Crossref
journal-article
Elsevier BV
Trends in Biochemical Sciences (78)
References
250
Referenced
490
10.1016/j.cell.2011.10.053
/ Cell / Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins by Slattery (2011)10.1016/j.celrep.2013.03.014
/ Cell Rep. / Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape by Gordân (2013)10.1016/j.molcel.2010.05.004
/ Mol. Cell / Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities by Heinz (2010)10.1101/gr.132811.111
/ Genome Res. / Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding by Yanez-Cuna (2012)10.1093/bioinformatics/16.1.16
/ Bioinformatics / DNA binding sites: representation and discovery by Stormo (2000)10.1146/annurev.biophys.36.040306.132725
/ Annu. Rev. Biophys. Biomol. Struct. / Predictive modeling of genome-wide mRNA expression: from modules to molecules by Bussemaker (2007)10.1126/science.1162327
/ Science / Diversity and complexity in DNA recognition by transcription factors by Badis (2009)10.1038/nrg2845
/ Nat. Rev. Genet. / Determining the specificity of protein–DNA interactions by Stormo (2010)10.1038/nbt.2486
/ Nat. Biotechnol. / Evaluation of methods for modeling transcription factor sequence specificity by Weirauch (2013)10.1016/j.cell.2012.12.009
/ Cell / DNA-binding specificities of human transcription factors by Jolma (2013)10.1073/pnas.1307449110
/ Proc. Natl. Acad. Sci. U.S.A. / Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks by White (2013)10.1126/science.1164265
/ Science / DNA binding site sequence directs glucocorticoid receptor structure and activity by Meijsing (2009)10.1038/nature08473
/ Nature / The role of DNA shape in protein–DNA recognition by Rohs (2009)10.1126/science.1229223
/ Science / Probing allostery through DNA by Kim (2013)10.1038/nsmb.2595
/ Nat. Struct. Mol. Biol. / The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals by Watson (2013)10.1038/msb.2011.89
/ Mol. Syst. Biol. / Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex by Siggers (2011)10.1016/j.sbi.2007.12.002
/ Curr. Opin. Struct. Biol. / The enhanceosome by Panne (2008)10.1101/gr.093450.109
/ Genome Res. / An ensemble model of competitive multi-factor binding of the genome by Wasson (2009)10.1038/nsmb.1800
/ Nat. Struct. Mol. Biol. / Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs by Kitayner (2010)10.1101/gr.5655606
/ Genome Res. / Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection by Liu (2006)10.1038/nature07667
/ Nature / The DNA-encoded nucleosome organization of a eukaryotic genome by Kaplan (2009)10.1016/j.tig.2010.08.003
/ Trends Genet. / Gene regulation by nucleosome positioning by Bai (2010)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 Kaplan (2011)10.1101/gr.112623.110
/ Genome Res. / Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data by Pique-Regi (2011)10.1101/gr.139105.112
/ Genome Res. / Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors by Wang (2012)10.1128/MCB.23.5.1623-1632.2003
/ Mol. Cell. Biol. / Collaborative competition mechanism for gene activation in vivo by Miller (2003)10.1073/pnas.0913805107
/ Proc. Natl. Acad. Sci. U.S.A. / Nucleosome-mediated cooperativity between transcription factors by Mirny (2010)10.1016/j.sbi.2011.02.003
/ Curr. Opin. Struct. Biol. / Recognizing and remodeling the nucleosome by Glatt (2011)10.1016/j.molcel.2014.04.006
/ Mol. Cell / Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers by Barozzi (2014)10.1073/pnas.1216822110
/ Proc. Natl. Acad. Sci. U.S.A. / Probing DNA shape and methylation state on a genomic scale with DNase I by Lazarovici (2013)10.1371/journal.pcbi.1000916
/ PLoS Comput. Biol. / High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions by Agius (2010)10.1016/S1097-2765(01)00392-6
/ Mol. Cell / Recognition of specific DNA sequences by Garvie (2001)10.1146/annurev.biophys.34.040204.144521
/ Annu. Rev. Biophys. Biomol. Struct. / From ‘simple’ DNA–protein interactions to the macromolecular machines of gene expression by von Hippel (2007){'key': '10.1016/j.tibs.2014.07.002_bib0170', 'series-title': 'Protein–Nucleic Acid Interactions: Structural Biology', 'first-page': '47', 'article-title': 'Structural basis for sequence-specific DNA recognition by transcription factors and their complexes', 'author': 'Hong', 'year': '2008'}
/ Protein–Nucleic Acid Interactions: Structural Biology / Structural basis for sequence-specific DNA recognition by transcription factors and their complexes by Hong (2008){'key': '10.1016/j.tibs.2014.07.002_bib0175', 'series-title': 'Protein–Nucleic Acid Interactions: Structural Biology', 'first-page': '66', 'article-title': 'Indirect readout of DNA sequence by proteins', 'author': 'Lawson', 'year': '2008'}
/ Protein–Nucleic Acid Interactions: Structural Biology / Indirect readout of DNA sequence by proteins by Lawson (2008)10.1038/nsmb.1441
/ Nat. Struct. Mol. Biol. / Visualizing one-dimensional diffusion of proteins along DNA by Gorman (2008)10.1016/S0070-2153(09)88003-4
/ Curr. Top. Dev. Biol. / Hox specificity unique roles for cofactors and collaborators by Mann (2009)10.1016/j.tig.2009.12.003
/ Trends Genet. / Mechanisms of transcription factor selectivity by Pan (2010)10.1146/annurev-biochem-060408-091030
/ Annu. Rev. Biochem. / Origins of specificity in protein–DNA recognition by Rohs (2010)10.1016/j.sbi.2011.03.002
/ Curr. Opin. Struct. Biol. / DNA shape, genetic codes, and evolution by Parker (2011)10.1146/annurev-genet-110711-155437
/ Annu. Rev. Genet. / Disentangling the many layers of eukaryotic transcriptional regulation by Lelli (2012)10.1016/j.sbi.2012.01.004
/ Curr. Opin. Struct. Biol. / Towards a molecular view of transcriptional control by Zakrzewska (2012)10.1007/s40484-013-0012-4
/ Quant. Biol. / Modeling the specificity of protein–DNA interactions by Stormo (2013)10.1016/j.ceb.2013.07.006
/ Curr. Opin. Cell Biol. / Lineages, cell types and functional states: a genomic view by Ostuni (2013)10.1007/s00439-013-1413-1
/ Hum. Genet. / The grammar of transcriptional regulation by Weingarten-Gabbay (2014)10.1038/nrg3682
/ Nat. Rev. Genet. / Transcriptional enhancers: from properties to genome-wide predictions by Shlyueva (2014)10.1093/nar/gkt1112
/ Nucleic Acids Res. / Protein–DNA binding: complexities and multi-protein codes by Siggers (2014)10.1038/nrg3684
/ Nat. Rev. Genet. / In pursuit of design principles of regulatory sequences by Levo (2014)10.1016/j.sbi.2009.03.002
/ Curr. Opin. Struct. Biol. / Nuance in the double-helix and its role in protein–DNA recognition by Rohs (2009)10.1093/nar/28.1.235
/ Nucleic Acids Res. / The Protein Data Bank by Berman (2000)10.1101/gad.1900610
/ Genes Dev. / The shape of the DNA minor groove directs binding by the DNA-bending protein Fis by Stella (2010)10.1093/nar/gkt357
/ Nucleic Acids Res. / Control of DNA minor groove width and Fis protein binding by the purine 2-amino group by Hancock (2013)10.1093/nar/gkt584
/ Nucleic Acids Res. / Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion by Chen (2013)10.1016/j.celrep.2013.03.002
/ Cell Rep. / Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen by Chang (2013)10.1002/bmb.20650
/ Biochem. Mol. Biol. Educ. / Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes by Dantas Machado (2012)10.1016/j.celrep.2012.10.012
/ Cell Rep. / DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation by Chen (2012)10.1093/nar/gkt1219
/ Nucleic Acids Res. / Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling by Zhang (2014)10.1016/j.str.2005.07.005
/ Structure / Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites by Rohs (2005)10.1016/j.cell.2007.05.019
/ Cell / An atomic model of the interferon-beta enhanceosome by Panne (2007){'key': '10.1016/j.tibs.2014.07.002_bib0300', 'first-page': '28', 'article-title': 'Fitting a mixture model by expectation maximization to discover motifs in biopolymers', 'volume': '2', 'author': 'Bailey', 'year': '1994', 'journal-title': 'Proc. Internat. Conf. Intell. Syst. Mol. Biol.'}
/ Proc. Internat. Conf. Intell. Syst. Mol. Biol. / Fitting a mixture model by expectation maximization to discover motifs in biopolymers by Bailey (1994)10.1038/nbt1098-939
/ Nat. Biotechnol. / Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation by Roth (1998){'key': '10.1016/j.tibs.2014.07.002_bib0310', 'first-page': '269', 'article-title': 'Combinatorial approaches to finding subtle signals in DNA sequences', 'volume': '8', 'author': 'Pevzner', 'year': '2000', 'journal-title': 'Proc. Int. Conf. Intell. Syst. Mol. Biol.'}
/ Proc. Int. Conf. Intell. Syst. Mol. Biol. / Combinatorial approaches to finding subtle signals in DNA sequences by Pevzner (2000){'key': '10.1016/j.tibs.2014.07.002_bib0315', 'series-title': 'RECOMB’03 Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology', 'first-page': '28', 'article-title': 'Modeling dependencies in protein–DNA binding sites', 'author': 'Barash', 'year': '2003'}
/ RECOMB’03 Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology / Modeling dependencies in protein–DNA binding sites by Barash (2003)10.1093/nar/5.9.3157
/ Nucleic Acids Res. / DNAse footprinting: a simple method for the detection of protein–DNA binding specificity by Galas (1978)10.1093/nar/9.13.3047
/ Nucleic Acids Res. / A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system by Garner (1981)10.1038/nbt1053
/ Nat. Biotechnol. / Assessing computational tools for the discovery of transcription factor binding sites by Tompa (2005)10.1186/1745-6150-1-11
/ Biol. Direct / A survey of motif discovery methods in an integrated framework by Sandve (2006)10.1093/nar/gki439
/ Nucleic Acids Res. / enoLOGOS: a versatile web tool for energy normalized sequence logos by Workman (2005)10.1093/nar/29.12.2471
/ Nucleic Acids Res. / Non-independence of Mnt repressor–operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay by Man (2001)10.1093/nar/30.5.1255
/ Nucleic Acids Res. / Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors by Bulyk (2002)10.1093/bioinformatics/btm055
/ Bioinformatics / Position dependencies in transcription factor binding sites by Tomovic (2007)10.1371/journal.pcbi.1000154
/ PLoS Comput. Biol. / A feature-based approach to modeling protein–DNA interactions by Sharon (2008)10.1534/genetics.112.138685
/ Genetics / Improved models for transcription factor binding site identification using nonindependent interactions by Zhao (2012)10.1093/bioinformatics/btt221
/ Bioinformatics / Stability selection for regression-based models of transcription factor-DNA binding specificity by Mordelet (2013)10.1093/nar/gkn361
/ Nucleic Acids Res. / Extracting sequence features to predict protein–DNA interactions: a comparative study by Zhou (2008)10.1073/pnas.95.19.11163
/ Proc. Natl. Acad. Sci. U.S.A. / DNA sequence-dependent deformability deduced from protein–DNA crystal complexes by Olson (1998){'key': '10.1016/j.tibs.2014.07.002_bib0385', 'series-title': 'Oxford Handbook of Nucleic Acid Structures', 'first-page': '455', 'article-title': 'DNA bending by adenine–thymine tracts', 'author': 'Crothers', 'year': '1999'}
/ Oxford Handbook of Nucleic Acid Structures / DNA bending by adenine–thymine tracts by Crothers (1999)10.1093/nar/gkt437
/ Nucleic Acids Res. / DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale by Zhou (2013)10.1093/nar/gkt1087
/ Nucleic Acids Res. / TFBSshape: a motif database for DNA shape features of transcription factor binding sites by Yang (2014)10.1093/nar/gkt862
/ Nucleic Acids Res. / Covariation between homeodomain transcription factors and the shape of their DNA binding sites by Dror (2014)10.1093/bioinformatics/btl565
/ Bioinformatics / Predicting transcription factor affinities to DNA from a biophysical model by Roider (2007)10.1371/journal.pcbi.1000590
/ PLoS Comput. Biol. / Inferring binding energies from selected binding sites by Zhao (2009)10.1093/nar/gkt250
/ Nucleic Acids Res. / TherMos: estimating protein–DNA binding energies from in vivo binding profiles by Sun (2013)10.1093/nar/26.10.2306
/ Nucleic Acids Res. / Quantitative parameters for amino acid-base interaction: implications for prediction of protein–DNA binding sites by Mandel-Gutfreund (1998)10.1016/j.jmb.2004.09.029
/ J. Mol. Biol. / A simple physical model for the prediction and design of protein–DNA interactions by Havranek (2004)10.1093/nar/gki875
/ Nucleic Acids Res. / Protein–DNA binding specificity predictions with structural models by Morozov (2005)10.1371/journal.pcbi.0010001
/ PLoS Comput. Biol. / Ab initio prediction of transcription factor targets using structural knowledge by Kaplan (2005)10.1016/j.jmb.2004.11.010
/ J. Mol. Biol. / Structural alignment of protein–DNA interfaces: insights into the determinants of binding specificity by Siggers (2005)10.1093/nar/gkl1155
/ Nucleic Acids Res. / Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry by Siggers (2007)10.1016/j.sbi.2012.06.002
/ Curr. Opin. Struct. Biol. / Atomistic modeling of protein–DNA interaction specificity: progress and applications by Liu (2012)10.1093/nar/gks771
/ Nucleic Acids Res. / Improved predictions of transcription factor binding sites using physicochemical features of DNA by Maienschein-Cline (2012)10.1093/nar/gks283
/ Nucleic Acids Res. / A flexible integrative approach based on random forest improves prediction of transcription factor binding sites by Hooghe (2012)10.1186/1471-2105-14-S10-S2
/ BMC bioinformatics / Evaluating a linear k-mer model for protein–DNA interactions using high-throughput SELEX data by Kahara (2013)10.1038/nbt1246
/ Nat. Biotechnol. / Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities by Berger (2006)10.1186/gb-2011-12-7-r70
/ Genome Biol. / Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits by Wong (2011)10.1038/ni.2151
/ Nat. Immunol. / Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-kappaB family DNA binding by Siggers (2012)10.1101/gr.5113606
/ Genome Res. / Extensive low-affinity transcriptional interactions in the yeast genome by Tanay (2006)10.1016/j.ygeno.2010.01.002
/ Genomics / Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites by Jaeger (2010)10.1101/gad.1890410
/ Genes Dev. / Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity by Rowan (2010)10.1038/msb.2012.48
/ Mol. Syst. Biol. / A model of spatially restricted transcription in opposing gradients of activators and repressors by White (2012)10.1126/science.1131007
/ Science / A systems approach to measuring the binding energy landscapes of transcription factors by Maerkl (2007)10.1016/j.cell.2008.05.023
/ Cell / Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites by Noyes (2008)10.1093/nar/gkp424
/ Nucleic Acids Res. / Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays by Bonham (2009)10.1186/gb-2011-12-12-r125
/ Genome Biol. / Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights by Gordân (2011)10.1073/pnas.1310430110
/ Proc. Natl. Acad. Sci. U.S.A. / DNA-binding specificity changes in the evolution of forkhead transcription factors by Nakagawa (2013)10.1016/j.cell.2008.05.024
/ Cell / Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences by Berger (2008)10.1101/gr.139014.112
/ Genome Res. / Exploring the DNA-recognition potential of homeodomains by Chu (2012)10.1038/nbt.1882
/ Nat. Biotechnol. / Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument by Nutiu (2011)10.1093/nar/23.13.2531
/ Nucleic Acids Res. / Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains by Kim (1995)10.1101/gr.100552.109
/ Genome Res. / Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities by Jolma (2010)10.1073/pnas.1212457109
/ Proc. Natl. Acad. Sci. U.S.A. / Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses by Fordyce (2012)10.1016/B978-0-12-800046-5.00002-3
/ Int. Rev. Cell Mol. Biol. / The crowded nucleus by Hancock (2014)10.1007/s00018-013-1267-7
/ Cell. Mol. Life Sci. / Changes to cellular water and element content induced by nucleolar stress: investigation by a cryo-correlative nano-imaging approach by Nolin (2013)10.1002/bmb.20494
/ Biochem. Mol. Biol. Educ. / Miniseries: Illustrating the machinery of life: eukaryotic cell panorama by Goodsell (2011)10.1126/science.1243490
/ Science / Exonic transcription factor binding directs codon choice and affects protein evolution by Stergachis (2013)10.1038/nrg2814
/ Nat. Rev. Genet. / Annotating non-coding regions of the genome by Alexander (2010)10.1186/1471-2164-11-581
/ BMC Genomics / The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation by Lin (2010)10.1093/hmg/dds389
/ Hum. Mol. Genet. / A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat–Wilson syndrome phenotypes by El-Kasti (2012)10.1128/MCB.05065-11
/ Mol. Cell. Biol. / An NK and T cell enhancer lies 280 kilobase pairs 3′ to the gata3 structural gene by Hosoya-Ohmura (2011)10.1182/blood-2012-08-447839
/ Blood / A far downstream enhancer for murine Bcl11b controls its T-cell specific expression by Li (2013)10.1101/gr.169243.113
/ Genome Res. / Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features by Yanez-Cuna (2014)10.1093/bfgp/els034
/ Brief. Funct. Genomics / Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster by Slattery (2012)10.1126/science.1232542
/ Science / Genome-wide quantitative enhancer activity maps identified by STARR-seq by Arnold (2013)10.1038/nmeth.2558
/ Nat. Methods / Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos by Gisselbrecht (2013)10.1016/j.celrep.2012.09.010
/ Cell Rep. / A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster by Jory (2012)10.1016/j.celrep.2012.09.009
/ Cell Rep. / A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS by Manning (2012)10.1016/j.celrep.2012.09.011
/ Cell Rep. / A GAL4-driver line resource for Drosophila neurobiology by Jenett (2012)10.1038/nbt.2136
/ Nat. Biotechnol. / Massively parallel functional dissection of mammalian enhancers in vivo by Patwardhan (2012)10.1016/j.molcel.2014.02.026
/ Mol. Cell / Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin by Shlyueva (2014)10.1038/nature13395
/ Nature / Genome-scale functional characterization of Drosophila developmental enhancers in vivo by Kvon (2014)10.1016/j.tig.2011.01.001
/ Trends Genet. / Genome-wide transcription factor binding: beyond direct target regulation by MacQuarrie (2011)10.1038/nrg2636
/ Nat. Rev. Genet. / Insights from genomic profiling of transcription factors by Farnham (2009)10.1016/j.devcel.2011.09.008
/ Dev. Cell / Animal transcription networks as highly connected, quantitative continua by Biggin (2011)10.1371/journal.pbio.0060027
/ PLoS Biol. / Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm by Li (2008)10.1073/pnas.1209589110
/ Proc. Natl. Acad. Sci. U.S.A. / DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila by Fisher (2012)10.1016/j.tig.2009.08.003
/ Trends Genet. / Different gene regulation strategies revealed by analysis of binding motifs by Wunderlich (2009)10.1016/j.cell.2013.09.011
/ Cell / Mapping human epigenomes by Rivera (2013)10.1016/j.cell.2011.08.008
/ Cell / Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification by Tan (2011)10.1016/j.bbagrm.2014.03.001
/ Biochim. Biophys. Acta / Interpreting the language of histone and DNA modifications by Rothbart (2014)10.1016/j.gde.2012.02.013
/ Curr. Opin. Genet. Dev. / Combinatorial complexity in chromatin structure and function: revisiting the histone code by Rando (2012)10.1101/gr.144840.112
/ Genome Res. / Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types by Ernst (2013)10.1093/nar/gkt1319
/ Nucleic Acids Res. / Nucleosomes accelerate transcription factor dissociation by Luo (2014)10.1038/nature11232
/ Nature / The accessible chromatin landscape of the human genome by Thurman (2012)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 Li (2011)10.1038/nmeth.2441
/ Nat. Methods / Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics by Simicevic (2013)10.1371/journal.pone.0083506
/ PLoS ONE / Widespread misinterpretable ChIP-seq bias in yeast by Park (2013)10.1073/pnas.1316064110
/ Proc. Natl. Acad. Sci. U.S.A. / Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins by Teytelman (2013)10.1371/journal.pgen.1003571
/ PLoS Genet. / Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy by Cheng (2013)10.1101/gr.5533506
/ Genome Res. / FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin by Giresi (2007)10.1101/gr.121541.111
/ Genome Res. / Open chromatin defined by DNase I and FAIRE identifies regulatory elements that shape cell-type identity by Song (2011)10.1038/nmeth.1313
/ Nat. Methods / Global mapping of protein–DNA interactions in vivo by digital genomic footprinting by Hesselberth (2009)10.1038/nmeth.2688
/ Nat. Methods / Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position by Buenrostro (2013)10.1038/nbt.2798
/ Nat. Biotechnol. / Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape by Sherwood (2014)10.1016/j.tig.2011.07.002
/ Trends Genet. / Pioneer factors: directing transcriptional regulators within the chromatin environment by Magnani (2011)10.1101/gad.176826.111
/ Genes Dev. / Pioneer transcription factors: establishing competence for gene expression by Zaret (2011)10.1101/pdb.top070060
/ Cold Spring Harb. Protoc. / Confirming the functional importance of a protein–DNA interaction by Carey (2012)10.1534/genetics.112.146647
/ Genetics / The relationship between long-range chromatin occupancy and polymerization of the Drosophila ETS family transcriptional repressor Yan by Webber (2013)10.1016/j.cell.2013.03.035
/ Cell / Master transcription factors and mediator establish super-enhancers at key cell identity genes by Whyte (2013)10.1016/j.cell.2013.09.053
/ Cell / Super-enhancers in the control of cell identity and disease by Hnisz (2013)10.1038/msb.2010.35
/ Mol. Syst. Biol. / Dynamic CRM occupancy reflects a temporal map of developmental progression by Wilczynski (2010)10.1038/ng.808
/ Nat. Genet. / High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species by He (2011)10.1371/journal.pgen.1003753
/ PLoS Genet. / Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning by Slattery (2013)10.1371/journal.pgen.1003748
/ PLoS Genet. / Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression by Paris (2013)10.1038/nprot.2011.420
/ Nat. Protoc. / A computational pipeline for comparative ChIP-seq analyses by Bardet (2012)10.1038/nature09990
/ Nature / A cis-regulatory map of the Drosophila genome by Negre (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 Yip (2012)10.1101/gad.188052.112
/ Genes Dev. / HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature by Kvon (2012)10.1101/gr.168807.113
/ Genome Res. / Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster by Slattery (2014)10.1038/nmeth.2766
/ Nat. Methods / High-resolution mapping of transcription factor binding sites on native chromatin by Kasinathan (2014)10.1016/j.cell.2014.01.062
/ Cell / Single-molecule dynamics of enhanceosome assembly in embryonic stem cells by Chen (2014)10.1126/science.1101270
/ Science / Biochemistry. Completing the view of transcriptional regulation by von Hippel (2004){'key': '10.1016/j.tibs.2014.07.002_bib0860', 'series-title': 'Innovations in Biomolecular Modeling and Simulations', 'first-page': '53', 'article-title': 'Opposites attract: shape and electrostatic complementarity in protein–DNA complexes', 'author': 'Harris', 'year': '2012'}
/ Innovations in Biomolecular Modeling and Simulations / Opposites attract: shape and electrostatic complementarity in protein–DNA complexes by Harris (2012)10.1016/j.bpj.2013.08.033
/ Biophys. J. / Positive and negative design for nonconsensus protein–DNA binding affinity in the vicinity of functional binding sites by Afek (2013)10.1016/j.bpj.2013.01.038
/ Biophys. J. / Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein–DNA binding by Afek (2013)10.1016/j.bpj.2011.04.037
/ Biophys. J. / DNA sequence correlations shape nonspecific transcription factor–DNA binding affinity by Sela (2011)10.1093/nar/gku117
/ Nucleic Acids Res. / A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data by Orenstein (2014)10.1016/0092-8674(95)90136-1
/ Cell / Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome by Thanos (1995)10.1016/j.molcel.2007.04.022
/ Mol. Cell / Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer by Escalante (2007)10.1073/pnas.0400611101
/ Proc. Natl. Acad. Sci. U.S.A. / Coordinate enhancers share common organizational features in the Drosophila genome by Erives (2004)10.1371/journal.pbio.0060263
/ PLoS Biol. / Evolution acts on enhancer organization to fine-tune gradient threshold readouts by Crocker (2008)10.1016/j.cub.2007.09.035
/ Curr. Biol. / A rationale for the enhanceosome and other evolutionarily constrained enhancers by Papatsenko (2007)10.1371/journal.pgen.1002796
/ PLoS Genet. / Role of architecture in the function and specificity of two Notch-regulated transcriptional enhancer modules by Liu (2012)10.1016/j.devcel.2009.12.026
/ Dev. Cell / Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer by Swanson (2010)10.1016/j.cub.2011.05.056
/ Curr. Biol. / Rapid evolutionary rewiring of a structurally constrained eye enhancer by Swanson (2011)10.1093/nar/gkt598
/ Nucleic Acids Res. / Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development by Kazemian (2013)10.1038/emboj.2012.179
/ EMBO J. / The cis-regulatory code of Hox function in Drosophila by Sorge (2012)10.1002/jcb.20352
/ J. Cell. Biochem. / Transcriptional enhancers: intelligent enhanceosomes or flexible billboards? by Arnosti (2005)10.1242/dev.00890
/ Development / Information display by transcriptional enhancers by Kulkarni (2003)10.1093/nar/gkt1302
/ Nucleic Acids Res. / CCAT: Combinatorial Code Analysis Tool for transcriptional regulation by Jiang (2014)10.1186/gb-2013-14-8-r86
/ Genome Biol. / Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization by Menoret (2013)10.1038/ng.2713
/ Nat. Genet. / Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model by Smith (2013)10.1371/journal.pgen.1004060
/ PLoS Genet. / Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity by Erceg (2014)10.1016/j.cell.2012.01.030
/ Cell / A transcription factor collective defines cardiac cell fate and reflects lineage history by Junion (2012)10.1016/j.devcel.2011.04.008
/ Dev. Cell / Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators by Tijssen (2011)10.1016/j.molcel.2010.01.016
/ Mol. Cell / Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs by Giorgetti (2010)10.1016/j.cub.2013.10.004
/ Curr. Biol. / Gene regulation: when analog beats digital by Lorberbaum (2013)10.1016/j.cub.2013.09.043
/ Curr. Biol. / Msn2 coordinates a stoichiometric gene expression program by Stewart-Ornstein (2013)10.1016/j.cell.2012.01.056
/ Cell / Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity by Zhang (2012)10.1186/gb-2013-14-1-r5
/ Genome Biol. / Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs by Kudron (2013)10.1186/gb-2012-13-9-r52
/ Genome Biol. / Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 by Frietze (2012)10.1371/journal.pgen.1003288
/ PLoS Genet. / SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state by Lodato (2013)10.1016/j.cub.2013.11.017
/ Curr. Biol. / cis-regulatory requirements for tissue-specific programs of the circadian clock by Meireles-Filho (2014)10.1101/gr.135681.111
/ Genome Res. / Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner by Gertz (2012)10.1016/j.molcel.2013.08.037
/ Mol. Cell / Distinct properties of cell-type-specific and shared transcription factor binding sites by Gertz (2013)10.1038/nature08531
/ Nature / Combinatorial binding predicts spatio-temporal cis-regulatory activity by Zinzen (2009)10.1371/journal.pgen.1001114
/ PLoS Genet. / Chromatin landscape dictates HSF binding to target DNA elements by Guertin (2010)10.1038/ng.545
/ Nat. Genet. / Nucleosome dynamics define transcriptional enhancers by He (2010)10.1038/ng.759
/ Nat. Genet. / Chromatin accessibility pre-determines glucocorticoid receptor binding patterns by John (2011)10.1016/j.cell.2013.07.020
/ Cell / Developmental fate and cellular maturity encoded in human regulatory DNA landscapes by Stergachis (2013)10.1186/gb-2011-12-5-r43
/ Genome Biol. / Dynamic reprogramming of chromatin accessibility during Drosophila embryo development by Thomas (2011)10.1126/science.1196914
/ Science / Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project by Gerstein (2010)10.1101/gad.234534.113
/ Genes Dev. / Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila by Xu (2014)10.1016/j.devcel.2012.09.003
/ Dev. Cell / Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis by Xu (2012)10.1016/S0959-437X(02)00344-1
/ Curr. Opin. Genet. Dev. / Molecular mechanisms of selector gene function and evolution by Mann (2002)10.1038/nn.3467
/ Nat. Neurosci. / Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity by Mazzoni (2013)10.1093/nar/gks281
/ Nucleic Acids Res. / Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies by Bresnick (2012)10.1073/pnas.1108440108
/ Proc. Natl. Acad. Sci. U.S.A. / Genetic framework for GATA factor function in vascular biology by Linnemann (2011)10.1182/blood-2011-09-380634
/ Blood / Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis by Dore (2012)10.1016/j.molcel.2009.11.002
/ Mol. Cell / Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis by Yu (2009)10.1016/j.molcel.2012.05.051
/ Mol. Cell / Cofactor-mediated restriction of GATA-1 chromatin occupancy coordinates lineage-specific gene expression by Chlon (2012)10.1016/j.stem.2010.07.016
/ Cell Stem Cell / Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators by Wilson (2010){'key': '10.1016/j.tibs.2014.07.002_bib1110', 'first-page': '163', 'article-title': 'GATA factor switching during erythroid differentiation', 'volume': '17', 'author': 'Kaneko', 'year': '2010', 'journal-title': 'Curr. Opin. Hematol.'}
/ Curr. Opin. Hematol. / GATA factor switching during erythroid differentiation by Kaneko (2010)10.1182/blood-2010-10-313031
/ Blood / Context-dependent function of ‘GATA switch’ sites in vivo by Snow (2011)10.1182/blood-2013-01-476911
/ Blood / The Gata1 5′ region harbors distinct cis-regulatory modules that direct gene activation in erythroid cells and gene inactivation in HSCs by Takai (2013)10.1016/j.molcel.2009.11.001
/ Mol. Cell / Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy by Fujiwara (2009)10.1101/gr.125088.111
/ Genome Res. / Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration by Wu (2011)10.1111/gtc.12086
/ Genes Cells / GATA factor switching from GATA2 to GATA1 contributes to erythroid differentiation by Suzuki (2013)10.1016/j.molcel.2006.05.015
/ Mol. Cell / Structural basis of DNA recognition by p53 tetramers by Kitayner (2006)10.1016/S0022-2836(02)00386-8
/ J. Mol. Biol. / Solvent mediated interactions in the structure of the nucleosome core particle at 1.9Å resolution by Davey (2002)10.1371/journal.pone.0009722
/ PLoS ONE / Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix by Siddharthan (2010)10.1371/journal.pcbi.1003214
/ PLoS Comput. Biol. / The next generation of transcription factor binding site prediction by Mathelier (2013)10.1093/nar/gkt831
/ Nucleic Acids Res. / A general approach for discriminative de novo motif discovery from high-throughput data by Grau (2013)10.1371/journal.pone.0020059
/ PLoS ONE / A linear model for transcription factor binding affinity prediction in protein binding microarrays by Annala (2011)10.1093/bioinformatics/bti410
/ Bioinformatics / Identification of transcription factor binding sites with variable-order Bayesian networks by Ben-Gal (2005)10.1093/nar/14.16.6661
/ Nucleic Acids Res. / Quantitative analysis of the relationship between nucleotide sequence and functional activity by Stormo (1986)10.1101/gr.1271603
/ Genome Res. / A biophysical approach to transcription factor binding site discovery by Djordjevic (2003)10.1093/bioinformatics/btl223
/ Bioinformatics / Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE by Foat (2006)10.1371/journal.pcbi.0030215
/ PLoS Comput. Biol. / A nucleosome-guided map of transcription factor binding sites in yeast by Narlikar (2007)10.1101/gr.127712.111
/ Genome Res. / Sequence and chromatin determinants of cell-type-specific transcription factor binding by Arvey (2012)10.1126/science.290.5500.2306
/ Science / Genome-wide location and function of DNA binding proteins by Ren (2000)10.1126/science.1141319
/ Science / Genome-wide mapping of in vivo protein–DNA interactions by Johnson (2007)10.1016/j.cell.2011.11.013
/ Cell / Comprehensive genome-wide protein–DNA interactions detected at single-nucleotide resolution by Rhee (2011)10.1016/S0076-6879(06)10016-6
/ Methods Enzymol. / DamID: mapping of in vivo protein–genome interactions using tethered DNA adenine methyltransferase by Greil (2006)10.1016/j.cell.2007.12.014
/ Cell / High-resolution mapping and characterization of open chromatin across the genome by Boyle (2008)10.2144/000112049
/ Biotechniques / Counter-selectable marker for bacterial-based interaction trap systems by Meng (2006)10.1038/nprot.2008.195
/ Nat. Protoc. / Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors by Berger (2009)10.1073/pnas.0509843102
/ Proc. Natl. Acad. Sci. U.S.A. / Defining the sequence-recognition profile of DNA-binding molecules by Warren (2006)10.1038/nbt.1675
/ Nat. Biotechnol. / De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis by Fordyce (2010)10.1101/gr.072942.107
/ Genome Res. / High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes by Tantin (2008)10.1093/nar/gkp802
/ Nucleic Acids Res. / Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing by Zykovich (2009)
@article{Slattery_2014, title={Absence of a simple code: how transcription factors read the genome}, volume={39}, ISSN={0968-0004}, url={http://dx.doi.org/10.1016/j.tibs.2014.07.002}, DOI={10.1016/j.tibs.2014.07.002}, number={9}, journal={Trends in Biochemical Sciences}, publisher={Elsevier BV}, author={Slattery, Matthew and Zhou, Tianyin and Yang, Lin and Dantas Machado, Ana Carolina and Gordân, Raluca and Rohs, Remo}, year={2014}, month=sep, pages={381–399} }