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Citations per year

Number of citations per year for the bioinformatics software tool CTCFBSDB

Tool usage distribution map

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


Unique identifier OMICS_00530
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Version 2.0
Maintained Yes


  • CTCFBS Prediction Tool


  • person_outline Yan Cui

Publications for CTCFBSDB

CTCFBSDB citations


The long range interaction map of ribosomal DNA arrays

PLoS Genet
PMCID: 5865718
PMID: 29570716
DOI: 10.1371/journal.pgen.1007258

[…] ed. Third, information on replication timing along the genome was downloaded from the Replication Domain Database (www.replicationdomain.org). Finally, CTCF binding coordinates were obtained from the CTCFBSDB database []. We extracted the coordinates for all the segments in each annotation and addressed its density of rDNA contacts. BEDTools was used to assess the number of mapped reads that overl […]


Association studies of WD repeat domain 3 and chitobiosyldiphosphodolichol beta mannosyltransferase genes with schizophrenia in a Japanese population

PLoS One
PMCID: 5757935
PMID: 29309433
DOI: 10.1371/journal.pone.0190991
call_split See protocol

[…] Select algorithm to evaluate the selection of the SNPs []. Additionally, we added SNPs from the insulator regions (CTCF binding site) between the target and adjacent gene as an effective region using CTCFBSDB 2.0 (http://insulatordb.uthsc.edu/) [].SNP genotyping was performed by TaqMan SNP genotyping assays (Applied Biosystems, Foster City, CA, USA). We used an ABI PRISM 7900HT (Applied Biosystems […]


Identification and characterization of two functional variants in the human longevity gene FOXO3

Nat Commun
PMCID: 5727304
PMID: 29234056
DOI: 10.1038/s41467-017-02183-y

[…] culating IGF-1 remains to be clarified.The CTCF supershift experiments indicated a slightly stronger binding of CTCF to the oligonucleotide containing the major allele C of rs12206094, confirming the CTCFBSDB 2.027 prediction. However, our functional experiments with the rs12206094 allele-specific constructs suggested that the binding strength of CTCF did not influence the luciferase promoter acti […]


Alternatively spliced MEFV transcript lacking exon 2 and its protein isoform pyrin 2d implies an epigenetic regulation of the gene in inflammatory cell culture models

Genet Mol Biol
PMCID: 5596369
PMID: 28863210
DOI: 10.1590/1678-4685-GMB-2016-0234

[…] methylation (). Adversely, another protein, CTCF, was found to play a role in the recognition of a weak exon signal in the CD45 gene in the absence of DNA methylation (). Although our research on the CTCFBSDB database, a database for CTCF binding sites, has shown the absence of CTCF in the MEFV gene in HL-60 cells, the CTCF prediction tool on the same site predicts a binding site 35 bp from the ex […]


Expansion of epigenetic alterations in EFEMP1 promoter predicts malignant formation in pancreatobiliary intraductal papillary mucinous neoplasms

PMCID: 4899496
PMID: 27095449
DOI: 10.1007/s00432-016-2164-x

[…] t various regions in previous studies (Kobayashi et al. ; Nomoto et al. ; Sadr-Nabavi et al. ; Wang et al. , ; Yang et al. ; Yue et al. ; Zhu et al. ). In this study, we searched CTCF biding sites by CTCFBSDB 2.0 (http://insulatordb.uthsc.edu/) in promoter region of the EFEMP1 gene and found a CTCF biding site ‘TGACATCTGTTGGG,’ called as the EMBL_M1 motifs (Schmidt et al. ). CTCF, also known as CC […]


Jointly characterizing epigenetic dynamics across multiple human cell types

Nucleic Acids Res
PMCID: 5772166
PMID: 27095202
DOI: 10.1093/nar/gkw278

[…] contribute to the performance difference observed here.We next evaluated CTCF occupancy prediction using manually curated CTCF sites and experimentally validated CTCF sites from non-ENCODE studies in CTCFBSDB2.0 (). The CTCF-labeled states for IDEAS captured substantially more CTCF sites (57.7%) than for ChromHMM (21.2%) and Segway (25.0%), respectively, on the manually curated CTCF. Similarly, th […]

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CTCFBSDB institution(s)
Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN, USA
CTCFBSDB funding source(s)
Supported by the UT Center for Integrative and Translational Genomics; Department of Defense [W81XHW-05-01- 0227].

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