4.6 Article

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemistry & Molecular Biology

The emerging structural complexity of G-quadruplex RNAs

Michael T. Banco et al.

Summary: Recent studies have discovered unprecedented complexity in RNA G4 structures, deviating from the traditional belief that these structures are relatively simple. This deviation from the requirement of consecutive nucleotides for guanine stacks has expanded the structural possibilities of RNA G-quadruplexes.
Article Biology

Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution

Feng Wu et al.

Summary: Wu, Niu, Cui et al characterized G4 motifs across 37 species by bioinformatics, revealing that G4 complexity increases with evolution, as well as an antagonistic relationship between the potential G4s and DNA methylation sites.

COMMUNICATIONS BIOLOGY (2021)

Article Multidisciplinary Sciences

Genome-wide discovery of G-quadruplexes in barley

H. Busra Cagirici et al.

Summary: This study identified and compared G4 motifs in barley with other monocot species, revealing their genomic distribution and molecular functions. The distribution of G4 motifs around genic regions was found to be relatively similar in the species studied, except for Arabidopsis.

SCIENTIFIC REPORTS (2021)

Article Biochemical Research Methods

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions

Vincent Rocher et al.

Summary: DNA is a complex molecule that carries instructions for organism development, living, and reproduction, with G4 being an important structure in DNA that plays a key role in cells. DeepG4 is a novel convolutional neural network that accurately predicts cell-type specific active G4 regions, identifying multiple predictive DNA motifs for G4 region activity.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Biochemical Research Methods

Performance of Regression Models as a Function of Experiment Noise

Gang Li et al.

Summary: This study introduces a new method to estimate the upper bound of model performance on test data, which can assist researchers in developing machine learning regression models that reach their maximum potential. The upper bound estimate, validated via Monte Carlo simulations, has been successfully used as a performance-guiding tool for regression models on biological datasets.

BIOINFORMATICS AND BIOLOGY INSIGHTS (2021)

Article Genetics & Heredity

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles

H. Busra Cagirici et al.

G3-GENES GENOMES GENETICS (2020)

Article Multidisciplinary Sciences

The barley pan-genome reveals the hidden legacy of mutation breeding

Murukarthick Jayakodi et al.

NATURE (2020)

Article Multidisciplinary Sciences

Multiple wheat genomes reveal global variation in modern breeding

Sean Walkowiak et al.

NATURE (2020)

Review Chemistry, Multidisciplinary

The Structure and Function of DNA G-Quadruplexes

Jochen Spiegel et al.

TRENDS IN CHEMISTRY (2020)

Article Biochemistry & Molecular Biology

Whole genome experimental maps of DNA G-quadruplexes in multiple species

Giovanni Marsico et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Machine learning algorithm validation with a limited sample size

Andrius Vabalas et al.

PLOS ONE (2019)

Article Biochemistry & Molecular Biology

MaizeGDB 2018: the maize multi-genome genetics and genomics database

John L. Portwood et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure

Anita Kotar et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Cecile Monat et al.

GENOME BIOLOGY (2019)

Article Biophysics

Prediction of the secondary structure of short DNA aptamers

Arina Afanasyeva et al.

BIOPHYSICS AND PHYSICOBIOLOGY (2019)

Article Biochemistry & Molecular Biology

G4RNA screener web server: User focused interface for RNA G-quadruplex prediction

Jean-Michel Garant et al.

BIOCHIMIE (2018)

Article Chemistry, Medicinal

Classifiers and their Metrics Quantified

J. B. Brown

MOLECULAR INFORMATICS (2018)

Letter Biochemistry & Molecular Biology

Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes

Daniel B. Sloan et al.

PLANT CELL (2018)

Article Chemistry, Multidisciplinary

Major G-Quadruplex Form of HIV-1 LTR Reveals a (3+1) Folding Topology Containing a Stem-Loop

Elena Butovskaya et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Multidisciplinary Sciences

A chromosome conformation capture ordered sequence of the barley genome

Martin Mascher et al.

NATURE (2017)

Article Multidisciplinary Sciences

Machine learning model for sequence-driven DNA G-quadruplex formation

Aleksandr B. Sahakyan et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

The expanding repertoire of G4 DNA structures

Anna Varizhuk et al.

BIOCHIMIE (2017)

Article Biochemistry & Molecular Biology

G-quadruplexes as novel cis-elements controlling transcription during embryonic development

Aldana P. David et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Re-evaluation of G-quadruplex propensity with G4Hunter

Amina Bedrat et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

Junjie U. Guo et al.

SCIENCE (2016)

Review Chemistry, Multidisciplinary

Metal Cations in G-Quadruplex Folding and Stability

Debmalya Bhattacharyya et al.

FRONTIERS IN CHEMISTRY (2016)

Article Biotechnology & Applied Microbiology

High-throughput sequencing of DNA G-quadruplex structures in the human genome

Vicki S. Chambers et al.

NATURE BIOTECHNOLOGY (2015)

Article Cell Biology

Post-transcriptional Regulation of Nkx2-5 by RHAU in Heart Development

Junwei Nie et al.

CELL REPORTS (2015)

Article Multidisciplinary Sciences

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

Andrew L. Wolfe et al.

NATURE (2014)

Article Biochemistry & Molecular Biology

New scoring system to identify RNA G-quadruplex folding

Jean-Denis Beaudoin et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Chemistry, Physical

Effect of Loops and G-Quartets on the Stability of RNA G-Quadruplexes

Satyaprakash Pandey et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Multidisciplinary

Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences

Vineeth Thachappilly Mukundan et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Article Computer Science, Artificial Intelligence

Gradient boosting machines, a tutorial

Alexey Natekin et al.

FRONTIERS IN NEUROROBOTICS (2013)

Review Genetics & Heredity

DNA secondary structures: stability and function of G-quadruplex structures

Matthew L. Bochman et al.

NATURE REVIEWS GENETICS (2012)

Article Biochemical Research Methods

ViennaRNA Package 2.0

Ronny Lorenz et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

G-quadruplex-induced instability during leading-strand replication

Judith Lopes et al.

EMBO JOURNAL (2011)

Article Chemistry, Multidisciplinary

Inhibition of Translation by Small RNA-Stabilized mRNA Structures in Human Cells

Kenichiro Ito et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Review Biochemistry & Molecular Biology

Structure, location and interactions of G-quadruplexes

Julian L. Huppert

FEBS JOURNAL (2010)

Article Biochemistry & Molecular Biology

RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles

Melissa A. Mullen et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

How long is too long? Effects of loop size on G-quadruplex stability

Aurore Guedin et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex

Gavin W. Collie et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

CENTROIDFOLD: a web server for RNA secondary structure prediction

Kengo Sato et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

Telomerase recruitment by the telomere end binding protein-β facilitates G-quadruplex DNA unfolding in ciliates

Katrin Paeschke et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2008)

Review Biochemistry & Molecular Biology

Stability and kinetics of G-quadruplex structures

Andrew N. Lane et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Multidisciplinary Sciences

The map-based sequence of the rice genome

T Matsumoto et al.

NATURE (2005)

Article Biochemistry & Molecular Biology

Prevalence of quadruplexes in the human genome

JL Huppert et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Finishing the euchromatic sequence of the human genome

FS Collins et al.

NATURE (2004)

Article Biochemistry & Molecular Biology

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker

NUCLEIC ACIDS RESEARCH (2003)

Article Multidisciplinary Sciences

Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription

A Siddiqui-Jain et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)