Mechanisms of Intron-Mediated Enhancement of Expression: Welcome to the Hotel California

Deep learning in regulatory genomics: from identification to design

(2023) Xuehai Hu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Incorporating Machine Learning into Established Bioinformatics Frameworks

(2021) Noam Auslander et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy

(2021) Simna SP et al.   CURRENT GENE THERAPY

Emerging role of non‐coding RNA in health and disease

(2021) Gurjit Kaur Bhatti et al.   METABOLIC BRAIN DISEASE

Gene Architecture Facilitates Intron-Mediated Enhancement of Transcription

(2021) Katherine Dwyer et al.   Frontiers in Molecular Biosciences

Proximity to the Promoter and Terminator Regions Regulates the Transcription Enhancement Potential of an Intron

(2021) Katherine Dwyer et al.   Frontiers in Molecular Biosciences

Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits

(2021) Jennifer P. C. To et al.   Frontiers in Plant Science

Insights Into Genetic and Molecular Elements for Transgenic Crop Development

(2020) Marcos Fernando Basso et al.   Frontiers in Plant Science

A Review on the Application of Deep Learning in Bioinformatics

(2020) Yongqing Zhang et al.   Current Bioinformatics

Multiple information carried by RNAs: total eclipse or a light at the end of the tunnel?

(2020) Baptiste Bogard et al.   RNA Biology

Introns mediate post-transcriptional enhancement of nuclear gene expression in the green microalga Chlamydomonas reinhardtii

(2020) Thomas Baier et al.   PLoS Genetics

First Come, First Served: Sui Generis Features of the First Intron

(2020) David Zalabák et al.   Plants-Basel

Crosstalk of promoter and terminator during RNA polymerase II transcription cycle

(2020) Nadra Al-Husini et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Introns as Gene Regulators: A Brick on the Accelerator

(2019) Alan B. Rose   Frontiers in Genetics

Analysis of the Functional Relevance of Epigenetic Chromatin Marks in the First Intron Associated with Specific Gene Expression Patterns

(2019) Shin-Sang Jo et al.   Genome Biology and Evolution

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Machine learning approaches and their current application in plant molecular biology: A systematic review

(2019) Jose Cleydson F. Silva et al.   PLANT SCIENCE

Alternative Splicing and Protein Diversity: Plants Versus Animals

(2019) Saurabh Chaudhary et al.   Frontiers in Plant Science

An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana

(2019) Jenna E. Gallegos et al.   Scientific Reports

Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing

(2019) Charlie F Rowlands et al.   Cells

The exon–intron gene structure upstream of the initiation codon predicts translation efficiency

(2018) Chun Shen Lim et al.   NUCLEIC ACIDS RESEARCH

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

How introns enhance gene expression

(2017) Orit Shaul   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Intron DNA Sequences Can Be More Important Than the Proximal Promoter in Determining the Site of Transcript Initiation

(2017) Jenna E. Gallegos et al.   PLANT CELL

Ten quick tips for machine learning in computational biology

(2017) Davide Chicco   BioData Mining

Intron-Mediated Enhancement: A Tool for Heterologous Gene Expression in Plants?

(2017) Miriam Laxa   Frontiers in Plant Science

Co-transcriptional splicing and the CTD code

(2016) Noélia Custódio et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs

(2016) Agnieszka M. Gromadzka et al.   NUCLEIC ACIDS RESEARCH

Intron sequences that stimulate gene expression in Arabidopsis

(2016) Alan B. Rose et al.   PLANT MOLECULAR BIOLOGY

The 5′UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II

(2016) Miriam Laxa et al.   PLANT PHYSIOLOGY

Exon Junction Complexes: Supervising the Gene Expression Assembly Line

(2016) Volker Boehm et al.   TRENDS IN GENETICS

Enhancement of Transcription by a Splicing-Competent Intron Is Dependent on Promoter Directionality

(2016) Neha Agarwal et al.   PLoS Genetics

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

The exon junction complex as a node of post-transcriptional networks

(2015) Hervé Le Hir et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The enduring mystery of intron-mediated enhancement

(2015) Jenna E. Gallegos et al.   PLANT SCIENCE

Unique Aspects of Plant Nonsense-Mediated mRNA Decay

(2015) Orit Shaul   TRENDS IN PLANT SCIENCE

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

(2014) Seung Park et al.   BMC GENOMICS

Characterization of the promoter and 5′-UTR intron of oleic acid desaturase (FAD2) gene in Brassica napus

(2014) Gang Xiao et al.   GENE

Functional characterization of the plant ubiquitin regulatory X (UBX) domain-containing protein AtPUX7 in Arabidopsis thaliana

(2013) Jean-Luc Gallois et al.   GENE

The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5′ UTR intron

(2013) Tsofit Akua et al.   JOURNAL OF EXPERIMENTAL BOTANY

The effects of a stimulating intron on the expression of heterologous genes inArabidopsis thaliana

(2013) Shahram Emami et al.   PLANT BIOTECHNOLOGY JOURNAL

The intron from the 5′-UTR of the FBP11 gene in petunia displays promoter- and enhancer-like functions

(2013) Liao Liao et al.   SCIENTIA HORTICULTURAE

Origin and evolution of spliceosomal introns

(2012) Igor B Rogozin et al.   Biology Direct

Differences in intron-mediated enhancement of gene expression by the first intron of cytosolic superoxide dismutase gene from rice in monocot and dicot plants

(2012) Shigeto Morita et al.   Plant Biotechnology

Role for gene looping in intron-mediated enhancement of transcription

(2012) A. M. Moabbi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

The Function of Introns

(2012) Michal Chorev et al.   Frontiers in Genetics

Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity

(2011) Deng-Ke Niu et al.   Biology Direct

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

(2011) G. Parra et al.   NUCLEIC ACIDS RESEARCH

Pre-mRNA splicing is a determinant of histone H3K36 methylation

(2011) S. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement

(2011) Alan B. Rose et al.   Frontiers in Plant Science

The leader intron of AtMHX can elicit, in the absence of splicing, low-level intron-mediated enhancement that depends on the internal intron sequence

(2010) Tsofit Akua et al.   BMC PLANT BIOLOGY

Testing the IMEter on rice introns and other aspects of intron-mediated enhancement of gene expression

(2010) Laura Morello et al.   JOURNAL OF EXPERIMENTAL BOTANY

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Promoter deletion analysis elucidates the role ofciselements and 5'UTR intron in spatiotemporal regulation ofAtPht1;4expression in Arabidopsis

(2009) Athikkattuvalasu S. Karthikeyan et al.   PHYSIOLOGIA PLANTARUM

Plant Spliceosomal Introns: Not Only Cut and Paste

(2008) L. Morello et al.   CURRENT GENOMICS

A 5′ Splice Site Enhances the Recruitment of Basal Transcription Initiation Factors In Vivo

(2008) Christian Kroun Damgaard et al.   MOLECULAR CELL

Transcriptional and post-transcriptional enhancement of gene expression by the 5′ UTR intron of rice rubi3 gene in transgenic rice cells

(2008) Partha Samadder et al.   MOLECULAR GENETICS AND GENOMICS

Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression

(2008) A. B. Rose et al.   PLANT CELL

Activity of the 5′ regulatory regions of the rice polyubiquitin rubi3 gene in transgenic rice plants as analyzed by both GUS and GFP reporter genes

(2008) Jianli Lu et al.   PLANT CELL REPORTS

RNA Silencing in Plants: Yesterday, Today, and Tomorrow

(2008) A. Eamens et al.   PLANT PHYSIOLOGY

Longer First Introns Are a General Property of Eukaryotic Gene Structure

(2008) Keith R. Bradnam et al.   PLoS One

Splicing promotes rapid and efficient mRNA export in mammalian cells

(2008) P. Valencia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In trangenic rice, α- and β-tubulin regulatory sequences control GUS amount and distribution through intron mediated enhancement and intron dependent spatial expression

(2008) Silvia Gianì et al.   TRANSGENIC RESEARCH