Published in Nucleic Acids Res on December 01, 2009
Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods (2011) 6.90
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell (2011) 3.40
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell (2013) 2.03
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res (2010) 1.88
Quantitative analysis of TALE-DNA interactions suggests polarity effects. Nucleic Acids Res (2013) 1.88
Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci (2014) 1.84
RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol Cell (2014) 1.68
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol (2011) 1.40
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res (2011) 1.26
Adding fingers to an engineered zinc finger nuclease can reduce activity. Biochemistry (2011) 1.17
Highly active zinc-finger nucleases by extended modular assembly. Genome Res (2012) 1.17
The generation of zinc finger proteins by modular assembly. Methods Mol Biol (2010) 1.15
Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res (2013) 1.09
Mapping yeast transcriptional networks. Genetics (2013) 1.06
Experimental strategies for studying transcription factor-DNA binding specificities. Brief Funct Genomics (2010) 1.01
Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon. Nat Protoc (2013) 0.97
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res (2011) 0.97
Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc (2012) 0.97
Determining the specificities of TALENs, Cas9, and other genome-editing enzymes. Methods Enzymol (2014) 0.93
Atomistic modeling of protein-DNA interaction specificity: progress and applications. Curr Opin Struct Biol (2012) 0.88
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Genetics (2014) 0.86
Mutational interference mapping experiment (MIME) for studying RNA structure and function. Nat Methods (2015) 0.85
To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins. Trends Genet (2016) 0.85
Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol (2015) 0.83
Miz-1 activates gene expression via a novel consensus DNA binding motif. PLoS One (2014) 0.82
An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example. PLoS One (2013) 0.81
The prospect of molecular therapy for Angelman syndrome and other monogenic neurologic disorders. BMC Neurosci (2014) 0.81
Spec-seq: determining protein-DNA-binding specificity by sequencing. Brief Funct Genomics (2014) 0.80
Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain. Mol Ther (2016) 0.79
Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage. Epigenetics Chromatin (2015) 0.79
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS One (2011) 0.79
Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells. Nucleic Acids Res (2012) 0.79
Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing. Nucleic Acids Res (2016) 0.77
Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators. Comput Struct Biotechnol J (2016) 0.77
Optimization of high-throughput sequencing kinetics for determining enzymatic rate constants of thousands of RNA substrates. Anal Biochem (2016) 0.77
Combinatorial bZIP dimers display complex DNA-binding specificity landscapes. Elife (2017) 0.77
Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics (2014) 0.76
The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity. Nucleic Acids Res (2016) 0.76
A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq. PLoS One (2016) 0.76
Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PLoS One (2016) 0.75
Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites. PLoS One (2014) 0.75
SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics. Sci Rep (2016) 0.75
Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput Biol (2017) 0.75
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science (1990) 35.96
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science (1991) 15.97
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods (2008) 11.61
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol (1996) 5.74
Zinc-finger nucleases: the next generation emerges. Mol Ther (2008) 5.69
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. Proc Natl Acad Sci U S A (1999) 4.87
Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site. Mol Cell Biol (1991) 3.54
A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci U S A (2000) 3.35
OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-Smad and Olf signaling pathways. Cell (2000) 3.12
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol (2002) 3.04
DNA-binding specificity of NGFI-A and related zinc finger transcription factors. Mol Cell Biol (1995) 2.78
Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J Mol Biol (2000) 2.32
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol (2005) 2.28
Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J Mol Biol (2006) 1.91
Critical parameters for genome editing using zinc finger nucleases. Mini Rev Med Chem (2008) 1.85
Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz. Mol Cell Biol (1998) 1.75
Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol (2005) 1.64
Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. BMC Evol Biol (2008) 1.51
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinformatics (2008) 1.42
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res (2007) 1.40
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res (2005) 1.27
A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. Comb Chem High Throughput Screen (2006) 1.21
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Res (2007) 1.17
ZIFIBI: Prediction of DNA binding sites for zinc finger proteins. Biochem Biophys Res Commun (2008) 1.15
Multiconnection of identical zinc finger: implication for DNA binding affinity and unit modulation of the three zinc finger domain. Biochemistry (2001) 0.90
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics (2007) 12.21
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res (2007) 6.48
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Assessing the gene space in draft genomes. Nucleic Acids Res (2008) 4.03
R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell (2012) 3.56
Design, construction and in vitro testing of zinc finger nucleases. Nat Protoc (2006) 3.51
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res (2003) 3.18
Custom zinc-finger nucleases for use in human cells. Mol Ther (2005) 3.04
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res (2009) 2.74
Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem (2005) 2.69
Designing transcription factor architectures for drug discovery. Mol Pharmacol (2004) 2.44
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys (2008) 1.95
Quantitative analysis of TALE-DNA interactions suggests polarity effects. Nucleic Acids Res (2013) 1.88
The human placenta methylome. Proc Natl Acad Sci U S A (2013) 1.86
Critical parameters for genome editing using zinc finger nucleases. Mini Rev Med Chem (2008) 1.85
GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res (2013) 1.71
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol (2013) 1.65
A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Res (2004) 1.60
Zinc-finger nucleases transition to the CoDA. Nat Methods (2011) 1.55
Longer first introns are a general property of eukaryotic gene structure. PLoS One (2008) 1.41
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics (2010) 1.40
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One (2011) 1.34
Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res (2011) 1.34
Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell (2008) 1.34
DNA sequence-enabled reassembly of the green fluorescent protein. J Am Chem Soc (2005) 1.31
Fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc finger protein E2C direct integration of viral DNA into specific sites. J Virol (2004) 1.20
Adding fingers to an engineered zinc finger nuclease can reduce activity. Biochemistry (2011) 1.17
Restricted spacer tolerance of a zinc finger nuclease with a six amino acid linker. Bioorg Med Chem Lett (2009) 1.17
Highly active zinc-finger nucleases by extended modular assembly. Genome Res (2012) 1.17
Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics. Mol Biosyst (2006) 1.17
The generation of zinc finger proteins by modular assembly. Methods Mol Biol (2010) 1.15
Sequence-enabled reassembly of beta-lactamase (SEER-LAC): a sensitive method for the detection of double-stranded DNA. Biochemistry (2006) 1.12
Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Res (2011) 1.10
Chimeric piggyBac transposases for genomic targeting in human cells. Nucleic Acids Res (2012) 1.09
The prospects for designer single-stranded RNA-binding proteins. Nat Struct Mol Biol (2011) 1.07
Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides? Trends Biochem Sci (2013) 1.07
Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site. J Virol (2006) 1.07
The protein-binding potential of C2H2 zinc finger domains. Cell Biochem Biophys (2008) 1.03
Transcription activator like effector (TALE)-directed piggyBac transposition in human cells. Nucleic Acids Res (2013) 1.01
Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics Chromatin (2011) 1.00
Site-specific detection of DNA methylation utilizing mCpG-SEER. J Am Chem Soc (2006) 0.98
Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc (2012) 0.97
Site-directed genome modification: derivatives of DNA-modifying enzymes as targeting tools. Trends Biotechnol (2005) 0.96
A zinc finger protein array for the visual detection of specific DNA sequences for diagnostic applications. Nucleic Acids Res (2010) 0.95
Site-directed genome modification: nucleic acid and protein modules for targeted integration and gene correction. Trends Biotechnol (2005) 0.93
Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics (2013) 0.92
Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections. J Virol (2014) 0.92
Active integration: new strategies for transgenesis. Transgenic Res (2007) 0.91
Toward a general approach for RNA-templated hierarchical assembly of split-proteins. J Am Chem Soc (2010) 0.90
Split beta-lactamase sensor for the sequence-specific detection of DNA methylation. Anal Chem (2007) 0.90
Engineering zinc finger protein transcription factors to downregulate the epithelial glycoprotein-2 promoter as a novel anti-cancer treatment. Mol Carcinog (2007) 0.89
Generation and functional analysis of zinc finger nucleases. Methods Mol Biol (2008) 0.89
Breadth by depth: expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing. DNA Repair (Amst) (2011) 0.88
Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement. Front Plant Sci (2011) 0.85
New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217. J Biol Chem (2013) 0.85
Comparative genomics of carp herpesviruses. J Virol (2012) 0.84
Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development. J Proteome Res (2015) 0.82
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics (2012) 0.82
The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana. Plant Biotechnol J (2013) 0.81
Modular assembly of RanBP2-type zinc finger domains to target single-stranded RNA. Angew Chem Int Ed Engl (2012) 0.80
Systematic evaluation of split-fluorescent proteins for the direct detection of native and methylated DNA. Bioorg Med Chem Lett (2009) 0.80
Uranyl acetate as a direct inhibitor of DNA-binding proteins. Chem Res Toxicol (2007) 0.79
From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One (2013) 0.79
Crystallization and preliminary X-ray crystallographic analysis of Aart, a designed six-finger zinc-finger peptide, bound to DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.77
Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA. Angew Chem Int Ed Engl (2014) 0.77
Allele-Specific Reduction of the Mutant Huntingtin Allele Using Transcription Activator-Like Effectors in Human Huntington's Disease Fibroblasts. Cell Transplant (2016) 0.76
Carlos F. Barbas III (1964-2014): Visionary at the interface of chemistry and biology. ACS Chem Biol (2014) 0.75
Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature (2017) 0.75
Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). Methods Mol Biol (2010) 0.75