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Citations per year

Number of citations per year for the bioinformatics software tool SELEX
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Tool usage distribution map

This map represents all the scientific publications referring to SELEX per scientific context
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SELEX specifications

Information


Unique identifier OMICS_17445
Name SELEX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12.0
Stability Stable
Requirements
R(>=2.7.0), Biostrings(>=2.26.0), rJava(>=0.5-0)
Maintained Yes

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Maintainer


  • person_outline Harmen Bussemaker

SELEX citations

 (5)
library_books

Accurate and sensitive quantification of protein DNA binding affinity

2018
Proc Natl Acad Sci U S A
PMCID: 5910815
PMID: 29610332
DOI: 10.1073/pnas.1714376115

[…] ries were gel-purified as described previously (, ). R0 and R1 indexed experiments were pooled and sequenced using the v2 high-output 75 cycles kit on an Illumina NEXTSeq Series desktop sequencer. R1 SELEX-seq for MAX protein was performed as described previously () and sequenced with Illumina’s HiSeq system at the New York Genome Center. […]

library_books

The RNA binding protein Celf1 post transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development

2018
PLoS Genet
PMCID: 5889275
PMID: 29565969
DOI: 10.1371/journal.pgen.1007278

[…] n assays (), suggesting that Celf1 directly associates with p27Kip1 mRNA in the developing mouse lens. Several studies have shown that Celf1 binds to GU-rich motifs in target RNAs. These are based on SELEX (systematic evolution of ligands by exponential enrichment) assays [] and by identifying conserved motifs within various Celf1-controlled transcripts [–]. Further, the structural bases for the s […]

library_books

A unified approach for quantifying and interpreting DNA shape readout by transcription factors

2018
Mol Syst Biol
PMCID: 5822049
PMID: 29472273
DOI: 10.15252/msb.20177902

[…] ma et al, ; Slattery et al, ; Zhao et al, ). A detailed description of NRLB, along with benchmarking results and biological applications of such models, is being prepared for separate publication.The SELEX process starts with a library of DNA probes containing a L‐bp random region flanked by constant adaptor sequences (Jolma et al, ; Slattery et al, ). This library is incubated with the TF of inte […]

library_books

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT content

2017
PLoS Genet
PMCID: 5756049
PMID: 29267285
DOI: 10.1371/journal.pgen.1007102

[…] vivo determination of Hmga2 binding preference, the identified motif (consensus of 49 sequences) was a simple repetition of W nucleotides (either A or T) []. This is in contrast with a low-throughput SELEX assessment of Hmga2 affinity, which resulted in a high-information-content DNA logo []. In another study, a ChIP-chip experiment was performed in the MKN28 gastrinoma cell line overexpressing Hm […]

library_books

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation

2017
PMCID: 5323403
PMID: 28286470
DOI: 10.3389/fnmol.2017.00045

[…] ical, they are useful for motif identification and can complement other antibody-based methods to separate falsely identified RNA targets. Systematic evolution of Ligands by EXponentional Enrichment (SELEX) was developed in the 1990s as a way of assessing the binding affinity of proteins to a pool of random oligonucleotides. The oligonucleotide library is incubated with the target protein of inter […]


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