Published in Nucleic Acids Res on April 27, 2011
Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci U S A (2011) 1.39
The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive. PLoS One (2013) 0.91
Targeted gene therapies: tools, applications, optimization. Crit Rev Biochem Mol Biol (2012) 0.91
Genome editing and the next generation of antiviral therapy. Hum Genet (2016) 0.88
LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. Nucleic Acids Res (2012) 0.87
Home and away- the evolutionary dynamics of homing endonucleases. BMC Evol Biol (2011) 0.83
Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res (2014) 0.80
The brown algae Pl.LSU/2 group II intron-encoded protein has functional reverse transcriptase and maturase activities. PLoS One (2013) 0.80
Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi. Int J Mol Sci (2016) 0.75
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics (1989) 105.30
Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol (2008) 14.75
Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol (2009) 12.40
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci U S A (2008) 6.59
Homing endonuclease structure and function. Q Rev Biophys (2005) 5.27
Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature (2009) 4.71
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol (2009) 3.63
InBase: the Intein Database. Nucleic Acids Res (2002) 3.51
Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res (2005) 3.47
REBASE--enzymes and genes for DNA restriction and modification. Nucleic Acids Res (2007) 3.44
Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Appl Environ Microbiol (2004) 3.11
Generation of knockout rats with X-linked severe combined immunodeficiency (X-SCID) using zinc-finger nucleases. PLoS One (2010) 3.09
Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Curr Gene Ther (2007) 2.56
Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci U S A (1999) 2.42
A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res (2006) 2.38
Archaeal genetics - the third way. Nat Rev Genet (2005) 2.34
Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease. Nucleic Acids Res (2009) 2.14
Improved production and purification of minicircle DNA vector free of plasmid bacterial sequences and capable of persistent transgene expression in vivo. Hum Gene Ther (2005) 2.06
Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J Mol Biol (2003) 1.93
Homing endonuclease genes: the rise and fall and rise again of a selfish element. Curr Opin Genet Dev (2004) 1.93
Molecular dissection of mitotic recombination in the yeast Saccharomyces cerevisiae. Mol Cell Biol (2003) 1.83
Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells. J Mol Biol (2007) 1.68
Targeted genome modifications using integrase-deficient lentiviral vectors. Mol Ther (2007) 1.60
Coevolution of a homing endonuclease and its host target sequence. J Mol Biol (2007) 1.49
Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing. J Mol Biol (1996) 1.49
Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks. Nucleic Acids Res (2008) 1.43
High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Res (2009) 1.43
Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci (2003) 1.40
Detection of mutations in the DNA polymerase delta gene of human sporadic colorectal cancers and colon cancer cell lines. Int J Cancer (1999) 1.38
Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases. Nucleic Acids Res (2001) 1.36
A highly sensitive selection method for directed evolution of homing endonucleases. Nucleic Acids Res (2005) 1.34
In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination. Nucleic Acids Res (2005) 1.26
Efficient in toto targeted recombination in mouse liver by meganuclease-induced double-strand break. J Gene Med (2006) 1.20
Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites. Proc Natl Acad Sci U S A (2001) 1.19
GISSD: Group I Intron Sequence and Structure Database. Nucleic Acids Res (2007) 1.17
Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene. J Mol Biol (2004) 1.13
The mechanism of intein-mediated protein splicing: variations on a theme. Protein Pept Lett (2005) 1.07
Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements. BMC Evol Biol (2009) 1.04
Suitability of Anabaena PCC7120 expressing mosquitocidal toxin genes from Bacillus thuringiensis subsp. israelensis for biotechnological application. Appl Microbiol Biotechnol (2001) 0.94
Gas exchange in the filamentous cyanobacterium Nostoc punctiforme strain ATCC 29133 and Its hydrogenase-deficient mutant strain NHM5. Appl Environ Microbiol (2004) 0.92
Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage. Nucleic Acids Res (2008) 0.92
Adaptation of intronic homing endonuclease for successful horizontal transmission. FEBS J (2005) 0.91
Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts. Yeast (2003) 0.91
Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis. Mol Biol Evol (2005) 0.90
Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease. J Biol Chem (2007) 0.90
In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii. PLoS One (2011) 0.87
The nuclear-encoded inteins of fungi. Fungal Genet Biol (2006) 0.86
Bioabsorption of chromium from retan chrome liquor by cyanobacteria. Microbiol Res (2007) 0.85
Zinc-finger nucleases meet iPS cells: Zinc positive: tailored genome engineering meets reprogramming. Gene Ther (2009) 0.82
Sexual mating of Botrytis cinerea illustrates PRP8 intein HEG activity. Fungal Genet Biol (2010) 0.81
Shuttle-vector system for Saccharomyces cerevisiae designed to produce C-terminal-Myc-tagged fusion proteins. Biotechniques (1998) 0.81
Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions. Biochem Soc Trans (2011) 0.81
Robust cell line development using meganucleases. Methods Mol Biol (2008) 0.80
The vacuolar ATPase in bone cells: a potential therapeutic target in osteoporosis. Mol Biol Rep (2010) 0.79
Toxicity and uptake of iron ions by Synechocystis sp. E35 isolated from Kucukcekmece Lagoon, Istanbul. J Hazard Mater (2009) 0.78
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res (2010) 9.68
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature (2012) 7.00
Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J Mol Evol (2005) 7.00
Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. Mol Cell (2006) 4.11
The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle. EMBO J (2004) 3.87
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62
ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci U S A (2004) 3.49
Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A (2010) 3.40
Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet (2006) 3.25
A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc Natl Acad Sci U S A (2004) 3.21
Adaptive prediction of environmental changes by microorganisms. Nature (2009) 3.19
GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res (2010) 2.95
Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr Biol (2012) 2.67
A structural EM algorithm for phylogenetic inference. J Comput Biol (2002) 2.67
Finding a match: how do homologous sequences get together for recombination? Nat Rev Genet (2008) 2.41
An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39
Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A (2008) 2.23
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res (2007) 2.21
Elg1, the major subunit of an alternative RFC complex, interacts with SUMO-processing proteins. Cell Cycle (2011) 2.16
The evolution of modularity in bacterial metabolic networks. Proc Natl Acad Sci U S A (2008) 1.96
Distinct Microbiotas are Associated with Ileum-Restricted and Colon-Involving Crohn's Disease. Inflamm Bowel Dis (2016) 1.96
Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog (2009) 1.94
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res (2007) 1.86
Molecular dissection of mitotic recombination in the yeast Saccharomyces cerevisiae. Mol Cell Biol (2003) 1.83
Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol (2009) 1.80
The average common substring approach to phylogenomic reconstruction. J Comput Biol (2006) 1.79
DSB repair: the yeast paradigm. DNA Repair (Amst) (2004) 1.77
The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res (2010) 1.75
Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun (2011) 1.75
ELG1, a yeast gene required for genome stability, forms a complex related to replication factor C. Proc Natl Acad Sci U S A (2003) 1.73
The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins (2005) 1.72
Genotype is a stronger determinant than sex of the mouse gut microbiota. Microb Ecol (2010) 1.63
Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61
Chromosomal duplication is a transient evolutionary solution to stress. Proc Natl Acad Sci U S A (2012) 1.61
Computational characterization of B-cell epitopes. Mol Immunol (2007) 1.60
Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol (2007) 1.60
A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol (2005) 1.59
Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics (2009) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet (2007) 1.53
KLF6-SV1 drives breast cancer metastasis and is associated with poor survival. Sci Transl Med (2013) 1.53
FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res (2012) 1.52
A combined empirical and mechanistic codon model. Mol Biol Evol (2006) 1.52
Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics (2005) 1.52
Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. Proc Natl Acad Sci U S A (2013) 1.51
Effect of nuclear architecture on the efficiency of double-strand break repair. Nat Cell Biol (2013) 1.45
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45
Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol (2009) 1.44
The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol (2010) 1.44
Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep (2012) 1.41
A machine-learning approach for predicting B-cell epitopes. Mol Immunol (2008) 1.40
Toward accurate reconstruction of functional protein networks. Mol Syst Biol (2009) 1.40
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium. Mol Syst Biol (2005) 1.36
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol (2008) 1.35
Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins (2007) 1.31
A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics (2005) 1.30
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29
Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29
Opposite effects of tor1 and tor2 on nitrogen starvation responses in fission yeast. Genetics (2006) 1.28
Regulation of leucine uptake by tor1+ in Schizosaccharomyces pombe is sensitive to rapamycin. Genetics (2004) 1.28
A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol Syst Biol (2008) 1.27
The "alternative" choice of constitutive exons throughout evolution. PLoS Genet (2007) 1.27
DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array. Proc Natl Acad Sci U S A (2013) 1.25
Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res (2011) 1.24
A Saccharomyces cerevisiae mutant with increased virulence. Proc Natl Acad Sci U S A (2003) 1.23
Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23
The checkpoint protein Rad24 of Saccharomyces cerevisiae is involved in processing double-strand break ends and in recombination partner choice. Mol Cell Biol (2003) 1.22
Multilocus sequence typing (MLST) of Escherichia coli O78 strains. FEMS Microbiol Lett (2003) 1.21
A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res (2009) 1.20
The yeast VPS genes affect telomere length regulation. Curr Genet (2004) 1.18
The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release. J Virol (2004) 1.18
In silico identification of functional regions in proteins. Bioinformatics (2005) 1.18
The Elg1 replication factor C-like complex: a novel guardian of genome stability. DNA Repair (Amst) (2005) 1.18
Systematic identification of gene annotation errors in the widely used yeast mutation collections. Nat Methods (2012) 1.17
The ELG1 clamp loader plays a role in sister chromatid cohesion. PLoS One (2009) 1.17
Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16
A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci (2008) 1.16
Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol (2011) 1.15
Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biol (2007) 1.13
Elg1, an alternative subunit of the RFC clamp loader, preferentially interacts with SUMOylated PCNA. EMBO J (2010) 1.12
New insights into the mechanism of homologous recombination in yeast. Mutat Res (2004) 1.11
Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res (2011) 1.10
Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. Bioinformatics (2007) 1.10
Proteasome nuclear activity affects chromosome stability by controlling the turnover of Mms22, a protein important for DNA repair. PLoS Genet (2010) 1.10