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Citations per year

Number of citations per year for the bioinformatics software tool SELEX

Tool usage distribution map

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


Unique identifier OMICS_17445
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
R(>=2.7.0), Biostrings(>=2.26.0), rJava(>=0.5-0)
Maintained Yes




No version available


  • person_outline Harmen Bussemaker

SELEX citations


Accurate and sensitive quantification of protein DNA binding affinity

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. […]


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

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 […]


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

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 […]


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

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 […]


Screening the Molecular Framework Underlying Local Dendritic mRNA Translation

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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