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DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-47396-0
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- Publication type:
- Article
The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain.
- Published in:
- Nucleic Acids Research, 2023, v. 51, n. 2, p. 574, doi. 10.1093/nar/gkac1188
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- Publication type:
- Article
Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements.
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- Molecular Systems Biology, 2022, v. 18, n. 8, p. 1, doi. 10.15252/msb.202110473
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- Publication type:
- Article
Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue.
- Published in:
- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02574-x
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- Publication type:
- Article
Context and number of noncanonical repeat variable diresidues impede the design of TALE proteins with improved DNA targeting.
- Published in:
- Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 2, p. 606, doi. 10.1002/pro.3801
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- Publication type:
- Article
CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types.
- Published in:
- Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1062-5
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- Publication type:
- Article
Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation.
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- PLoS Genetics, 2016, v. 12, n. 7, p. 1, doi. 10.1371/journal.pgen.1006120
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- Publication type:
- Article
Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. 6, p. 2538, doi. 10.1093/nar/gkv1244
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- Publication type:
- Article
Nuclear respiratory factor 2 induces SIRT3 expression.
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- Aging Cell, 2015, v. 14, n. 5, p. 818, doi. 10.1111/acel.12360
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- Publication type:
- Article
Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development.
- Published in:
- Genesis: The Journal of Genetics & Development, 2015, v. 53, n. 9, p. 573, doi. 10.1002/dvg.22875
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- Publication type:
- Article
Context influences on TALE-DNA binding revealed by quantitative profiling.
- Published in:
- Nature Communications, 2015, v. 6, n. 6, p. 7440, doi. 10.1038/ncomms8440
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- Publication type:
- Article
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. D1, p. D117, doi. 10.1093/nar/gku1045
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- Publication type:
- Article
Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks.
- Published in:
- Molecular Biology & Evolution, 2014, v. 31, n. 10, p. 2672, doi. 10.1093/molbev/msu213
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- Publication type:
- Article
5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy.
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- Journal of Clinical Investigation, 2014, v. 124, n. 3, p. 1364, doi. 10.1172/JCI70108
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- Publication type:
- Article
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.
- Published in:
- Nature Methods, 2013, v. 10, n. 8, p. 774, doi. 10.1038/nmeth.2558
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- Publication type:
- Article
Contribution of Distinct Homeodomain DNA Binding Specificities to <i>Drosophila</i> Embryonic Mesodermal Cell-Specific Gene Expression Programs.
- Published in:
- PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0069385
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- Publication type:
- Article
Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers.
- Published in:
- Bioinformatics, 2013, v. 29, n. 11, p. 1390, doi. 10.1093/bioinformatics/btt152
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- Publication type:
- Article
LOESS correction for length variation in gene set-based genomic sequence analysis.
- Published in:
- Bioinformatics, 2012, v. 28, n. 11, p. 1446, doi. 10.1093/bioinformatics/bts155
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- Publication type:
- Article
An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud.
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- PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0038568
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- Publication type:
- Article
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.
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- Human Molecular Genetics, 2012, v. 21, n. 10, p. 2194, doi. 10.1093/hmg/dds034
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- Publication type:
- Article
Meta-Profiles of Gene Expression during Aging: Limited Similarities between Mouse and Human and an Unexpectedly Decreased Inflammatory Signature.
- Published in:
- PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0033204
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- Publication type:
- Article
Bioinformatic and molecular investigation of Sirt3 expression.
- Published in:
- 2012
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- Publication type:
- Abstract
Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-?B family DNA binding.
- Published in:
- Nature Immunology, 2012, v. 13, n. 1, p. 95, doi. 10.1038/ni.2151
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- Publication type:
- Article
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
- Published in:
- Genome Biology, 2011, v. 12, n. 12, p. 1, doi. 10.1186/gb-2011-12-12-r125
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- Publication type:
- Article
Jury remains out on simple models of transcription factor specificity.
- Published in:
- 2011
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- Publication type:
- Letter
Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants.
- Published in:
- Nucleic Acids Research, 2011, v. 39, n. 11, p. 4553, doi. 10.1093/nar/gkr070
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- Publication type:
- Article
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions.
- Published in:
- Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D124, doi. 10.1093/nar/gkq992
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- Publication type:
- Article
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.
- Published in:
- Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.89
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- Publication type:
- Article
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences.
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- Nucleic Acids Research, 2010, v. 38, n. 22, p. 7927, doi. 10.1093/nar/gkq714
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- Publication type:
- Article
Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example.
- Published in:
- Nucleic Acids Research, 2010, v. 38, n. 21, p. 7422, doi. 10.1093/nar/gkq683
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- Publication type:
- Article
Notch and MAML-1 Complexation Do Not Detectably Alter the DNA Binding Specificity of the Transcription Factor CSL.
- Published in:
- PLoS ONE, 2010, v. 5, n. 11, p. 1, doi. 10.1371/journal.pone.0015034
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- Publication type:
- Article
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.
- Published in:
- EMBO Journal, 2010, v. 29, n. 13, p. 2147, doi. 10.1038/emboj.2010.106
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- Publication type:
- Article
Inferring condition‐specific transcription factor function from DNA binding and gene expression data.
- Published in:
- 2010
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- Publication type:
- Correction Notice
Predicting the binding preference of transcription factors to individual DNA k-mers.
- Published in:
- Bioinformatics, 2009, v. 25, n. 8, p. 1012, doi. 10.1093/bioinformatics/btn645
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- Publication type:
- Article
Short-Term Calorie Restriction in Male Mice Feminizes Gene Expression and Alters Key Regulators of Conserved Aging Regulatory Pathways.
- Published in:
- PLoS ONE, 2009, v. 4, n. 4, p. 1, doi. 10.1371/journal.pone.0005242
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- Publication type:
- Article
UniPROBE: an online database of protein binding microarray data on protein–DNA interactions.
- Published in:
- Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D77, doi. 10.1093/nar/gkn660
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- Publication type:
- Article
The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.
- Published in:
- Molecular Microbiology, 2008, v. 70, n. 1, p. 76, doi. 10.1111/j.1365-2958.2008.06389.x
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- Publication type:
- Article
Systematic identification of mammalian regulatory motifs' target genes and functions.
- Published in:
- Nature Methods, 2008, v. 5, n. 4, p. 347, doi. 10.1038/nmeth.1188
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- Publication type:
- Article
Inferring condition-specific transcription factor function from DNA binding and gene expression data.
- Published in:
- Molecular Systems Biology, 2007, v. 3, n. 1, p. 100, doi. 10.1038/msb4100140
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- Publication type:
- Article
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
- Published in:
- Nature Biotechnology, 2006, v. 24, n. 11, p. 1429, doi. 10.1038/nbt1246
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- Publication type:
- Article
Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells.
- Published in:
- PLoS Computational Biology, 2006, v. 2, n. 5, p. e53, doi. 10.1371/journal.pcbi.0020053
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- Publication type:
- Article
Biological code breaking in the 21st century.
- Published in:
- Molecular Systems Biology, 2006, v. 2, n. 1, p. E1, doi. 10.1038/msb4100062
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- Publication type:
- Article
Discovering DNA regulatory elements with bacteria.
- Published in:
- Nature Biotechnology, 2005, v. 23, n. 8, p. 942, doi. 10.1038/nbt0805-942
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- Publication type:
- Article
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
- Published in:
- Nature Genetics, 2004, v. 36, n. 12, p. 1331, doi. 10.1038/ng1473
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- Publication type:
- Article
A Statistical Model for Investigating Binding Probabilities of DNA Nucleotide Sequences Using Microarrays.
- Published in:
- Biometrics, 2002, v. 58, n. 4, p. 981, doi. 10.1111/j.0006-341X.2002.00981.x
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- Publication type:
- Article
Additivity in protein–DNA interactions: how good an approximation is it?
- Published in:
- Nucleic Acids Research, 2002, v. 30, n. 20, p. 4442, doi. 10.1093/nar/gkf578
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- Publication type:
- Article
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.
- Published in:
- Nucleic Acids Research, 2002, v. 30, n. 5, p. 1255, doi. 10.1093/nar/30.5.1255
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- Publication type:
- Article
Computational comparison of two draft sequences of the human genome.
- Published in:
- Nature, 2001, v. 409, n. 6822, p. 856, doi. 10.1038/35057055
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- Publication type:
- Article
Quantifying DNA?protein interactions by double-stranded DNA arrays.
- Published in:
- Nature Biotechnology, 1999, v. 17, n. 6, p. 573, doi. 10.1038/9878
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- Publication type:
- Article