A broad analysis of splicing regulation in yeast using a large library of synthetic introns

A first exon termination checkpoint preferentially suppresses extragenic transcription

(2021) Liv M. I. Austenaa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing

(2019) Pablo Baeza-Centurion et al.   CELL

Constitutive splicing and economies of scale in gene expression

(2019) Fangyuan Ding et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A unified mechanism for intron and exon definition and back-splicing

(2019) Xueni Li et al.   NATURE

Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms

(2019) Idan Frumkin et al.   PLOS BIOLOGY

Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries

(2019) Martin Mikl et al.   Nature Communications

RNA Splicing by the Spliceosome

(2019) Max E. Wilkinson et al.   Annual Review of Biochemistry

Random sequences rapidly evolve into de novo promoters

(2018) Avihu H. Yona et al.   Nature Communications

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

(2018) Rocky Cheung et al.   MOLECULAR CELL

Structure of a spliceosome remodelled for exon ligation

(2017) Sebastian M. Fica et al.   NATURE

High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection

(2017) Alper Celik et al.   RNA

Postcatalytic spliceosome structure reveals mechanism of 3′–splice site selection

(2017) Max E. Wilkinson et al.   SCIENCE

A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ 54 Promoters

(2017) Lior Levy et al.   Cell Reports

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

(2017) Bing Feng et al.   Scientific Reports

5´-UTR introns enhance protein expression in the yeast Saccharomyces cerevisiae

(2016) Hisashi Hoshida et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein geneCirbp

(2016) Ivana Gotic et al.   GENES & DEVELOPMENT

Structure of a yeast step II catalytically activated spliceosome

(2016) Chuangye Yan et al.   SCIENCE

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

AK-fold averaging cross-validation procedure

(2015) Yoonsuh Jung et al.   JOURNAL OF NONPARAMETRIC STATISTICS

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

(2015) Ophir Shalem et al.   PLoS Genetics

Intron Evolution in Saccharomycetaceae

(2014) Katarzyna B. Hooks et al.   Genome Biology and Evolution

U2AF1mutations alter splice site recognition in hematological malignancies

(2014) Janine O. Ilagan et al.   GENOME RESEARCH

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae

(2014) Ido Yofe et al.   PLoS Genetics

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Patterns of missplicing due to somatic U2AF1 mutations in myeloid neoplasms

(2013) B. Przychodzen et al.   BLOOD

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

RF-Cloning.org: an online tool for the design of restriction-free cloning projects

(2012) S. R. Bond et al.   NUCLEIC ACIDS RESEARCH

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

(2012) Y. Harigaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae

(2012) M. Plass et al.   RNA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes

(2011) Julie Parenteau et al.   CELL

The intronome of budding yeasts

(2011) Cécile Neuvéglise et al.   COMPTES RENDUS BIOLOGIES

Deciphering 3′ss Selection in the Yeast Genome Reveals an RNA Thermosensor that Mediates Alternative Splicing

(2011) Markus Meyer et al.   MOLECULAR CELL

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

(2011) Timothy A Graubert et al.   NATURE GENETICS

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Key features of the two-intron Saccharomyces cerevisiae gene SUS1 contribute to its alternative splicing

(2011) Munshi Azad Hossain et al.   NUCLEIC ACIDS RESEARCH

The mechanism of the second step of pre-mRNA splicing

(2011) David S. Horowitz   Wiley Interdisciplinary Reviews-RNA

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

Alternative Splicing of PTC7 in Saccharomyces cerevisiae Determines Protein Localization

(2009) K. Juneau et al.   GENETICS

The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression

(2008) Stefanie E. Grund et al.   JOURNAL OF CELL BIOLOGY

Widespread Impact of Nonsense-Mediated mRNA Decay on the Yeast Intronome

(2008) Shakir Sayani et al.   MOLECULAR CELL