| scholarly article | Q13442814 |
| P819 | ADS bibcode | 2010PNAS..10722534M |
| P818 | arXiv ID | 0901.2905 |
| P356 | DOI | 10.1073/PNAS.0913805107 |
| P953 | full work available at URL | https://doi.org/10.1073/pnas.0913805107 |
| https://europepmc.org/articles/PMC3012490 | ||
| https://europepmc.org/articles/pmc3012490?pdf=render | ||
| https://europepmc.org/articles/PMC3012490?pdf=render | ||
| https://pnas.org/doi/pdf/10.1073/pnas.0913805107 | ||
| P932 | PMC publication ID | 3012490 |
| P698 | PubMed publication ID | 21149679 |
| P5875 | ResearchGate publication ID | 49675503 |
| P2093 | author name string | Leonid A. Mirny | |
| P2860 | cites work | A genomic code for nucleosome positioning | Q24650238 |
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| ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL | Q27861036 | ||
| Large-scale turnover of functional transcription factor binding sites in Drosophila | Q33260343 | ||
| Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation | Q33347127 | ||
| G+C content dominates intrinsic nucleosome occupancy | Q33520380 | ||
| High nucleosome occupancy is encoded at human regulatory sequences | Q33531768 | ||
| Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila | Q33948085 | ||
| Allosteric mechanisms of signal transduction | Q33987546 | ||
| A single GAL4 dimer can maximally activate transcription under physiological conditions | Q33997974 | ||
| The pitch of chromatin DNA is reflected in its nucleotide sequence | Q34273471 | ||
| Nucleosomes facilitate their own invasion | Q34333992 | ||
| The eve stripe 2 enhancer employs multiple modes of transcriptional synergy | Q34371968 | ||
| Rapid spontaneous accessibility of nucleosomal DNA. | Q34373646 | ||
| Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? | Q34391887 | ||
| A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome | Q34588290 | ||
| Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters | Q34646654 | ||
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| The DNA-encoded nucleosome organization of a eukaryotic genome | Q34907179 | ||
| Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. | Q35004175 | ||
| Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins | Q35126514 | ||
| Getting into chromatin: how do transcription factors get past the histones? | Q35191526 | ||
| Nucleosome positioning signals in genomic DNA | Q35914766 | ||
| Transcriptional regulation by the numbers: models. | Q36083228 | ||
| DNA looping: the consequences and its control. | Q36484063 | ||
| Chromatin decouples promoter threshold from dynamic range | Q36732068 | ||
| Spontaneous access to DNA target sites in folded chromatin fibers | Q36787090 | ||
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| Using DNA mechanics to predict in vitro nucleosome positions and formation energies. | Q37298599 | ||
| Nucleosome organization in the Drosophila genome. | Q37326387 | ||
| Synergistic transcriptional enhancement does not depend on the number of acidic activation domains bound to the promoter | Q37363097 | ||
| An ensemble model of competitive multi-factor binding of the genome | Q37417297 | ||
| Discovery of functional noncoding elements by digital analysis of chromatin structure | Q37695799 | ||
| Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. | Q37697997 | ||
| Interaction of the glucocorticoid receptor with the chromatin landscape | Q38292692 | ||
| Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative | Q38298166 | ||
| A systems approach to measuring the binding energy landscapes of transcription factors | Q38305871 | ||
| Collaborative competition mechanism for gene activation in vivo | Q39740430 | ||
| Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences | Q41131282 | ||
| Different gene regulation strategies revealed by analysis of binding motifs | Q41412074 | ||
| Incorporating nucleosomes into thermodynamic models of transcription regulation | Q41909104 | ||
| Synergistic activation of transcription by multiple binding sites for NF-kappa B even in absence of co-operative factor binding to DNA. | Q43968321 | ||
| Alternative Models for Describing the Acid Unfolding of the Apomyoglobin Folding Intermediate | Q46177546 | ||
| Automated image analysis of protein localization in budding yeast | Q46701810 | ||
| Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays | Q50725987 | ||
| A probabilistic method to detect regulatory modules | Q50792656 | ||
| Comparative binding of p53 to its promoter and DNA recognition elements | Q51503955 | ||
| Targeting gene expression to the head: the Drosophila orthodenticle gene is a direct target of the Bicoid morphogen | Q52184102 | ||
| How different eukaryotic transcriptional activators can cooperate promiscuously. | Q54713258 | ||
| Evidence for nucleosome depletion at active regulatory regions genome-wide | Q54998820 | ||
| Dynamics of Replication-Independent Histone Turnover in Budding Yeast | Q57233862 | ||
| A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites | Q71093565 | ||
| Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation | Q71566510 | ||
| Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites | Q73472047 | ||
| Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions | Q74460820 | ||
| Nucleosome positions predicted through comparative genomics | Q80238247 | ||
| Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast | Q81836844 | ||
| P433 | issue | 52 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | genetic model | Q67149661 |
| P1104 | number of pages | 6 | |
| P304 | page(s) | 22534-22539 | |
| P577 | publication date | 2010-12-13 | |
| P1433 | published in | Proceedings of the National Academy of Sciences of the United States of America | Q1146531 |
| P1476 | title | Nucleosome-mediated cooperativity between transcription factors | |
| P478 | volume | 107 |
| Q37392303 | A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution. |
| Q34887134 | A framework for modelling gene regulation which accommodates non-equilibrium mechanisms |
| Q34111752 | Absence of a simple code: how transcription factors read the genome |
| Q48245982 | Acceleration of bursty multiprotein target search kinetics on DNA by colocalisation. |
| Q90067785 | Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation |
| Q91530448 | Allele-selective transcriptional repression of mutant HTT for the treatment of Huntington's disease |
| Q37417297 | An ensemble model of competitive multi-factor binding of the genome |
| Q30367987 | An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding. |
| Q55517950 | BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization. |
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| Q37916761 | Basic statistical recipes for the emergence of biochemical discernment |
| Q86043904 | Biophysics of protein-DNA interactions and chromosome organization |
| Q83227416 | CTCF confers local nucleosome resiliency after DNA replication and during mitosis |
| Q91187980 | Chromatin accessibility and the regulatory epigenome |
| Q27320948 | Chromatin loops as allosteric modulators of enhancer-promoter interactions |
| Q28083608 | Chromatin regulation at the frontier of synthetic biology |
| Q90603640 | Clock-controlled rhythmic transcription: is the clock enough and how does it work? |
| Q35091271 | Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association |
| Q64068601 | Combinatorial Control through Allostery |
| Q33746438 | Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos |
| Q34428720 | Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli |
| Q33362219 | Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes |
| Q89997445 | Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies |
| Q37061181 | Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers |
| Q28535025 | Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy |
| Q33556999 | Computational models for large-scale simulations of facilitated diffusion |
| Q42273867 | Concentration dependent chromatin states induced by the bicoid morphogen gradient |
| Q35865022 | Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells |
| Q57250268 | Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants |
| Q34785860 | Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding |
| Q35164635 | Cooperative transcription factor associations discovered using regulatory variation |
| Q57358066 | Cooperativity Principles in Self-Assembled Nanomedicine |
| Q34361479 | Cooperativity and rapid evolution of cobound transcription factors in closely related mammals |
| Q35877421 | Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions |
| Q41989913 | DNA Sequence Correlations Shape Nonspecific Transcription Factor-DNA Binding Affinity |
| Q36368758 | DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells |
| Q37561098 | DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation |
| Q27702589 | DNA-dependent formation of transcription factor pairs alters their binding specificity |
| Q36408973 | DNase I sensitivity QTLs are a major determinant of human expression variation |
| Q28591313 | Deciphering the Sox-Oct partner code by quantitative cooperativity measurements |
| Q36079749 | Defining cooperativity in gene regulation locally through intrinsic noise. |
| Q37080405 | Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection |
| Q36279083 | Differential Sox10 genomic occupancy in myelinating glia |
| Q38303257 | Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize |
| Q26865492 | Disentangling the many layers of eukaryotic transcriptional regulation |
| Q36096560 | Disrupted cooperation between transcription factors across diverse cancer types. |
| Q83232121 | Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity |
| Q39321147 | Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells |
| Q35686044 | Dynamic regulation of transcription factors by nucleosome remodeling |
| Q35068557 | Dynamic regulation of transcriptional states by chromatin and transcription factors. |
| Q35834497 | Dynamics of Transcription Factor Binding Site Evolution. |
| Q38866012 | Effect of natural genetic variation on enhancer selection and function. |
| Q34372573 | Epigenomics of macrophages |
| Q39013266 | Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution |
| Q90429904 | Factor cooperation for chromosome discrimination in Drosophila |
| Q90006561 | Genome reading by the NF-κB transcription factors |
| Q55362433 | Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. |
| Q30277994 | Genome-wide predictors of NF-κB recruitment and transcriptional activity |
| Q49552110 | Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts |
| Q98164641 | Global reference mapping of human transcription factor footprints |
| Q92060125 | Help from my friends-cooperation of BMAL1 with noncircadian transcription factors |
| Q84705617 | Hierarchical cooperativity mediated by chromatin remodeling; the model of the MMTV transcription regulation |
| Q33531768 | High nucleosome occupancy is encoded at human regulatory sequences |
| Q27026122 | Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression |
| Q38104719 | Human genetic variation within neural crest enhancers: molecular and phenotypic implications |
| Q30853426 | Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data |
| Q42180396 | Information Integration and Energy Expenditure in Gene Regulation |
| Q37860833 | Information transmission in genetic regulatory networks: a review |
| Q41090628 | Inherent limitations of probabilistic models for protein-DNA binding specificity |
| Q37985244 | Intra-nuclear mobility and target search mechanisms of transcription factors: A single-molecule perspective on gene expression |
| Q41947132 | Intrinsic limits to gene regulation by global crosstalk |
| Q47203571 | Local sequence features that influence AP-1 cis-regulatory activity |
| Q50746835 | Mathematical model of a gene regulatory network reconciles effects of genetic perturbations on hematopoietic stem cell emergence |
| Q92292857 | Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response |
| Q37098224 | Napoleon Is in Equilibrium |
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| Q34408957 | Noise and information transmission in promoters with multiple internal States. |
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| Q39170272 | Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast |
| Q34976936 | Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. |
| Q34695671 | Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes |
| Q36739541 | Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm |
| Q37272420 | Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer |
| Q34356274 | One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data |
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| Q35743239 | Pattern Formation by Graded and Uniform Signals in the Early Drosophila Embryo |
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| Q37649488 | Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq. |
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