Published in Nucleic Acids Res on August 04, 2010
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res (2010) 2.16
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol (2011) 1.32
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res (2014) 1.31
Aniridia. Eur J Hum Genet (2012) 1.24
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res (2011) 1.15
Notch and MAML-1 complexation do not detectably alter the DNA binding specificity of the transcription factor CSL. PLoS One (2010) 0.93
Functional dissection of the paired domain of Pax6 reveals molecular mechanisms of coordinating neurogenesis and proliferation. Development (2013) 0.91
Computational models for large-scale simulations of facilitated diffusion. Mol Biosyst (2012) 0.90
Atomistic modeling of protein-DNA interaction specificity: progress and applications. Curr Opin Struct Biol (2012) 0.88
Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations. Mol Syst Biol (2014) 0.86
Towards computational specificity screening of DNA-binding proteins. Nucleic Acids Res (2011) 0.85
Gene regulation by PAX6: structural-functional correlations of missense mutants and transcriptional control of Trpm3/miR-204. Mol Vis (2014) 0.81
Assessing the correlation between mutant rhodopsin stability and the severity of retinitis pigmentosa. Mol Vis (2014) 0.78
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. Nucleic Acids Res (2014) 0.78
A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL. Nucleic Acids Res (2014) 0.77
Impact of the 237th residue on the folding of human carbonic anhydrase II. Int J Mol Sci (2011) 0.76
Structure-based prediction of transcription factor binding specificity using an integrative energy function. Bioinformatics (2016) 0.76
The yin-yang of kinase activation and unfolding explains the peculiarity of Val600 in the activation segment of BRAF. Elife (2016) 0.75
Specificity determinants for the abscisic acid response element. FEBS Open Bio (2013) 0.75
Structure-based activity prediction of CYP21A2 stability variants: A survey of available gene variations. Sci Rep (2016) 0.75
Pathogenic mutations in retinitis pigmentosa 2 predominantly result in loss of RP2 protein stability in humans and zebrafish. J Biol Chem (2017) 0.75
Structure-based modeling of protein: DNA specificity. Brief Funct Genomics (2014) 0.75
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science (1990) 35.96
In vitro selection of RNA molecules that bind specific ligands. Nature (1990) 30.19
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res (2004) 19.32
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res (2008) 6.83
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
Pax6 is required for the multipotent state of retinal progenitor cells. Cell (2001) 4.65
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc (2009) 3.48
Computational prediction of transcription-factor binding site locations. Genome Biol (2003) 3.39
Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. J Biol Chem (1994) 3.22
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 3.02
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res (2006) 2.81
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes Dev (1999) 2.54
Getting your Pax straight: Pax proteins in development and disease. Trends Genet (2002) 2.48
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
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
Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development. Genes Dev (2001) 2.18
PAX6 in sensory development. Hum Mol Genet (2002) 2.05
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol (2005) 2.04
Concise review: Pax6 transcription factor contributes to both embryonic and adult neurogenesis as a multifunctional regulator. Stem Cells (2008) 1.99
Mutations of the PAX6 gene detected in patients with a variety of optic-nerve malformations. Am J Hum Genet (2003) 1.94
A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol (2004) 1.90
Missense mutations in the most ancient residues of the PAX6 paired domain underlie a spectrum of human congenital eye malformations. Hum Mol Genet (1999) 1.86
Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics (2008) 1.74
PAX6 mutations: genotype-phenotype correlations. BMC Genet (2005) 1.65
Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A (2007) 1.46
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res (2007) 1.40
Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. Genome Res (2002) 1.39
Clinical and molecular aspects of aniridia. Clin Genet (2010) 1.34
Loss- and gain-of-function analyses reveal targets of Pax6 in the developing mouse telencephalon. Mol Cell Neurosci (2006) 1.34
Regulatory pathway analysis by high-throughput in situ hybridization. PLoS Genet (2007) 1.28
The Human PAX6 Mutation Database. Nucleic Acids Res (1998) 1.28
Toward the rational design of p53-stabilizing drugs: probing the surface of the oncogenic Y220C mutant. Chem Biol (2010) 1.27
Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet (2007) 1.24
Identification of pax6-dependent gene regulatory networks in the mouse lens. PLoS One (2009) 1.19
Kinetic stabilization of the native state by protein engineering: implications for inhibition of transthyretin amyloidogenesis. J Mol Biol (2005) 1.14
Looking into DNA recognition: zinc finger binding specificity. Nucleic Acids Res (2004) 1.13
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Proteins (2008) 1.07
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics (2008) 1.07
Functional analysis of paired box missense mutations in the PAX6 gene. Hum Mol Genet (1997) 1.06
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci U S A (2008) 1.01
The third helix of the homeodomain of paired class homeodomain proteins acts as a recognition helix both for DNA and protein interactions. Nucleic Acids Res (2005) 0.99
Weight matrices for protein-DNA binding sites from a single co-crystal structure. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.98
Focus on molecules: Pax-6, the eye master. Exp Eye Res (2006) 0.98
Predicting transcription factor specificity with all-atom models. Nucleic Acids Res (2008) 0.86
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res (2008) 6.83
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell (2010) 5.67
High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J (2010) 4.78
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc (2009) 3.48
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A (2008) 3.10
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 3.02
Structure-based assembly of protein complexes in yeast. Science (2004) 2.89
Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science (2011) 2.78
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
From in vivo to in silico biology and back. Nature (2006) 2.74
Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci U S A (2003) 2.71
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res (2005) 2.69
Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol (2006) 2.69
De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59
Systematic identification of mammalian regulatory motifs' target genes and functions. Nat Methods (2008) 2.58
Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51
Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell (2010) 2.43
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
O-glycosylated cell wall proteins are essential in root hair growth. Science (2011) 2.34
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
The stability effects of protein mutations appear to be universally distributed. J Mol Biol (2007) 2.25
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res (2010) 2.16
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. Mol Microbiol (2008) 2.11
Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol (2006) 2.10
Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth. Structure (2005) 2.09
Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res (2009) 2.05
A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J Mol Biol (2004) 2.05
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol (2005) 2.04
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep (2013) 2.03
Analysis and description of HOLTIN service provision for AECG monitoring in complex indoor environments. Sensors (Basel) (2013) 2.02
Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol Biol (2006) 2.00
Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells. Cancer Res (2009) 1.97
Rational design of a CD4 mimic that inhibits HIV-1 entry and exposes cryptic neutralization epitopes. Nat Biotechnol (2002) 1.95
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol (2005) 1.91
Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol (2002) 1.89
Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells. PLoS Comput Biol (2006) 1.88
Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci U S A (2004) 1.83
LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr Biol (2011) 1.78
Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol (2005) 1.76
Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae. Genome Res (2007) 1.75
Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res (2008) 1.74
Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. Nat Immunol (2011) 1.72
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68
Microarray analyses of newborn mouse ovaries lacking Nobox. Biol Reprod (2007) 1.67
Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64
Strand-specific deep sequencing of the transcriptome. Genome Res (2010) 1.58
A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics (2002) 1.54
A graphical interface for the FoldX forcefield. Bioinformatics (2011) 1.50
Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol (2005) 1.48
Design of compact, universal DNA microarrays for protein binding microarray experiments. J Comput Biol (2008) 1.45
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci U S A (2006) 1.45
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
A detailed thermodynamic analysis of ras/effector complex interfaces. J Mol Biol (2004) 1.42
The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41
Energy estimation in protein design. Curr Opin Struct Biol (2002) 1.39
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. Genes Dev (2010) 1.39
PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol Syst Biol (2011) 1.34
Towards cellular systems in 4D. Cell (2005) 1.33
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol (2005) 1.33
Modulefinder: a tool for computational discovery of cis regulatory modules. Pac Symp Biocomput (2005) 1.33
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol (2011) 1.32
Analyzing protein interaction networks using structural information. Annu Rev Biochem (2008) 1.32
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics (2006) 1.28
Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways. PLoS One (2009) 1.28
Design of a wearable device for ECG continuous monitoring using wireless technology. Conf Proc IEEE Eng Med Biol Soc (2004) 1.28
Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27
Space as the final frontier in stochastic simulations of biological systems. FEBS Lett (2005) 1.25
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev (2012) 1.24
Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet (2007) 1.24
Engineering signal transduction pathways. Cell (2010) 1.21
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res (2010) 1.19
Computational design of peptide ligands. Trends Biotechnol (2011) 1.19