Published in Nucleic Acids Res on May 30, 2007
Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods (2011) 6.90
Genome engineering with zinc-finger nucleases. Genetics (2011) 4.66
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res (2009) 1.88
Modular system for the construction of zinc-finger libraries and proteins. Nat Protoc (2010) 1.87
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Res (2009) 1.43
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res (2011) 1.27
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
Determining the specificities of TALENs, Cas9, and other genome-editing enzymes. Methods Enzymol (2014) 0.93
In vitro Fab display: a cell-free system for IgG discovery. Protein Eng Des Sel (2014) 0.82
Evaluation of novel design strategies for developing zinc finger nucleases tools for treating human diseases. Biotechnol Res Int (2014) 0.79
Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res (1998) 96.63
Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature (2005) 19.15
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science (1991) 15.97
Chimeric nucleases stimulate gene targeting in human cells. Science (2003) 12.12
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol (2001) 6.68
DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct (2000) 6.61
Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc Natl Acad Sci U S A (1998) 5.46
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure (1996) 5.30
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science (1997) 4.93
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
Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics (2006) 4.47
Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006) 4.06
Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat Biotechnol (2003) 4.03
Expressing the human genome. Nature (2001) 3.45
Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A. J Biol Chem (2001) 3.38
Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem (2001) 3.35
A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci U S A (2000) 3.35
Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci U S A (2003) 3.29
Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol (1999) 3.20
A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat Biotechnol (2001) 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
Drug discovery with engineered zinc-finger proteins. Nat Rev Drug Discov (2003) 2.63
Physical basis of a protein-DNA recognition code. Curr Opin Struct Biol (1997) 2.53
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol (2005) 2.28
Zinc-finger protein-targeted gene regulation: genomewide single-gene specificity. Proc Natl Acad Sci U S A (2003) 2.24
Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol (2002) 2.23
Quantitative specificity of the Mnt repressor. J Mol Biol (1997) 1.91
Sequence discrimination by alternatively spliced isoforms of a DNA binding zinc finger domain. Science (1992) 1.81
Genetic analysis of prokaryotic and eukaryotic DNA-binding proteins in Escherichia coli. Nucleic Acids Res (1998) 1.60
Rapid, high-throughput engineering of sequence-specific zinc finger DNA-binding proteins. Methods Enzymol (2001) 1.49
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc (2006) 1.36
Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry (2002) 1.26
A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions. Comb Chem High Throughput Screen (2006) 1.21
Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing. Biotechniques (1998) 1.17
Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site. J Virol (2006) 1.07
Genetic reprogramming of tumor cells by zinc finger transcription factors. Proc Natl Acad Sci U S A (2005) 1.07
Improved DNA sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators. Genome Res (1999) 0.97
One-step selection of artificial transcription factors using an in vivo screening system. Mol Cells (2006) 0.97
Fluorescent dye terminator sequencing methods for quantitative determination of replication fitness of human immunodeficiency virus type 1 containing the codon 74 and 184 mutations in reverse transcriptase. J Clin Microbiol (2003) 0.96
A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res (2004) 0.89
Counter-selectable marker for bacterial-based interaction trap systems. Biotechniques (2006) 0.87
Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol (2013) 21.32
International network of cancer genome projects. Nature (2010) 20.35
High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol (2013) 18.01
FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol (2012) 12.97
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell (2008) 11.24
Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol (2008) 10.29
Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell (2009) 8.97
Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods (2010) 8.86
High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature (2009) 7.19
Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol (2011) 7.05
Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods (2011) 6.90
Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS One (2009) 6.67
Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods (2008) 6.51
A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science (2010) 5.84
Zinc-finger nucleases: the next generation emerges. Mol Ther (2008) 5.69
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A (2010) 4.78
CRISPR RNA-guided activation of endogenous human genes. Nat Methods (2013) 4.69
Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc (2006) 4.16
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther (2007) 3.94
Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol (2013) 3.82
Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet (2011) 3.66
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res (2010) 3.59
Direct interaction between Nrf2 and p21(Cip1/WAF1) upregulates the Nrf2-mediated antioxidant response. Mol Cell (2009) 3.50
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res (2007) 3.47
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet (2011) 3.43
Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs. Nucleic Acids Res (2012) 3.41
Surgery with molecular fluorescence imaging using activatable cell-penetrating peptides decreases residual cancer and improves survival. Proc Natl Acad Sci U S A (2010) 3.41
Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci U S A (2003) 3.29
Activatable cell penetrating peptides linked to nanoparticles as dual probes for in vivo fluorescence and MR imaging of proteases. Proc Natl Acad Sci U S A (2010) 3.03
Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays. Nat Protoc (2009) 3.01
A noncanonical mechanism of Nrf2 activation by autophagy deficiency: direct interaction between Keap1 and p62. Mol Cell Biol (2010) 2.93
Robust, synergistic regulation of human gene expression using TALE activators. Nat Methods (2013) 2.89
Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat Biotechnol (2013) 2.89
Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol Ther (2008) 2.87
Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PLoS One (2013) 2.74
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Targeted mutagenesis in zebrafish using customized zinc-finger nucleases. Nat Protoc (2009) 2.67
In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases. Stem Cells (2011) 2.52
Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays. Hepatology (2010) 2.51
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins. Nucleic Acids Res (2008) 2.42
A synthetic biology framework for programming eukaryotic transcription functions. Cell (2012) 2.32
Efficient and robust feature extraction by maximum margin criterion. IEEE Trans Neural Netw (2006) 2.32
Roscovitine targets, protein kinases and pyridoxal kinase. J Biol Chem (2005) 2.31
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene (2006) 2.31
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res (2008) 2.30
In vivo characterization of activatable cell penetrating peptides for targeting protease activity in cancer. Integr Biol (Camb) (2009) 2.30
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol (2005) 2.28
Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects. Nucleic Acids Res (2012) 2.26
Brusatol enhances the efficacy of chemotherapy by inhibiting the Nrf2-mediated defense mechanism. Proc Natl Acad Sci U S A (2011) 2.22
Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol (2011) 2.15
Chemokine signaling guides regional patterning of the first embryonic artery. Genes Dev (2009) 2.14
MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. J Comput Biol (2007) 2.14
The Mg-chelatase H subunit of Arabidopsis antagonizes a group of WRKY transcription repressors to relieve ABA-responsive genes of inhibition. Plant Cell (2010) 2.13
Genomic segmental polymorphisms in inbred mouse strains. Nat Genet (2004) 1.93
Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics (2011) 1.93
Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion. Nucleic Acids Res (2010) 1.92
Efficient inference of haplotypes from genotypes on a pedigree. J Bioinform Comput Biol (2003) 1.89
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res (2010) 1.88
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res (2008) 1.87
Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs). PLoS One (2012) 1.85
TALEN-based gene correction for epidermolysis bullosa. Mol Ther (2013) 1.84
An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods (2012) 1.84
Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology (2013) 1.83
Understanding high grade glioma: molecular mechanism, therapy and comprehensive management. Cancer Lett (2013) 1.82
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res (2010) 1.81
Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming. J Comput Biol (2005) 1.78
Systemic in vivo distribution of activatable cell penetrating peptides is superior to that of cell penetrating peptides. Integr Biol (Camb) (2009) 1.78
IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. J Comput Biol (2011) 1.76
MiR-221 and miR-222 target PUMA to induce cell survival in glioblastoma. Mol Cancer (2010) 1.74
Inference of isoforms from short sequence reads. J Comput Biol (2011) 1.72
Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish. Dev Cell (2011) 1.72
Regulation of renal lipid metabolism, lipid accumulation, and glomerulosclerosis in FVBdb/db mice with type 2 diabetes. Diabetes (2005) 1.70
Molecular classification of gliomas based on whole genome gene expression: a systematic report of 225 samples from the Chinese Glioma Cooperative Group. Neuro Oncol (2012) 1.66
Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science (2014) 1.66
Assignment of orthologous genes via genome rearrangement. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.66
A small-molecule inducer of the antioxidant response element. Chem Biol (2010) 1.65
ChemmineR: a compound mining framework for R. Bioinformatics (2008) 1.64
Regulation of renal fatty acid and cholesterol metabolism, inflammation, and fibrosis in Akita and OVE26 mice with type 1 diabetes. Diabetes (2006) 1.64
Repression of phase-variable cup gene expression by H-NS-like proteins in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A (2005) 1.60
Crosstalk between Aurora-A and p53: frequent deletion or downregulation of Aurora-A in tumors from p53 null mice. Cancer Cell (2007) 1.59
Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development (2014) 1.59
Targeted chromosomal deletions and inversions in zebrafish. Genome Res (2013) 1.57
Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet (2011) 1.54
Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development (2011) 1.54
The Wilms tumor gene, Wt1, is critical for mouse spermatogenesis via regulation of sertoli cell polarity and is associated with non-obstructive azoospermia in humans. PLoS Genet (2013) 1.52
Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med (2011) 1.52
Circulating microRNAs in cancer: origin, function and application. J Exp Clin Cancer Res (2012) 1.50