Literature DB >> 31943112

A guide to computational methods for G-quadruplex prediction.

Emilia Puig Lombardi1, Arturo Londoño-Vallejo1.   

Abstract

Year:  2020        PMID: 31943112      PMCID: PMC7026631          DOI: 10.1093/nar/gkaa033

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


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Nucleic Acids Research, 2019, gkz1097, https://doi.org/10.1093/nar/gkz1097 During the preparation of the revised version of this survey, another relevant article appeared in Bioinformatics. For completeness, a citation has been added to the end of the Concluding Remarks: … Currently, two algorithms are designed to predict higher-order, or multimeric, quadruplex structures: G4-iM Grinder, also intended as a tool for i-motif identification (98); and QPARSE, a tool specifically developed for the prediction of both multimeric quadruplex structures and G4s with long, hairpin loops (113). This addition does not affect the results and conclusion of the study.
  1 in total

1.  QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable.

Authors:  Michele Berselli; Enrico Lavezzo; Stefano Toppo
Journal:  Bioinformatics       Date:  2020-01-15       Impact factor: 6.937

  1 in total
  12 in total

1.  G-quadruplex structural variations in human genome associated with single-nucleotide variations and their impact on gene activity.

Authors:  Jia-Yuan Gong; Cui-Jiao Wen; Ming-Liang Tang; Rui-Fang Duan; Juan-Nan Chen; Jia-Yu Zhang; Ke-Wei Zheng; Yi-de He; Yu-Hua Hao; Qun Yu; Su-Ping Ren; Zheng Tan
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-25       Impact factor: 11.205

2.  G-quadruplexes in H1N1 influenza genomes.

Authors:  Václav Brázda; Otília Porubiaková; Alessio Cantara; Natália Bohálová; Jan Coufal; Martin Bartas; Miroslav Fojta; Jean-Louis Mergny
Journal:  BMC Genomics       Date:  2021-01-23       Impact factor: 3.969

3.  MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif.

Authors:  Amen Shamim; Maria Razzaq; Kyeong Kyu Kim
Journal:  Int J Mol Sci       Date:  2020-12-23       Impact factor: 5.923

Review 4.  RNA G-quadruplexes (rG4s): genomics and biological functions.

Authors:  Kaixin Lyu; Eugene Yui-Ching Chow; Xi Mou; Ting-Fung Chan; Chun Kit Kwok
Journal:  Nucleic Acids Res       Date:  2021-06-04       Impact factor: 16.971

Review 5.  Impact of G-Quadruplexes and Chronic Inflammation on Genome Instability: Additive Effects during Carcinogenesis.

Authors:  MaryElizabeth Stein; Kristin A Eckert
Journal:  Genes (Basel)       Date:  2021-11-09       Impact factor: 4.096

6.  R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences.

Authors:  Václav Brázda; Jan Havlík; Jan Kolomazník; Oldřich Trenz; Jiří Šťastný
Journal:  Int J Mol Sci       Date:  2021-11-27       Impact factor: 5.923

Review 7.  The Dynamic Regulation of G-Quadruplex DNA Structures by Cytosine Methylation.

Authors:  Aaron John Stevens; Lucy de Jong; Martin Alexander Kennedy
Journal:  Int J Mol Sci       Date:  2022-02-22       Impact factor: 5.923

Review 8.  How bioinformatics resources work with G4 RNAs.

Authors:  Joanna Miskiewicz; Joanna Sarzynska; Marta Szachniuk
Journal:  Brief Bioinform       Date:  2021-05-20       Impact factor: 11.622

Review 9.  Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions.

Authors:  Lucie Poggi; Guy-Franck Richard
Journal:  Microbiol Mol Biol Rev       Date:  2020-12-23       Impact factor: 11.056

10.  A CpG island promoter drives the CXXC5 gene expression.

Authors:  Pelin Yaşar; Gizem Kars; Kerim Yavuz; Gamze Ayaz; Çerağ Oğuztüzün; Ecenaz Bilgen; Zeynep Suvacı; Özgül Persil Çetinkol; Tolga Can; Mesut Muyan
Journal:  Sci Rep       Date:  2021-08-02       Impact factor: 4.379

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