Published in Nucleic Acids Res on August 02, 2004
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
Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism. Nucleic Acids Res (2007) 0.98
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Res (2009) 0.93
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Genetics (2014) 0.86
Predicting transcription factor specificity with all-atom models. Nucleic Acids Res (2008) 0.86
Hybrid incompatibility arises in a sequence-based bioenergetic model of transcription factor binding. Genetics (2014) 0.85
Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. Proc Natl Acad Sci U S A (2007) 0.83
Spec-seq: determining protein-DNA-binding specificity by sequencing. Brief Funct Genomics (2014) 0.80
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Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
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Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83
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Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
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High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol (2002) 3.04
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Mining genome databases to identify and understand new gene regulatory systems. Curr Opin Microbiol (2002) 1.02
One-hybrid systems for detecting protein-DNA interactions. Methods Mol Biol (2001) 0.89
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res (2002) 0.88
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13
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
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
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
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
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
An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods (2012) 1.84
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
Improved models for transcription factor binding site identification using nonindependent interactions. Genetics (2012) 1.61
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
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res (2011) 1.37
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
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
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol (2008) 1.12
PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum Mutat (2005) 1.12
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res (2007) 1.11
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics (2012) 1.09
Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res (2007) 1.07
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res (2013) 1.07
Molecular diagnostics in sepsis: from bedside to bench. J Am Coll Surg (2006) 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
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res (2011) 0.97
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLoS Comput Biol (2012) 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
Identification of cilia genes that affect cell-cycle progression using whole-genome transcriptome analysis in Chlamydomonas reinhardtti. G3 (Bethesda) (2013) 0.93
Editing efficiency of a Drosophila gene correlates with a distant splice site selection. RNA (2005) 0.92
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinformatics (2007) 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
Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays. Crit Care Med (2002) 0.92
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res (2013) 0.91
A nutrient-sensitive interaction between Sirt1 and HNF-1α regulates Crp expression. Aging Cell (2011) 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
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res (2002) 0.88
Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines. PLoS Comput Biol (2009) 0.88
Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2. BMC Genomics (2009) 0.88
Procom: a web-based tool to compare multiple eukaryotic proteomes. Bioinformatics (2004) 0.87
Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Nucleic Acids Res (2007) 0.87
Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling. Philos Trans R Soc Lond B Biol Sci (2002) 0.87
Exploring the DNA-recognition potential of homeodomains. Genome Res (2012) 0.83
Discriminative motif optimization based on perceptron training. Bioinformatics (2013) 0.81
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. G3 (Bethesda) (2012) 0.81
Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach. PLoS One (2007) 0.81
Spec-seq: determining protein-DNA-binding specificity by sequencing. Brief Funct Genomics (2014) 0.80
Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation. Proc IEEE Int Symp Bioinformatics Bioeng (2010) 0.79
A simplified homology-model builder toward highly protein-like structures: an inspection of restraining potentials. J Comput Chem (2012) 0.78
Fast, sensitive discovery of conserved genome-wide motifs. J Comput Biol (2012) 0.78
Assessing the effects of symmetry on motif discovery and modeling. PLoS One (2011) 0.77
Evolution. Heirlooms in the attic. Science (2003) 0.75
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans. Bioinformatics (2006) 0.75