Absence of a simple code: how transcription factors read the genome.

[1]  B. Strahl,et al.  Interpreting the language of histone and DNA modifications. , 2014, Biochimica et biophysica acta.

[2]  Manolis Kellis,et al.  Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster , 2014, Genome research.

[3]  E. Segal,et al.  In pursuit of design principles of regulatory sequences , 2014, Nature Reviews Genetics.

[4]  Lin Yang,et al.  Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers. , 2014, Molecular cell.

[5]  B. Dickson,et al.  Genome-scale functional characterization of Drosophila developmental enhancers in vivo , 2014, Nature.

[6]  Łukasz M. Boryń,et al.  Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. , 2014, Molecular cell.

[7]  Gerald Stampfel,et al.  Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features , 2014, Genome research.

[8]  Danyang Yu,et al.  Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila , 2014, Genes & development.

[9]  Wesley R. Legant,et al.  Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells , 2014, Cell.

[10]  A. Stark,et al.  Transcriptional enhancers: from properties to genome-wide predictions , 2014, Nature Reviews Genetics.

[11]  R. Shamir,et al.  A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data , 2014, Nucleic acids research.

[12]  Tatsunori B. Hashimoto,et al.  Discovery of non-directional and directional pioneer transcription factors by modeling DNase profile magnitude and shape , 2014, Nature Biotechnology.

[13]  A. Stark,et al.  cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock , 2014, Current Biology.

[14]  E. Segal,et al.  The grammar of transcriptional regulation , 2014, Human Genetics.

[15]  Lars Hufnagel,et al.  Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity , 2014, PLoS genetics.

[16]  Mona Singh,et al.  CCAT: Combinatorial Code Analysis Tool for transcriptional regulation , 2013, Nucleic acids research.

[17]  Michael G. Poirier,et al.  Nucleosomes accelerate transcription factor dissociation , 2013, Nucleic acids research.

[18]  Remo Rohs,et al.  Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling , 2013, Nucleic acids research.

[19]  R. Gordân,et al.  Protein–DNA binding: complexities and multi-protein codes , 2013, Nucleic acids research.

[20]  Lin Yang,et al.  TFBSshape: a motif database for DNA shape features of transcription factor binding sites , 2013, Nucleic Acids Res..

[21]  Remo Rohs,et al.  Covariation between homeodomain transcription factors and the shape of their DNA binding sites , 2013, Nucleic acids research.

[22]  Jens Keilwagen,et al.  A general approach for discriminative de novo motif discovery from high-throughput data , 2013, GCB.

[23]  R. Hancock.  The crowded nucleus. , 2014, International review of cell and molecular biology.

[24]  Alex P. Reynolds,et al.  Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution , 2013, Science.

[25]  Vishwanath R. Iyer,et al.  Widespread Misinterpretable ChIP-seq Bias in Yeast , 2013, PloS one.

[26]  Hana El-Samad,et al.  Msn2 Coordinates a Stoichiometric Gene Expression Program , 2013, Current Biology.

[27]  David S. Lorberbaum,et al.  Gene Regulation: When Analog Beats Digital , 2013, Current Biology.

[28]  Renato Ostuni,et al.  Lineages, cell types and functional states: a genomic view. , 2013, Current opinion in cell biology.

[29]  Masayuki Yamamoto,et al.  The Gata1 5' region harbors distinct cis-regulatory modules that direct gene activation in erythroid cells and gene inactivation in HSCs. , 2013, Blood.

[30]  H. Aburatani,et al.  GATA factor switching from GATA2 to GATA1 contributes to erythroid differentiation , 2013, Genes to cells : devoted to molecular & cellular mechanisms.

[31]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[32]  Alexander van Oudenaarden,et al.  Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins , 2013, Proceedings of the National Academy of Sciences.

[33]  Timothy E. Reddy,et al.  Distinct properties of cell-type-specific and shared transcription factor binding sites. , 2013, Molecular cell.

[34]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[35]  A. Afek,et al.  Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites. , 2013, Biophysical journal.

[36]  B. Ren,et al.  Mapping Human Epigenomes , 2013, Cell.

[37]  Kevin P. White,et al.  Divergent Transcriptional Regulatory Logic at the Intersection of Tissue Growth and Developmental Patterning , 2013, PLoS genetics.

[38]  Wyeth W. Wasserman,et al.  The Next Generation of Transcription Factor Binding Site Prediction , 2013, PLoS Comput. Biol..

[39]  Stein Aerts,et al.  Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization , 2013, Genome Biology.

[40]  Shane J. Neph,et al.  Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes , 2013, Cell.

[41]  Harri Lähdesmäki,et al.  Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data , 2013, BMC Bioinformatics.

[42]  H. Kueh,et al.  A far downstream enhancer for murine Bcl11b controls its T-cell specific expression. , 2013, Blood.

[43]  Remo Rohs,et al.  Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion , 2013, Nucleic acids research.

[44]  Charles Blatti,et al.  Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy , 2013, PLoS genetics.

[45]  J. Shendure,et al.  Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model , 2013, Nature Genetics.

[46]  Martha L. Bulyk,et al.  Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos , 2013, Nature Methods.

[47]  Saurabh Sinha,et al.  Program in Gene Function and Expression Publications and Presentations Program in Gene Function and Expression 9-2013 Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development , 2014 .

[48]  Martha L. Bulyk,et al.  DNA-binding specificity changes in the evolution of forkhead transcription factors , 2013, Proceedings of the National Academy of Sciences.

[49]  B. Cohen,et al.  Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks , 2013, Proceedings of the National Academy of Sciences.

[50]  Manolis Kellis,et al.  Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types , 2013, Genome research.

[51]  Carolyn A. Morrison,et al.  Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity , 2013, Nature Neuroscience.

[52]  Barbara E. Engelhardt,et al.  Stability selection for regression-based models of transcription factor–DNA binding specificity , 2013, Bioinform..

[53]  Lin Yang,et al.  DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale , 2013, Nucleic Acids Res..

[54]  Remo Rohs,et al.  Control of DNA minor groove width and Fis protein binding by the purine 2-amino group , 2013, Nucleic acids research.

[55]  K. Yamamoto,et al.  The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals , 2013, Nature Structural &Molecular Biology.

[56]  M. Bulyk,et al.  Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. , 2013, Cell reports.

[57]  Remo Rohs,et al.  Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen. , 2013, Cell reports.

[58]  Shyam Prabhakar,et al.  TherMos: Estimating protein–DNA binding energies from in vivo binding profiles , 2013, Nucleic acids research.

[59]  Frédérique Lisacek,et al.  Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics , 2013, Nature Methods.

[60]  Steven Henikoff,et al.  High-resolution mapping of transcription factor binding sites on native chromatin , 2013, Epigenetics & Chromatin.

[61]  Gary D. Stormo,et al.  Modeling the specificity of protein-DNA interactions , 2013, Quantitative Biology.

[62]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[63]  R. Sandstrom,et al.  Probing DNA shape and methylation state on a genomic scale with DNase I , 2013, Proceedings of the National Academy of Sciences.

[64]  Ariel Afek,et al.  Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding. , 2013, Biophysical journal.

[65]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[66]  Michael B. Eisen,et al.  Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression Permalink , 2013 .

[67]  Lijiang Yang,et al.  Probing Allostery Through DNA , 2013, Science.

[68]  G. Balossier,et al.  Changes to cellular water and element content induced by nucleolar stress: investigation by a cryo-correlative nano-imaging approach , 2013, Cellular and Molecular Life Sciences.

[69]  K. White,et al.  The Relationship Between Long-Range Chromatin Occupancy and Polymerization of the Drosophila ETS Family Transcriptional Repressor Yan , 2013, Genetics.

[70]  R. Jaenisch,et al.  SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State , 2013, PLoS genetics.

[71]  Atina G. Coté,et al.  Evaluation of methods for modeling transcription factor sequence specificity , 2013, Nature Biotechnology.

[72]  Juan M. Vaquerizas,et al.  DNA-Binding Specificities of Human Transcription Factors , 2013, Cell.

[73]  Michelle M. Kudron,et al.  Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs , 2013, Genome Biology.

[74]  Timothy Wells,et al.  A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes. , 2012, Human molecular genetics.

[75]  James B. Brown,et al.  DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila , 2012, Proceedings of the National Academy of Sciences.

[76]  Remo Rohs,et al.  DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation. , 2012, Cell reports.

[77]  R. Mann,et al.  Disentangling the many layers of eukaryotic transcriptional regulation. , 2012, Annual review of genetics.

[78]  Richard M Myers,et al.  Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner , 2012, Genome research.

[79]  R. Rohs,et al.  Multimedia in Biochemistry and Molecular Biology Education Proteopedia: 3D Visualization and Annotation of Transcription Factor–DNA Readout Modes , 2012 .

[80]  Gerald M Rubin,et al.  A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. , 2012, Cell reports.

[81]  Gerald M Rubin,et al.  A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS. , 2012, Cell reports.

[82]  Julie H. Simpson,et al.  A GAL4-driver line resource for Drosophila neurobiology. , 2012, Cell reports.

[83]  Polly M Fordyce,et al.  Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses , 2012, Proceedings of the National Academy of Sciences.

[84]  A. Stark,et al.  Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding , 2012, Genome research.

[85]  Zhiping Weng,et al.  Exploring the DNA-recognition potential of homeodomains , 2012, Genome research.

[86]  Luca Pinello,et al.  Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.

[87]  Scott Barolo,et al.  A model of spatially restricted transcription in opposing gradients of activators and repressors , 2012, Molecular systems biology.

[88]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[89]  Zhenqing Ye,et al.  Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 , 2012, Genome Biology.

[90]  K. White,et al.  Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. , 2012, Briefings in functional genomics.

[91]  William Stafford Noble,et al.  Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors , 2012, Genome research.

[92]  William Stafford Noble,et al.  Sequence and chromatin determinants of cell-type–specific transcription factor binding , 2012, Genome research.

[93]  J. Crispino,et al.  Cofactor-mediated restriction of GATA-1 chromatin occupancy coordinates lineage-specific gene expression. , 2012, Molecular cell.

[94]  Fangping Mu,et al.  Improved predictions of transcription factor binding sites using physicochemical features of DNA , 2012, Nucleic acids research.

[95]  Philip Bradley,et al.  Atomistic modeling of protein-DNA interaction specificity: progress and applications. , 2012, Current opinion in structural biology.

[96]  Martin H. Schaefer,et al.  The cis‐regulatory code of Hox function in Drosophila , 2012, The EMBO journal.

[97]  G. Stormo,et al.  Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions , 2012, Genetics.

[98]  C. Peterson,et al.  Confirming the functional importance of a protein-DNA interaction. , 2012, Cold Spring Harbor protocols.

[99]  J. Posakony,et al.  Role of Architecture in the Function and Specificity of Two Notch-Regulated Transcriptional Enhancer Modules , 2012, PLoS genetics.

[100]  Barry J Dickson,et al.  HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. , 2012, Genes & development.

[101]  Christopher D. Brown,et al.  Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis. , 2012, Blood.

[102]  B. Williams,et al.  Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity , 2012, Cell.

[103]  F. van Roy,et al.  A flexible integrative approach based on random forest improves prediction of transcription factor binding sites , 2012, Nucleic acids research.

[104]  Kirby D. Johnson,et al.  Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies , 2012, Nucleic acids research.

[105]  Richard Lavery,et al.  Towards a molecular view of transcriptional control. , 2012, Current opinion in structural biology.

[106]  O. Rando,et al.  Combinatorial complexity in chromatin structure and function: revisiting the histone code. , 2012, Current opinion in genetics & development.

[107]  Joseph B Hiatt,et al.  Massively parallel functional dissection of mammalian enhancers in vivo , 2012, Nature Biotechnology.

[108]  E. Birney,et al.  A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History , 2012, Cell.

[109]  J. Ragoussis,et al.  Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding , 2011, Nature Immunology.

[110]  J. Zeitlinger,et al.  A computational pipeline for comparative ChIP-seq analyses , 2011, Nature Protocols.

[111]  Kevin Y. Yip,et al.  Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors , 2012, Genome Biology.

[112]  Raluca Gordân,et al.  Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights , 2011, Genome Biology.

[113]  B. Pugh,et al.  Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.

[114]  R. Mann,et al.  Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins , 2011, Cell.

[115]  Martha L Bulyk,et al.  Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex , 2011, Molecular systems biology.

[116]  J. Carroll,et al.  Pioneer transcription factors: establishing competence for gene expression. , 2011, Genes & development.

[117]  J. Eeckhoute,et al.  Pioneer factors: directing transcriptional regulators within the chromatin environment. , 2011, Trends in genetics : TIG.

[118]  M. Biggin.  Animal transcription networks as highly connected, quantitative continua. , 2011, Developmental cell.

[119]  Nathan C. Sheffield,et al.  Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. , 2011, Genome research.

[120]  Manolis Kellis,et al.  Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. , 2011, Genome research.

[121]  Zhike Lu,et al.  Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.

[122]  Emery H. Bresnick,et al.  Genetic framework for GATA factor function in vascular biology , 2011, Proceedings of the National Academy of Sciences.

[123]  Martha Bulyk,et al.  Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits , 2011, Genome Biology.

[124]  S. Barolo,et al.  Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer , 2011, Current Biology.

[125]  D. B. Lukatsky,et al.  DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity. , 2011, Biophysical journal.

[126]  S. Luo,et al.  Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument , 2011, Nature Biotechnology.

[127]  C. Müller,et al.  Recognizing and remodeling the nucleosome. , 2011, Current opinion in structural biology.

[128]  Stephen C. J. Parker,et al.  DNA shape, genetic codes, and evolution. , 2011, Current opinion in structural biology.

[129]  H. Lähdesmäki,et al.  A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays , 2011, PloS one.

[130]  W. Ouwehand,et al.  Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators , 2011, Developmental cell.

[131]  R. Sandstrom,et al.  Dynamic reprogramming of chromatin accessibility during Drosophila embryo development , 2011, Genome Biology.

[132]  Tohru Fujiwara,et al.  Context-dependent function of "GATA switch" sites in vivo. , 2011, Blood.

[133]  J. Zeitlinger,et al.  High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species , 2011, Nature Genetics.

[134]  J. Stamatoyannopoulos,et al.  The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding , 2011, Genome Biology.

[135]  Abraham P. Fong,et al.  Genome-wide transcription factor binding: beyond direct target regulation. , 2011, Trends in genetics : TIG.

[136]  J. D. Engel,et al.  An NK and T Cell Enhancer Lies 280 Kilobase Pairs 3′ to the Gata3 Structural Gene , 2011, Molecular and Cellular Biology.

[137]  D. Goodsell.  Eukaryotic cell panorama , 2011, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[138]  Jacob F. Degner,et al.  Sequence and Chromatin Accessibility Data Accurate Inference of Transcription Factor Binding from Dna Material Supplemental Open Access , 2022 .

[139]  Robert L. Grossman,et al.  A cis-regulatory map of the Drosophila genome , 2011, Nature.

[140]  J. Stamatoyannopoulos,et al.  Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development , 2011, PLoS genetics.

[141]  J. Stamatoyannopoulos,et al.  Chromatin accessibility pre-determines glucocorticoid receptor binding patterns , 2011, Nature Genetics.

[142]  Raymond K. Auerbach,et al.  Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project , 2010, Science.

[143]  G. Stormo,et al.  Determining the specificity of protein–DNA interactions , 2010, Nature Reviews Genetics.

[144]  Alexandre V Morozov,et al.  Gene regulation by nucleosome positioning. , 2010, Trends in genetics : TIG.

[145]  Wei-Sheng Wu,et al.  The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation , 2010, BMC Genomics.

[146]  W. Ouwehand,et al.  Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. , 2010, Cell stem cell.

[147]  Michael J. Guertin,et al.  Chromatin Landscape Dictates HSF Binding to Target DNA Elements , 2010, PLoS genetics.

[148]  S. Quake,et al.  De Novo Identification and Biophysical Characterization of Transcription Factor Binding Sites with Microfluidic Affinity Analysis , 2010, Nature Biotechnology.

[149]  William Stafford Noble,et al.  High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions , 2010, PLoS Comput. Biol..

[150]  M. Gerstein,et al.  Annotating non-coding regions of the genome , 2010, Nature Reviews Genetics.

[151]  Bartek Wilczyński,et al.  Dynamic CRM occupancy reflects a temporal map of developmental progression , 2010, Molecular systems biology.

[152]  R. Mann,et al.  Origins of specificity in protein-DNA recognition. , 2010, Annual review of biochemistry.

[153]  Juan M. Vaquerizas,et al.  Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. , 2010, Genome research.

[154]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[155]  Martha L Bulyk,et al.  Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. , 2010, Genes & development.

[156]  Duilio Cascio,et al.  The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. , 2010, Genes & development.

[157]  Esther T. Chan,et al.  Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. , 2010, Genomics.

[158]  B. Honig,et al.  Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs , 2010, Nature Structural &Molecular Biology.

[159]  H. Rozenberg,et al.  Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3) , 2010 .

[160]  R. Siddharthan.  Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix , 2010, PloS one.

[161]  S. Barolo,et al.  Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer. , 2010, Developmental cell.

[162]  Clifford A. Meyer,et al.  Nucleosome Dynamics Define Transcriptional Enhancers , 2010, Nature Genetics.

[163]  Masayuki Yamamoto,et al.  GATA factor switching during erythroid differentiation , 2010, Current opinion in hematology.

[164]  Guido Tiana,et al.  Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. , 2010, Molecular cell.

[165]  R. Nussinov,et al.  Mechanisms of transcription factor selectivity. , 2010, Trends in genetics : TIG.

[166]  L. Mirny,et al.  Nucleosome-mediated cooperativity between transcription factors , 2009, Proceedings of the National Academy of Sciences.

[167]  Yue Zhao,et al.  Inferring Binding Energies from Selected Binding Sites , 2009, PLoS Comput. Biol..

[168]  Henriette O'Geen,et al.  Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. , 2009, Molecular cell.

[169]  Ernest Fraenkel,et al.  Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. , 2009, Molecular cell.

[170]  E. Furlong,et al.  Combinatorial binding predicts spatio-temporal cis-regulatory activity , 2009, Nature.

[171]  A. Hartemink,et al.  An ensemble model of competitive multi-factor binding of the genome. , 2009, Genome research.

[172]  I. Korf,et al.  Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing , 2009, Nucleic acids research.

[173]  L. Mirny,et al.  Different gene regulation strategies revealed by analysis of binding motifs. , 2009, Trends in genetics : TIG.

[174]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[175]  P. Farnham.  Insights from genomic profiling of transcription factors , 2009, Nature Reviews Genetics.

[176]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[177]  Andrew J. Bonham,et al.  Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays , 2009, Nucleic acids research.

[178]  K. Yamamoto,et al.  DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity , 2009, Science.

[179]  B. Honig,et al.  Nuance in the double-helix and its role in protein-DNA recognition. , 2009, Current opinion in structural biology.

[180]  Irene K. Moore,et al.  The DNA-encoded nucleosome organization of a eukaryotic genome , 2009, Nature.

[181]  William Stafford Noble,et al.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting , 2009, Nature Methods.

[182]  M. Berger,et al.  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors , 2009, Nature Protocols.

[183]  R. Mann,et al.  Chapter 3 Hox Specificity , 2009 .

[184]  R. Mann,et al.  Hox specificity unique roles for cofactors and collaborators. , 2009, Current Topics in Developmental Biology.

[185]  Justin Crocker,et al.  Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts , 2008, PLoS biology.

[186]  Eric C Greene,et al.  Visualizing one-dimensional diffusion of proteins along DNA , 2008, Nature Structural &Molecular Biology.

[187]  Daniel E. Newburger,et al.  Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences , 2008, Cell.

[188]  G. Stormo,et al.  Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites , 2008, Cell.

[189]  H. Berman,et al.  Chapter 4:Indirect Readout of DNA Sequence by Proteins , 2008 .

[190]  R. Marmorstein,et al.  Chapter 3:Structural Basis for Sequence-specific DNA Recognition by Transcription Factors and their Complexes , 2008 .

[191]  W. Fairbrother,et al.  High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes. , 2008, Genome research.

[192]  D. W. Knowles,et al.  Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm , 2008, PLoS biology.

[193]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[194]  Jun S. Liu,et al.  Extracting sequence features to predict protein–DNA interactions: a comparative study , 2008, Nucleic acids research.

[195]  Eran Segal,et al.  A Feature-Based Approach to Modeling Protein–DNA Interactions , 2007, RECOMB.

[196]  Dmitri Papatsenko,et al.  A rationale for the enhanceosome and other evolutionarily constrained enhancers , 2007, Current Biology.

[197]  Alexander J. Hartemink,et al.  A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast , 2007, PLoS Comput. Biol..

[198]  S. Harrison,et al.  An Atomic Model of the Interferon-β Enhanceosome , 2007, Cell.

[199]  Estanislao Nistal-Villán,et al.  Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer. , 2007, Molecular cell.

[200]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[201]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[202]  Barrett C. Foat,et al.  Predictive modeling of genome-wide mRNA expression: from modules to molecules. , 2007, Annual review of biophysics and biomolecular structure.

[203]  Edward J. Oakeley,et al.  Position dependencies in transcription factor binding sites , 2007, Bioinform..

[204]  B. Honig,et al.  Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry , 2007, Nucleic acids research.

[205]  S. Quake,et al.  A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors , 2007, Science.

[206]  Martin Vingron,et al.  Predicting transcription factor affinities to DNA from a biophysical model , 2007, Bioinform..

[207]  P. V. von Hippel,et al.  From "simple" DNA-protein interactions to the macromolecular machines of gene expression. , 2007, Annual review of biophysics and biomolecular structure.

[208]  Neil D Clarke,et al.  Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. , 2006, Genome research.

[209]  A. Philippakis,et al.  Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities , 2006, Nature Biotechnology.

[210]  Amos Tanay,et al.  Extensive low-affinity transcriptional interactions in the yeast genome. , 2006, Genome research.

[211]  Alexandre V. Morozov,et al.  Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE , 2006, ISMB.

[212]  M. Kitayner,et al.  Structural basis of DNA recognition by p53 tetramers. , 2006, Molecular cell.

[213]  G. K. Sandve,et al.  A survey of motif discovery methods in an integrated framework , 2006, Biology Direct.

[214]  J. Joung,et al.  Counter-selectable marker for bacterial-based interaction trap systems. , 2006, BioTechniques.

[215]  Christopher L. Warren,et al.  Defining the sequence-recognition profile of DNA-binding molecules. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[216]  B. van Steensel,et al.  DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. , 2006, Methods in enzymology.

[217]  D. Baker,et al.  Protein–DNA binding specificity predictions with structural models , 2005, Nucleic acids research.

[218]  R. Rohs,et al.  Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. , 2005, Structure.

[219]  Gary D. Stormo,et al.  enoLOGOS: a versatile web tool for energy normalized sequence logos , 2005, Nucleic Acids Res..

[220]  Armin Shmilovici,et al.  Identification of transcription factor binding sites with variable-order Bayesian networks , 2005, Bioinform..

[221]  Nir Friedman,et al.  Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge , 2005, PLoS Comput. Biol..

[222]  David N Arnosti,et al.  Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? , 2005, Journal of cellular biochemistry.

[223]  Antonina Silkov,et al.  Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity. , 2005, Journal of molecular biology.

[224]  William Stafford Noble,et al.  Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.

[225]  D. Baker,et al.  A simple physical model for the prediction and design of protein-DNA interactions. , 2004, Journal of molecular biology.

[226]  P. V. Hippel,et al.  Completing the View of Transcriptional Regulation , 2004 .

[227]  Michael Levine,et al.  Coordinate enhancers share common organizational features in the Drosophila genome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[228]  P. V. von Hippel,et al.  Biochemistry. Completing the view of transcriptional regulation. , 2004, Science.

[229]  D. Arnosti,et al.  Information display by transcriptional enhancers , 2003, Development.

[230]  Anirvan M. Sengupta,et al.  A biophysical approach to transcription factor binding site discovery. , 2003, Genome research.

[231]  Nir Friedman,et al.  Modeling dependencies in protein-DNA binding sites , 2003, RECOMB '03.

[232]  J. Widom,et al.  Collaborative Competition Mechanism for Gene Activation In Vivo , 2003, Molecular and Cellular Biology.

[233]  S. Carroll,et al.  Molecular mechanisms of selector gene function and evolution. , 2002, Current opinion in genetics & development.

[234]  T. Richmond,et al.  Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. , 2002, Journal of molecular biology.

[235]  G. Church,et al.  Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. , 2002, Nucleic acids research.

[236]  H. Rozenberg,et al.  DNA bending by an adenine–thymine tract and its role in gene regulation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[237]  G. Stormo,et al.  Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. , 2001, Nucleic acids research.

[238]  Pavel A. Pevzner,et al.  Combinatorial Approaches to Finding Subtle Signals in DNA Sequences , 2000, ISMB.

[239]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[240]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[241]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[242]  G. Church,et al.  Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation , 1998, Nature Biotechnology.

[243]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[244]  H. Margalit,et al.  Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. , 1998, Nucleic acids research.

[245]  T. Maniatis,et al.  Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome , 1995, Cell.

[246]  Joon Kim,et al.  Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains , 1995, Nucleic Acids Res..

[247]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[248]  T. D. Schneider,et al.  Quantitative analysis of the relationship between nucleotide sequence and functional activity. , 1986, Nucleic acids research.

[249]  M. M. Garner,et al.  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 , 1981, Nucleic Acids Res..

[250]  H. Weintraub.  Recognition of specific DNA sequences in eukaryotic chromosomes. , 1980, Nucleic acids research.

[251]  D. Galas,et al.  DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. , 1978, Nucleic acids research.