Published in Nucleic Acids Res on April 20, 2011
An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods (2012) 1.84
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev (2012) 1.11
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res (2014) 1.02
A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res (2015) 0.92
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res (2013) 0.91
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Genetics (2014) 0.86
Engineered zinc-finger proteins can compensate genetic haploinsufficiency by transcriptional activation of the wild-type allele: application to Willams-Beuren syndrome and supravalvular aortic stenosis. Hum Gene Ther (2012) 0.81
Spec-seq: determining protein-DNA-binding specificity by sequencing. Brief Funct Genomics (2014) 0.80
Assessing the effects of symmetry on motif discovery and modeling. PLoS One (2011) 0.77
Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. Trends Genet (2016) 0.76
LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression. Nucleic Acids Res (2016) 0.75
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
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol (1987) 17.53
DNA binding sites: representation and discovery. Bioinformatics (2000) 16.01
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36
Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science (1990) 9.54
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput (2001) 8.65
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol (1989) 5.23
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
A systems approach to measuring the binding energy landscapes of transcription factors. Science (2007) 5.06
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site. Mol Cell Biol (1991) 3.54
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol (2002) 3.04
Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res (2008) 2.30
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol (2005) 2.28
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol (2010) 2.05
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res (2010) 1.88
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res (2009) 1.88
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res (2010) 1.81
Selection of DNA binding sites by regulatory proteins. Trends Biochem Sci (1988) 1.73
Quantitative microarray profiling of DNA-binding molecules. J Am Chem Soc (2007) 1.30
CSI-FID: high throughput label-free detection of DNA binding molecules. Bioorg Med Chem Lett (2009) 0.96
Counter-selectable marker for bacterial-based interaction trap systems. Biotechniques (2006) 0.87
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol (2008) 10.29
Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell (2004) 6.10
Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics (2003) 5.99
A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science (2010) 5.84
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
The AP-1 transcription factor Batf controls T(H)17 differentiation. Nature (2009) 3.75
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol (2011) 2.58
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics (2005) 2.43
The neuropeptide pigment-dispersing factor coordinates pacemaker interactions in the Drosophila circadian system. J Neurosci (2004) 2.42
Target selectivity of vertebrate notch proteins. Collaboration between discrete domains and CSL-binding site architecture determines activation probability. J Biol Chem (2005) 2.33
Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc Natl Acad Sci U S A (2002) 2.33
Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development. Genes Dev (2006) 2.33
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res (2008) 2.30
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol (2005) 2.28
Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol (2002) 2.23
Is there a code for protein-DNA recognition? Probab(ilistical)ly. . . Bioessays (2002) 2.17
Chemokine signaling guides regional patterning of the first embryonic artery. Genes Dev (2009) 2.14
Direct, androgen receptor-mediated regulation of the FKBP5 gene via a distal enhancer element. Endocrinology (2005) 2.04
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics (2004) 1.89
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res (2010) 1.88
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res (2002) 1.87
Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication. Retrovirology (2008) 1.87
An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods (2012) 1.84
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res (2010) 1.81
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. Genome Res (2006) 1.78
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci U S A (2005) 1.72
Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish. Dev Cell (2011) 1.72
Improved models for transcription factor binding site identification using nonindependent interactions. Genetics (2012) 1.61
Automated retrieval of CT images of liver lesions on the basis of image similarity: method and preliminary results. Radiology (2010) 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
Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development (2011) 1.54
Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc (2004) 1.53
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinformatics (2008) 1.42
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol (2010) 1.40
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res (2011) 1.37
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat Protoc (2006) 1.36
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics (2004) 1.35
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics (2007) 1.32
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics (2005) 1.31
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res (2005) 1.27
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res (2005) 1.22
RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites. Proc Natl Acad Sci U S A (2004) 1.22
Arterial-venous network formation during brain vascularization involves hemodynamic regulation of chemokine signaling. Development (2011) 1.20
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Res (2007) 1.17
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol Syst Biol (2009) 1.17
Making connections between novel transcription factors and their DNA motifs. Genome Res (2005) 1.16
PromoLign: a database for upstream region analysis and SNPs. Hum Mutat (2004) 1.15
Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major. Mol Biochem Parasitol (2004) 1.14
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes. Genome Res (2004) 1.13
Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases. Genome Res (2012) 1.12
PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum Mutat (2005) 1.12
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol (2008) 1.12
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res (2007) 1.11
Pharmacognostic evaluation of Cayratia trifolia (Linn.) leaf. Asian Pac J Trop Biomed (2012) 1.09
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics (2012) 1.09
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res (2013) 1.07
Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res (2007) 1.07
Pandemic swine influenza virus (H1N1): A threatening evolution. Indian J Microbiol (2010) 1.05
Influenza A (H1N1) 2009: a pandemic alarm. J Biosci (2009) 1.05
Homocysteine- and cysteine-mediated growth defect is not associated with induction of oxidative stress response genes in yeast. Biochem J (2006) 1.04
Molecular diagnostics in sepsis: from bedside to bench. J Am Coll Surg (2006) 1.02
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res (2013) 1.02
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res (2014) 1.02
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes. Genome Res (2007) 1.01
Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III. J Eukaryot Microbiol (2003) 1.01
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics (2010) 0.98
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLoS Comput Biol (2012) 0.97
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet (2013) 0.97
The cis-regulatory map of Shewanella genomes. Nucleic Acids Res (2008) 0.96
ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res (2004) 0.96
Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields. Appl Environ Microbiol (2011) 0.96
Identification of cilia genes that affect cell-cycle progression using whole-genome transcriptome analysis in Chlamydomonas reinhardtti. G3 (Bethesda) (2013) 0.93
Allospecific CD154+ T cells identify rejection-prone recipients after pediatric small-bowel transplantation. Surgery (2009) 0.92
Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor. J Biol Chem (2012) 0.92
Editing efficiency of a Drosophila gene correlates with a distant splice site selection. RNA (2005) 0.92
Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria. Nucleic Acids Res (2003) 0.92
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor. Nucleic Acids Res (2004) 0.92
Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays. Crit Care Med (2002) 0.92
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinformatics (2007) 0.92
A nutrient-sensitive interaction between Sirt1 and HNF-1α regulates Crp expression. Aging Cell (2011) 0.91
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res (2013) 0.91
Modeling the quantitative specificity of DNA-binding proteins from example binding sites. PLoS One (2009) 0.91
Transcriptional profiles of human epithelial cells in response to heat: computational evidence for novel heat shock proteins. Shock (2008) 0.90
U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res (2013) 0.88
Nuclear-encoded DnaJ homologue of Plasmodium falciparum interacts with replication ori of the apicoplast genome. Mol Microbiol (2010) 0.88