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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen
Genome Biol. 2009; 10(7): R80. Published online 2009 July 23. doi: 10.1186/gb-2009-10-7-r80
PMCID:
PMC2728534
Abstract Full Text PDF–1.7M Supplementary Material

Is Cited by the Following 63 Articles in this Archive:

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
Timothy E. Reddy, Jason Gertz, Florencia Pauli, Katerina S. Kucera, Katherine E. Varley, Kimberly M. Newberry, Georgi K. Marinov, Ali Mortazavi, Brian A. Williams, Lingyun Song, Gregory E. Crawford, Barbara Wold, Huntington F. Willard, Richard M. Myers
Genome Res. 2012 May; 22(5): 860–869. doi: 10.1101/gr.131201.111
PMCID:
PMC3337432
Free in PMC on 2012/11/01
HOT DNAs: a novel class of developmental enhancers
Emma Farley, Michael Levine
Genes Dev. 2012 May 1; 26(9): 873–876. doi: 10.1101/gad.192583.112
PMCID:
PMC3347785
Free in PMC on 2012/11/01
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
Evgeny Z. Kvon, Gerald Stampfel, J. Omar Yáñez-Cuna, Barry J. Dickson, Alexander Stark
Genes Dev. 2012 May 1; 26(9): 908–913. doi: 10.1101/gad.188052.112
PMCID:
PMC3347788
Free in PMC on 2012/11/01
Genomewide protein-DNA binding dynamics suggest a clutch for transcription factor function
Colin R. Lickwar, Florian Mueller, Sean E. Hanlon, James G McNally, Jason D. Lieb
Nature. Author manuscript; available in PMC 2012 October 12.
Published in final edited form as: Nature. 2012 April 11; 484(7393): 251–255. doi: 10.1038/nature10985
PMCID:
PMC3341663
Free in PMC on 2012/10/12
Developmental regulation of chromatin conformation by Hox proteins in Drosophila
Marios Agelopoulos, Daniel J. McKay, Richard S. Mann
Cell Rep. Author manuscript; available in PMC 2012 April 20.
Published in final edited form as: Cell Rep. 2012 April 5; 1(4): 350–359. doi: 10.1016/j.celrep.2012.03.003
PMCID:
PMC3329935
Abstract Full Text PDF–1.9M Supplementary Material
The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
Rahul Satija, Robert K. Bradley
Genome Res. 2012 April; 22(4): 656–665. doi: 10.1101/gr.130682.111
PMCID:
PMC3317148
Abstract Full Text PDF–2.5M
A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis
Brian W. Busser, Leila Taher, Yongsok Kim, Terese Tansey, Molly J. Bloom, Ivan Ovcharenko, Alan M. Michelson
PLoS Genet. 2012 March; 8(3): e1002531. Published online 2012 March 8. doi: 10.1371/journal.pgen.1002531
PMCID:
PMC3297574
Abstract Full Text PDF–2.8M Supplementary Material
Transcription Factor Binding Site Redundancy in Embryonic Enhancers of the Drosophila Bithorax Complex
Robert A. Drewell
G3 (Bethesda) 2011 December; 1(7): 603–606. Published online 2011 December 1. doi: 10.1534/g3.111.001404
PMCID:
PMC3276168
Abstract Full Text PDF–875K
Pioneer transcription factors: establishing competence for gene expression
Kenneth S. Zaret, Jason S. Carroll
Genes Dev. 2011 November 1; 25(21): 2227–2241. doi: 10.1101/gad.176826.111
PMCID:
PMC3219227
Abstract Full Text PDF–389K
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles
Chao Cheng, Renqiang Min, Mark Gerstein
Bioinformatics. 2011 December 1; 27(23): 3221–3227. Published online 2011 October 29. doi: 10.1093/bioinformatics/btr552
PMCID:
PMC3223362
Free in PMC on 2012/12/01
A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila
Charless C. Fowlkes, Kelly B. Eckenrode, Meghan D. Bragdon, Miriah Meyer, Zeba Wunderlich, Lisa Simirenko, Cris L. Luengo Hendriks, Soile V. E. Keränen, Clara Henriquez, David W. Knowles, Mark D. Biggin, Michael B. Eisen, Angela H. DePace
PLoS Genet. 2011 October; 7(10): e1002346. Published online 2011 October 27. doi: 10.1371/journal.pgen.1002346
PMCID:
PMC3203197
Abstract Full Text PDF–8.2M Supplementary Material
The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset
Christian Feller, Matthias Prestel, Holger Hartmann, Tobias Straub, Johannes Söding, Peter B. Becker
Nucleic Acids Res. 2012 February; 40(4): 1509–1522. Published online 2011 October 27. doi: 10.1093/nar/gkr869
PMCID:
PMC3287193
Abstract Full Text PDF–4.5M Supplementary Material
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition
Melissa M. Harrison, Xiao-Yong Li, Tommy Kaplan, Michael R. Botchan, Michael B. Eisen
PLoS Genet. 2011 October; 7(10): e1002266. Published online 2011 October 20. doi: 10.1371/journal.pgen.1002266
PMCID:
PMC3197655
Abstract Full Text PDF–1.1M Supplementary Material
Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo
Chung-Yi Nien, Hsiao-Lan Liang, Stephen Butcher, Yujia Sun, Shengbo Fu, Tenzin Gocha, Nikolai Kirov, J. Robert Manak, Christine Rushlow
PLoS Genet. 2011 October; 7(10): e1002339. Published online 2011 October 20. doi: 10.1371/journal.pgen.1002339
PMCID:
PMC3197689
Abstract Full Text PDF–8.0M Supplementary Material
Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3
Zhe Liu, Devin R. Scannell, Michael B. Eisen, Robert Tjian
Cell. Author manuscript; available in PMC 2012 September 2.
Published in final edited form as: Cell. 2011 September 2; 146(5): 720–731. doi: 10.1016/j.cell.2011.08.005
PMCID:
PMC3191068
Free in PMC on 2012/09/02
Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs
Michael O. Starr, Margaret C. W. Ho, Eric J. M. Gunther, Yen-Kuei Tu, Andrey S. Shur, Sara E. Goetz, Matthew J. Borok, Victoria Kang, Robert A. Drewell
Dev Biol. Author manuscript; available in PMC 2012 November 15.
Published in final edited form as: Dev Biol. 2011 November 15; 359(2): 290–302. Published online 2011 July 28. doi: 10.1016/j.ydbio.2011.07.028
PMCID:
PMC3202680
Free in PMC on 2012/11/15
Cooperative transcription factor associations discovered using regulatory variation
Konrad J. Karczewski, Nicholas P. Tatonetti, Stephen G. Landt, Xinqiong Yang, Teri Slifer, Russ B. Altman, Michael Snyder
Proc Natl Acad Sci U S A. 2011 August 9; 108(32): 13353–13358. Published online 2011 July 26. doi: 10.1073/pnas.1103105108
PMCID:
PMC3156166
Abstract Full Text PDF–418K Supplementary Material
Whole-Embryo Modeling of Early Segmentation in Drosophila Identifies Robust and Fragile Expression Domains
Jonathan Bieler, Christian Pozzorini, Felix Naef
Biophys J. 2011 July 20; 101(2): 287–296. doi: 10.1016/j.bpj.2011.05.060
PMCID:
PMC3136765
Abstract Full Text PDF–1.0M Supplementary Material
Integrated Genome-Scale Prediction of Detrimental Mutations in Transcription Networks
Mirko Francesconi, Rob Jelier, Ben Lehner
PLoS Genet. 2011 May; 7(5): e1002077. Published online 2011 May 26. doi: 10.1371/journal.pgen.1002077
PMCID:
PMC3102745
Abstract Full Text PDF–1001K Supplementary Material
Genome surveyor 2.0: cis-regulatory analysis in Drosophila
Majid Kazemian, Michael H. Brodsky, Saurabh Sinha
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W79–W85. Published online 2011 May 18. doi: 10.1093/nar/gkr291
PMCID:
PMC3125742
Abstract Full Text PDF–7.7M
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos
Genome Biol. 2011; 12(5): R43. Published online 2011 May 11. doi: 10.1186/gb-2011-12-5-r43
PMCID:
PMC3219966
Abstract Full Text PDF–1.5M Supplementary Material
Chromatin: constructing the big picture
Bas van Steensel
EMBO J. 2011 May 18; 30(10): 1885–1895. Published online 2011 April 28. doi: 10.1038/emboj.2011.135
PMCID:
PMC3098493
Abstract Full Text PDF–784K Supplementary Material
Hairless is a cofactor for Runt-dependent transcriptional regulation
Pegine B. Walrad, Saiyu Hang, J. Peter Gergen
Mol Biol Cell. 2011 April 15; 22(8): 1364–1374. doi: 10.1091/mbc.E10-06-0483
PMCID:
PMC3078061
Abstract Full Text PDF–1.4M
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin
Genome Biol. 2011; 12(4): R34. Published online 2011 April 7. doi: 10.1186/gb-2011-12-4-r34
PMCID:
PMC3218860
Abstract Full Text PDF–787K Supplementary Material
Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila
Matthew Slattery, Lijia Ma, Nicolas Négre, Kevin P. White, Richard S. Mann
PLoS One. 2011; 6(4): e14686. Published online 2011 April 5. doi: 10.1371/journal.pone.0014686
PMCID:
PMC3071676
Abstract Full Text PDF–1.8M Supplementary Material
Genome-Wide Analysis of the Binding of the Hox Protein Ultrabithorax and the Hox Cofactor Homothorax in Drosophila
Siew Woh Choo, Robert White, Steven Russell
PLoS One. 2011; 6(4): e14778. Published online 2011 April 5. doi: 10.1371/journal.pone.0014778
PMCID:
PMC3071696
Abstract Full Text PDF–1.8M Supplementary Material
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
Anil Ozdemir, Katherine I. Fisher-Aylor, Shirley Pepke, Manoj Samanta, Leslie Dunipace, Kenneth McCue, Lucy Zeng, Nobuo Ogawa, Barbara J. Wold, Angelike Stathopoulos
Genome Res. 2011 April; 21(4): 566–577. doi: 10.1101/gr.104018.109
PMCID:
PMC3065704
Abstract Full Text PDF–1.7M
Defining the replication program through the chromatin landscape
Queying Ding, David M. MacAlpine
Crit Rev Biochem Mol Biol. Author manuscript; available in PMC 2012 April 1.
Published in final edited form as: Crit Rev Biochem Mol Biol. 2011 April; 46(2): 165–179. doi: 10.3109/10409238.2011.560139
PMCID:
PMC3074350
Abstract Full Text PDF–665K
Mathematical modeling of gene expression: a guide for the perplexed biologist
Ahmet Ay, David N. Arnosti
Crit Rev Biochem Mol Biol. Author manuscript; available in PMC 2012 April 1.
Published in final edited form as: Crit Rev Biochem Mol Biol. 2011 April; 46(2): 137–151. doi: 10.3109/10409238.2011.556597
PMCID:
PMC3086598
Abstract Full Text PDF–225K
A Cis-Regulatory Map of the Drosophila Genome
Nicolas Nègre, Christopher D. Brown, Lijia Ma, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Rebecca F. Spokony, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn, Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, Alec Victorsen, Nicholas A. Bild, A. Jason Grundstad, David Hanley, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White, Steven Russell, Robert L. Grossman, Bing Ren, Mark Gerstein, James W. Posakony, Manolis Kellis, Kevin P. White
Nature. Author manuscript; available in PMC 2011 September 23.
Published in final edited form as: Nature. 2011 March 24; 471(7339): 527–531. doi: 10.1038/nature09990
PMCID:
PMC3179250
Abstract Full Text PDF–1.2M Supplementary Material
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