 Jun 7;4(176):ra38. doi: 10.1126/scisignal.2002077.

5.

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.

He X, Samee MA, Blatti C, Sinha S.

PLoS Comput Biol. 2010 Sep 16;6(9). pii: e1000935. doi: 10.1371/journal.pcbi.1000935.

6.

Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog.

Dessaud E, Ribes V, Balaskas N, Yang LL, Pierani A, Kicheva A, Novitch BG, Briscoe J, Sasai N.

PLoS Biol. 2010 Jun 1;8(6):e1000382. doi: 10.1371/journal.pbio.1000382.

7.

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity.

Rowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL.

Genes Dev. 2010 May 15;24(10):980-5. doi: 10.1101/gad.1890410.

8.

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo.

Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti DN.

Mol Syst Biol. 2010;6:341. doi: 10.1038/msb.2009.97.

9.

Non-consensus GLI binding sites in Hedgehog target gene regulation.

Winklmayr M, Schmid C, Laner-Plamberger S, Kaser A, Aberger F, Eichberger T, Frischauf AM.

BMC Mol Biol. 2010 Jan 13;11:2. doi: 10.1186/1471-2199-11-2.

10.

Environment-specific combinatorial cis-regulation in synthetic promoters.

Gertz J, Cohen BA.

Mol Syst Biol. 2009;5:244. doi: 10.1038/msb.2009.1.

11.

Analysis of combinatorial cis-regulation in synthetic and genomic promoters.

Gertz J, Siggia ED, Cohen BA.

Nature. 2009 Jan 8;457(7226):215-8. doi: 10.1038/nature07521.

12.

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb.

Vokes SA, Ji H, Wong WH, McMahon AP.

Genes Dev. 2008 Oct 1;22(19):2651-63. doi: 10.1101/gad.1693008.

13.

GLI2-specific transcriptional activation of the bone morphogenetic protein/activin antagonist follistatin in human epidermal cells.

Eichberger T, Kaser A, Pixner C, Schmid C, Klingler S, Winklmayr M, Hauser-Kronberger C, Aberger F, Frischauf AM.

J Biol Chem. 2008 May 2;283(18):12426-37. doi: 10.1074/jbc.M707117200.

14.

Expression of Fgf15 is regulated by both activator and repressor forms of Gli2 in vitro.

Komada M, Saitsu H, Shiota K, Ishibashi M.

Biochem Biophys Res Commun. 2008 May 2;369(2):350-6. doi: 10.1016/j.bbrc.2008.02.015.

PMID:
18279667
15.

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U.

Nature. 2008 Jan 31;451(7178):535-40. doi: 10.1038/nature06496.

PMID:
18172436
16.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium., Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
17.

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.

Janssens H, Hou S, Jaeger J, Kim AR, Myasnikova E, Sharp D, Reinitz J.

Nat Genet. 2006 Oct;38(10):1159-65.

PMID:
16980977
18.

Selective modulation of Hedgehog/GLI target gene expression by epidermal growth factor signaling in human keratinocytes.

Kasper M, Schnidar H, Neill GW, Hanneder M, Klingler S, Blaas L, Schmid C, Hauser-Kronberger C, Regl G, Philpott MP, Aberger F.

Mol Cell Biol. 2006 Aug;26(16):6283-98.

19.

The interpretation of morphogen gradients.

Ashe HL, Briscoe J.

Development. 2006 Feb;133(3):385-94. Review.

20.

The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila.

Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4960-5.

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