High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

scientific article published on 8 July 2002

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1038/NBT718
P698PubMed publication ID12101405
P5875ResearchGate publication ID11275646

P50authorAnamaria Aranha CamargoQ37616056
P2093author name stringAndrew J G Simpson
Philipp Bucher
Nicolas Mermod
Emmanuelle Roulet
Stéphane Busso
P2860cites workBase-calling of automated sequencer traces using phred. I. Accuracy assessmentQ27860665
Serial analysis of gene expressionQ27860777
Prediction of complete gene structures in human genomic DNAQ27860780
In vitro selection of integration host factor binding sitesQ31289061
The mathematics of SELEX against complex targetsQ32062858
The eukaryotic promoter database (EPD).Q33611246
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.Q33939540
A quantitative analysis of nuclear factor I/DNA interactionsQ36005298
DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sitesQ38307243
All you wanted to know about SELEX.Q38313117
Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.Q38313939
Quantitative specificity of the Mnt repressorQ38343476
A flexible motif search technique based on generalized profiles.Q52308727
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.Q52603460
P433issue8
P304page(s)831-835
P577publication date2002-07-08
P1433published inNature BiotechnologyQ1893837
P1476titleHigh-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.
P478volume20

Reverse relations

cites work (P2860)
Q30377926A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq.
Q43159884A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
Q91011824A deep learning framework to predict binding preference of RNA constituents on protein surface
Q33878190A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
Q31089638A novel approach for transcription factor analysis using SELEX with high-throughput sequencing (TFAST).
Q44029544A novel high-throughput B1H-ChIP method for efficiently validating and screening specific regulator-target promoter interactions
Q34760479A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
Q42382121ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs
Q35018471An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example
Q37781733Analysis of DNA-protein interactions: from nitrocellulose filter binding assays to microarray studies.
Q37671981Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change
Q38295683Anti-Transcription Factor RNA Aptamers as Potential Therapeutics
Q35766840Applied bioinformatics for the identification of regulatory elements
Q34933446Aptamer database
Q38358691Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
Q40678062Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication
Q33395479Better estimation of protein-DNA interaction parameters improve prediction of functional sites
Q35008732Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.
Q45869978CTF/NF1 transcription factors act as potent genetic insulators for integrating gene transfer vectors
Q50610314Capturing the target genes of BldD in Saccharopolyspora erythraea using improved genomic SELEX method.
Q35335653Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells
Q28484847Challenges and opportunities for small molecule aptamer development
Q28487330Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein.
Q33554218Characterization of homing endonuclease binding and cleavage specificities using yeast surface display SELEX (YSD-SELEX)
Q38335472Characterization of protein-DNA interactions using protein microarrays
Q35744439Charting gene regulatory networks: strategies, challenges and perspectives.
Q40342981Chromatin immunoprecipitation identifies photoreceptor transcription factor targets in mouse models of retinal degeneration: new findings and challenges
Q24816299Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions
Q37318348Comparative analysis of regulatory motif discovery tools for transcription factor binding sites
Q35174797Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers
Q39026696Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges
Q24801531Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
Q43063731Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
Q38330611DIP-chip: rapid and accurate determination of DNA-binding specificity.
Q35038272Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets
Q33638356Designing anti-influenza aptamers: novel quantitative structure activity relationship approach gives insights into aptamer-virus interaction
Q28775981Detection of functional DNA motifs via statistical over-representation
Q37793836Determining the specificity of protein–DNA interactions
Q48076871Development of software facilities to characterize regulatory binding motifs and application to streptococcaceae
Q24654994Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
Q25256713EMBL Nucleotide Sequence Database: developments in 2005
Q33886716Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases
Q35557677Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits.
Q24641842FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1
Q33300800Finding regulatory elements and regulatory motifs: a general probabilistic framework
Q24609505FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
Q97542507Fully interpretable deep learning model of transcriptional control
Q36796414Genetic dissection of the consensus sequence for the class 2 and class 3 flagellar promoters
Q24618467Genome annotation by high-throughput 5' RNA end determination
Q36151076Genome-wide view of cell fate specification: ladybird acts at multiple levels during diversification of muscle and heart precursors
Q37788028Genome‐wide maps of transcription regulatory elements
Q34421960Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing
Q25257857HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites
Q38303102High-throughput assay for determining specificity and affinity of protein-DNA binding interactions
Q33280931Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system
Q38337637Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors.
Q89637567In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target
Q59102293In silico identification of metazoan transcriptional regulatory regions
Q38333905In situ imaging and isolation of proteins using dsDNA oligonucleotides
Q35652294In vitro analysis of DNA-protein interactions by proximity ligation
Q28469075Inference of splicing regulatory activities by sequence neighborhood analysis
Q46871344Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis.
Q38341005Inferring Protein–DNA Interaction Parameters from SELEX Experiments
Q28472054Inferring binding energies from selected binding sites
Q36280574Inferring direct DNA binding from ChIP-seq
Q41090628Inherent limitations of probabilistic models for protein-DNA binding specificity
Q27934300Linking DNA-binding proteins to their recognition sequences by using protein microarrays
Q28710347MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences
Q37590028Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.
Q33881396Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
Q30538110Nuclear Factor I genomic binding associates with chromatin boundaries
Q30499852Nuclear factor I revealed as family of promoter binding transcription activators
Q37972851Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects.
Q28075458Opportunities in the design and application of RNA for gene expression control
Q30817157Optimized mixed Markov models for motif identification
Q34924138Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome
Q38288287Poly(methyl methacrylate) microchip affinity capillary gel electrophoresis of aptamer-protein complexes for the analysis of thrombin in plasma.
Q36544912Prediction of cis-regulatory elements for drug-activated transcription factors in the regulation of drug-metabolising enzymes and drug transporters
Q33286236Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method
Q24803007Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts
Q36732432Protein binding microarrays for the characterization of DNA-protein interactions
Q36874479Putting numbers on the network connections
Q35652208Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy
Q39456981Quantitative Analysis of Protein-DNA Interaction by qDPI-ELISA.
Q36769443Quantitative analysis of TALE-DNA interactions suggests polarity effects.
Q37346433Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor
Q28477071Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
Q34611185Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic
Q56915345Recent Advances in the Computational Discovery of Transcription Factor Binding Sites
Q38848925Recent Progress in Aptamer-Based Functional Probes for Bioanalysis and Biomedicine.
Q38753507Recent advances in transcription factor assays in vitro
Q38958313Redefining Escherichia coli σ(70) promoter elements: -15 motif as a complement of the -10 motif
Q35750565Reliable scaling of position weight matrices for binding strength comparisons between transcription factors
Q35958678SELEX Modifications and Bioanalytical Techniques for Aptamer-Target Binding Characterization.
Q41098984SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics
Q47284764Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites
Q35022394Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA
Q47590465SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
Q35845621Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools
Q27674412Structure and Function of AvtR, a Novel Transcriptional Regulator from a Hyperthermophilic Archaeal Lipothrixvirus
Q37826102Systematic characterization of protein-DNA interactions
Q22001535THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves
Q38092497Taking into account nucleosomes for predicting gene expression
Q27006654Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?
Q26745628The in vitro selection world
Q35382148Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding
Q39209455Transcription factor-DNA binding: beyond binding site motifs.
Q57806574Transcription of the Human 5-Hydroxytryptamine Receptor 2B (HTR2B) Gene Is under the Regulatory Influence of the Transcription Factors NFI and RUNX1 in Human Uveal Melanoma
Q24655466UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

Search more.