Crossref
journal-article
Public Library of Science (PLoS)
PLoS Genetics (340)
References
68
Referenced
49
10.1126/science.1198374
/ Science / Identification of functional elements and regulatory circuits by Drosophila modENCODE by S Roy (2010)10.1371/journal.pbio.1001046
/ PLoS Biol / A user's guide to the encyclopedia of DNA elements (ENCODE) by RM Myers (2011)10.1186/gb-2012-13-9-r48
/ Genome Biol / Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors by KY Yip (2012)10.1038/nature11245
/ Nature / Architecture of the human regulatory network derived from ENCODE data by MB Gerstein (2012)10.1101/gr.132811.111
/ Genome Res / Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding by JO Yanez-Cuna (2012)10.1371/journal.pgen.1001290
/ PLoS Genet / Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development by T Kaplan (2011)10.1101/gr.112623.110
/ Genome Res / Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data by R Pique-Regi (2011)10.1016/j.cell.2008.05.024
/ Cell / Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences by MF Berger (2008)10.1016/j.cell.2008.05.023
/ Cell / Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites by MB Noyes (2008)10.1007/978-1-61779-292-2_6
/ Methods Mol Biol / MITOMI: a microfluidic platform for in vitro characterization of transcription factor-DNA interaction by S Rockel (2012)10.1016/j.bioeng.2007.06.001
/ Biomol Eng / SELEX–a (r)evolutionary method to generate high-affinity nucleic acid ligands by R Stoltenburg (2007)10.1016/j.cell.2011.10.053
/ Cell / Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins by M Slattery (2011)10.1074/jbc.M313200200
/ J Biol Chem / Repression by TTK69 of GAGA-mediated activation occurs in the absence of TTK69 binding to DNA and solely requires the contribution of the POZ/BTB domain of TTK69 by S Pagans (2004)10.1016/j.molcel.2011.05.025
/ Mol Cell / Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4 by X Zhou (2011)10.1126/science.1465613
/ Science / Nucleosome core displacement in vitro via a metastable transcription factor-nucleosome complex by JL Workman (1992)10.1126/science.8248805
/ Science / Nucleosome disruption by transcription factor binding in yeast by RH Morse (1993)10.1016/j.molcel.2012.07.003
/ Mol Cell / A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern by AL Hughes (2012)10.1101/gr.093450.109
/ Genome Res / An ensemble model of competitive multi-factor binding of the genome by T Wasson (2009)10.1186/gb-2011-12-4-r34
/ Genome Biol / The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding by XY Li (2011)10.1093/nar/gkq858
/ Nucleic Acids Res / FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system by LJ Zhu (2011)10.1038/nature09715
/ Nature / The developmental transcriptome of Drosophila melanogaster by BR Graveley (2011)10.1371/journal.pone.0008155
/ PLoS ONE / A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data by X He (2009)10.1093/bioinformatics/btl565
/ Bioinformatics / Predicting transcription factor affinities to DNA from a biophysical model by HG Roider (2007)10.1038/nature08531
/ Nature / Combinatorial binding predicts spatio-temporal cis-regulatory activity by RP Zinzen (2009)10.1016/S0968-0004(98)01187-6
/ Trends Biochem Sci / Specificity, free energy and information content in protein-DNA interactions by GD Stormo (1998)10.1093/emboj/20.9.2246
/ EMBO J / Local action of long-range repressors in the Drosophila embryo by Y Nibu (2001)10.1242/dev.01613
/ Development / Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb by T Sagai (2005)10.1101/gad.176826.111
/ Genes Dev / Pioneer transcription factors: establishing competence for gene expression by KS Zaret (2011)10.1371/journal.pgen.1002339
/ PLoS Genet / Temporal coordination of gene networks by Zelda in the early Drosophila embryo by CY Nien (2011)10.1371/journal.pgen.1002266
/ PLoS Genet / Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition by MM Harrison (2011)10.1101/gr.130682.111
/ Genome Res / The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo by R Satija (2012)10.1101/gad.188052.112
/ Genes Dev / HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature by EZ Kvon (2012)10.1016/S0960-9822(95)00048-0
/ Curr Biol / Chromatin. Ga-ga over GAGA factor by H Granok (1995)10.1016/j.tig.2003.11.005
/ Trends Genet / Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure by M Lehmann (2004)10.1128/MCB.22.17.6148-6157.2002
/ Mol Cell Biol / GAGA factor and the TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 promoter by BA Leibovitch (2002)10.1128/MCB.18.5.2455
/ Mol Cell Biol / Chromatin remodeling mediated by Drosophila GAGA factor and ISWI activates fushi tarazu gene transcription in vitro by M Okada (1998)10.1093/nar/gkg799
/ Nucleic Acids Res / Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information by VJ Makeev (2003)10.1126/science.1105776
/ Science / High-throughput mapping of a dynamic signaling network in mammalian cells by M Barrios-Rodiles (2005)10.1002/pmic.200900298
/ Proteomics / LuMPIS–a modified luminescence-based mammalian interactome mapping pull-down assay for the investigation of protein-protein interactions encoded by GC-low ORFs by MG Vizoso Pinto (2009)10.1242/dev.125.8.1433
/ Development / Medea is a Drosophila Smad4 homolog that is differentially required to potentiate DPP responses by RG Wisotzkey (1998)10.1091/mbc.9.8.2145
/ Mol Biol Cell / Interplay of signal mediators of decapentaplegic (Dpp): molecular characterization of mothers against dpp, Medea, and daughters against dpp by H Inoue (1998)10.1074/jbc.M506882200
/ J Biol Chem / Dpp-responsive silencers are bound by a trimeric Mad-Medea complex by S Gao (2005)10.1016/j.bbaexp.2007.05.006
/ Biochim Biophys Acta / Flexible interaction of Drosophila Smad complexes with bipartite binding sites by S Gao (2007)10.1242/dev.114.1.99
/ Development / The giant gene of Drosophila encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes by M Capovilla (1992)10.1146/annurev-genet-110711-155437
/ Annu Rev Genet / Disentangling the many layers of eukaryotic transcriptional regulation by KM Lelli (2012)10.1038/nprot.2006.33
/ Nat Protoc / High-throughput assay for determining specificity and affinity of protein-DNA binding interactions by O Hallikas (2006){'key': 'ref47', 'first-page': '423', 'article-title': 'The Drosophila retained/dead ringer gene and ARID gene family function during development', 'volume': '46', 'author': 'T Shandala', 'year': '2002', 'journal-title': 'Int J Dev Biol'}
/ Int J Dev Biol / The Drosophila retained/dead ringer gene and ARID gene family function during development by T Shandala (2002)10.1128/MCB.16.3.792
/ Mol Cell Biol / Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins by SL Gregory (1996)10.1002/dvdy.21873
/ Dev Dyn / The homeobox gene Mohawk represses transcription by recruiting the sin3A/HDAC co-repressor complex by DM Anderson (2009)10.1016/S1097-2765(02)00443-4
/ Mol Cell / CtBP, an unconventional transcriptional corepressor in development and oncogenesis by G Chinnadurai (2002)10.1371/journal.pgen.1002769
/ PLoS Genet / Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos by PH Holmqvist (2012)10.1101/gad.1509007
/ Genes Dev / A core transcriptional network for early mesoderm development in Drosophila melanogaster by T Sandmann (2007)10.1242/dev.125.20.3989
/ Development / The Drosophila SOX-domain protein Dichaete is required for the development of the central nervous system midline by NS Soriano (1998)10.1016/j.cell.2012.12.009
/ Cell / DNA-binding specificities of human transcription factors by A Jolma (2013)10.1093/bioinformatics/btn645
/ Bioinformatics / Predicting the binding preference of transcription factors to individual DNA k-mers by TM Alleyne (2009)10.1016/j.devcel.2011.09.008
/ Dev Cell / Animal transcription networks as highly connected, quantitative continua by MD Biggin (2011)10.1016/j.jmb.2011.07.032
/ J Mol Biol / Structural constraints in collaborative competition of transcription factors against the nucleosome by G Moyle-Heyrman (2011)10.1073/pnas.0913805107
/ Proc Natl Acad Sci U S A / Nucleosome-mediated cooperativity between transcription factors by LA Mirny (2010)10.1101/gr.094144.109
/ Genome Res / Distinguishing direct versus indirect transcription factor-DNA interactions by R Gordan (2009)10.1186/gb-2009-10-7-r80
/ Genome Biol / Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions by S MacArthur (2009)10.1038/459927a
/ Nature / Unlocking the secrets of the genome by SE Celniker (2009)10.1371/journal.pbio.1000013
/ PLoS Biol / Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos by B Schuettengruber (2009)10.1073/pnas.0930314100
/ Proc Natl Acad Sci U S A / On schemes of combinatorial transcription logic by NE Buchler (2003)- Boris Iglewicz DCH (1993) How to detect and handle outliers. Milwaukee: ASQC Quality Press.
10.1093/bioinformatics/btr064
/ Bioinformatics / FIMO: scanning for occurrences of a given motif by Charles E Grant (2011)- Abdi H (2007) Part (Semi Partial) and Partial Regression Coefficients. In: Salkind NJ, editor. Encyclopedia of Measurement and Statistics. New York: SAGE Publications.
10.1007/978-1-61779-043-0_17
/ Methods Mol Biol / Development of expression-ready constructs for generation of proteomic libraries by C Yu (2011)10.1038/nature07388
/ Nature / The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila by HL Liang (2008)
Dates
Type | When |
---|---|
Created | 12 years, 1 month ago (Aug. 1, 2013, 4:46 p.m.) |
Deposited | 3 years, 6 months ago (March 2, 2022, 3:14 p.m.) |
Indexed | 4 months, 2 weeks ago (April 17, 2025, 6:08 a.m.) |
Issued | 12 years, 1 month ago (Aug. 1, 2013) |
Published | 12 years, 1 month ago (Aug. 1, 2013) |
Published Online | 12 years, 1 month ago (Aug. 1, 2013) |
@article{Cheng_2013, title={Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy}, volume={9}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1003571}, DOI={10.1371/journal.pgen.1003571}, number={8}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Cheng, Qiong and Kazemian, Majid and Pham, Hannah and Blatti, Charles and Celniker, Susan E. and Wolfe, Scot A. and Brodsky, Michael H. and Sinha, Saurabh}, editor={Mann, Richard S.}, year={2013}, month=aug, pages={e1003571} }