Literature DB >> 23740745

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Fabian A Buske1, Denis C Bauer, John S Mattick, Timothy L Bailey.   

Abstract

SUMMARY: At the heart of many modern biotechnological and therapeutic applications lies the need to target specific genomic loci with pinpoint accuracy. Although landmark experiments demonstrate technological maturity in manufacturing and delivering genetic material, the genomic sequence analysis to find suitable targets lags behind. We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genomic architecture into account. AVAILABILITY: Source code and binaries are downloadable from www.bioinformatics.org.au/triplexator/inspector. CONTACT: t.bailey@uq.edu.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mesh：

Substances：

Year:  2013        PMID： 23740745      PMCID： PMC3712220          DOI： 10.1093/bioinformatics/btt315

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

1.  Circos: an information aesthetic for comparative genomics.

Authors:  Martin Krzywinski; Jacqueline Schein; Inanç Birol; Joseph Connors; Randy Gascoyne; Doug Horsman; Steven J Jones; Marco A Marra
Journal:  Genome Res       Date:  2009-06-18       Impact factor: 9.043

2.  PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules.

Authors:  M Egholm; O Buchardt; L Christensen; C Behrens; S M Freier; D A Driver; R H Berg; S K Kim; B Norden; P E Nielsen
Journal:  Nature       Date:  1993-10-07       Impact factor: 49.962

Review 3.  Potential in vivo roles of nucleic acid triple-helices.

Authors:  Fabian A Buske; John S Mattick; Timothy L Bailey
Journal:  RNA Biol       Date:  2011-05-01       Impact factor: 4.652

4.  Targeted gene modification of hematopoietic progenitor cells in mice following systemic administration of a PNA-peptide conjugate.

Authors:  Faye A Rogers; Sharon S Lin; Denise C Hegan; Diane S Krause; Peter M Glazer
Journal:  Mol Ther       Date:  2011-08-09       Impact factor: 11.454

5.  Triplex formation on DNA targets: how to choose the oligonucleotide.

Authors:  Pierre Vekhoff; Alexandre Ceccaldi; David Polverari; Jean Pylouster; Claudio Pisano; Paola B Arimondo
Journal:  Biochemistry       Date:  2008-11-25       Impact factor: 3.162

6.  Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids.

Authors:  Joanna Y Chin; Jean Y Kuan; Pallavi S Lonkar; Diane S Krause; Michael M Seidman; Kenneth R Peterson; Peter E Nielsen; Ryszard Kole; Peter M Glazer
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-29       Impact factor: 11.205

7.  Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.

Authors:  Fabian A Buske; Denis C Bauer; John S Mattick; Timothy L Bailey
Journal:  Genome Res       Date:  2012-05-01       Impact factor: 9.043
  7 in total
  13 in total

Review 1.  Towards a complete map of the human long non-coding RNA transcriptome.

Authors:  Barbara Uszczynska-Ratajczak; Julien Lagarde; Adam Frankish; Roderic Guigó; Rory Johnson
Journal:  Nat Rev Genet       Date:  2018-09       Impact factor: 53.242

2.  GT-Scan: identifying unique genomic targets.

Authors:  Aidan O'Brien; Timothy L Bailey
Journal:  Bioinformatics       Date:  2014-05-23       Impact factor: 6.937

3.  Long Noncoding RNA MEG3 Is an Epigenetic Determinant of Oncogenic Signaling in Functional Pancreatic Neuroendocrine Tumor Cells.

Authors:  Sucharitha Iyer; Sita D Modali; Sunita K Agarwal
Journal:  Mol Cell Biol       Date:  2017-10-27       Impact factor: 4.272

Review 4.  Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin.

Authors:  Emily J McFadden; Amanda E Hargrove
Journal:  Biochemistry       Date:  2016-02-24       Impact factor: 3.162

5.  Illuminating lncRNA Function Through Target Prediction.

Authors:  Hua-Sheng Chiu; Sonal Somvanshi; Ting-Wen Chen; Pavel Sumazin
Journal:  Methods Mol Biol       Date:  2021

6.  The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.

Authors:  Piroon Jenjaroenpun; Chee Siang Chew; Tai Pang Yong; Kiattawee Choowongkomon; Wimada Thammasorn; Vladimir A Kuznetsov
Journal:  Nucleic Acids Res       Date:  2014-10-16       Impact factor: 16.971

7.  Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets.

Authors:  Gunaseelan Goldsmith; Thenmalarchelvi Rathinavelan; Narayanarao Yathindra
Journal:  PLoS One       Date:  2016-03-24       Impact factor: 3.240

8.  p53 Specifically Binds Triplex DNA In Vitro and in Cells.

Authors:  Marie Brázdová; Vlastimil Tichý; Robert Helma; Pavla Bažantová; Alena Polášková; Aneta Krejčí; Marek Petr; Lucie Navrátilová; Olga Tichá; Karel Nejedlý; Martin L Bennink; Vinod Subramaniam; Zuzana Bábková; Tomáš Martínek; Matej Lexa; Matej Adámik
Journal:  PLoS One       Date:  2016-12-01       Impact factor: 3.240

Review 9.  Human Long Noncoding RNA Interactome: Detection, Characterization and Function.

Authors:  Marek Kazimierczyk; Marta K Kasprowicz; Marta E Kasprzyk; Jan Wrzesinski
Journal:  Int J Mol Sci       Date:  2020-02-04       Impact factor: 5.923

10.  Deep learning based DNA:RNA triplex forming potential prediction.

Authors:  Yu Zhang; Yahui Long; Chee Keong Kwoh
Journal:  BMC Bioinformatics       Date:  2020-11-12       Impact factor: 3.169
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.