Estimating the prevalence of functional exonic splice regulatory information

Both maintenance and avoidance of RNA-binding protein interactions constrain coding sequence evolution

(2017) Savisaar Rosina et al.   MOLECULAR BIOLOGY AND EVOLUTION

dbDSM: a manually curated database for deleterious synonymous mutations

(2016) Pengbo Wen et al.   BIOINFORMATICS

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

Purifying Selection on Exonic Splice Enhancers in Intronless Genes

(2016) Rosina Savisaar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation

(2016) S. Aylin Cakiroglu et al.   NUCLEIC ACIDS RESEARCH

Coding Regions of Intrinsic Disorder Accommodate Parallel Functions

(2016) Rita Pancsa et al.   TRENDS IN BIOCHEMICAL SCIENCES

How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing?

(2016) Dror Hollander et al.   TRENDS IN GENETICS

The Meaning of NMD: Translate or Perish

(2016) Saverio Brogna et al.   TRENDS IN GENETICS

The complete local genotype–phenotype landscape for the alternative splicing of a human exon

(2016) Philippe Julien et al.   Nature Communications

Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools

(2016) Omar Soukarieh et al.   PLoS Genetics

Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function

(2016) Mojca Tajnik et al.   PLoS Genetics

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

An Evolutionary Classification of Genomic Function

(2015) Dan Graur et al.   Genome Biology and Evolution

The Silent Sway of Splicing by Synonymous Substitutions

(2015) William F. Mueller et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Are Synonymous Sites in Primates and Rodents Functionally Constrained?

(2015) Nicholas Price et al.   JOURNAL OF MOLECULAR EVOLUTION

Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associatedcis-Motifs

(2015) XianMing Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Disentangling Sources of Selection on Exonic Transcriptional Enhancers

(2015) Rachel M. Agoglia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reassessing the “Duon” Hypothesis of Protein Evolution

(2015) Ke Xing et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of the Usage of Splice-Associatedcis-Motifs Predict the Distribution of Human Pathogenic SNPs

(2015) XianMing Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Specificity and nonspecificity in RNA–protein interactions

(2015) Eckhard Jankowsky et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Splice junctions are constrained by protein disorder

(2015) Ben Smithers et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

The alternative role of DNA methylation in splicing regulation

(2015) Galit Lev Maor et al.   TRENDS IN GENETICS

HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing

(2015) Ahuvi Yearim et al.   Cell Reports

Junk or functional DNA? ENCODE and the function controversy

(2014) Pierre-Luc Germain et al.   BIOLOGY & PHILOSOPHY

High-throughput characterization of protein-RNA interactions

(2014) K. B. Cook et al.   Briefings in Functional Genomics

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Identification of Splicing Defects Caused by Mutations in the Dysferlin Gene

(2014) Virginie Kergourlay et al.   HUMAN MUTATION

Purifying Selection on Splice-Related Motifs, Not Expression Level nor RNA Folding, Explains Nearly All Constraint on Human lincRNAs

(2014) Andreas Schüler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional Conservation of Both CDS- and 3′-UTR-Located MicroRNA Binding Sites between Species

(2014) Guojing Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of gene expression programmes by serine–arginine rich splicing factors

(2014) Minna-Liisa Änkö   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Reciprocal regulatory links between cotranscriptional splicing and chromatin

(2014) Sérgio Fernandes de Almeida et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Synonymous Constraint Elements Show a Tendency to Encode Intrinsically Disordered Protein Segments

(2014) Mauricio Macossay-Castillo et al.   PLoS Computational Biology

Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional Regulation

(2014) Ramon Y. Birnbaum et al.   PLoS Genetics

Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms

(2014) Fernando Racimo et al.   PLoS Genetics

The RNAissance family: SR proteins as multifaceted regulators of gene expression

(2014) Jonathan M. Howard et al.   Wiley Interdisciplinary Reviews-RNA

The translational landscape of the splicing factor SRSF1 and its role in mitosis

(2014) Magdalena M Maslon et al.   eLife

Open questions: A logic (or lack thereof) of genome organization

(2013) Laurence D Hurst   BMC BIOLOGY

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

The ENCODE project: Missteps overshadowing a success

(2013) Sean R. Eddy   CURRENT BIOLOGY

A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations

(2013) A. Kousathanas et al.   GENETICS

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation

(2013) J. Hausser et al.   GENOME RESEARCH

Functional Analysis of a Large set of BRCA2 exon 7 Variants Highlights the Predictive Value of Hexamer Scores in Detecting Alterations of Exonic Splicing Regulatory Elements

(2013) Daniela Di Giacomo et al.   HUMAN MUTATION

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

(2013) Shatakshi Pandit et al.   MOLECULAR CELL

Genome-wide inference of natural selection on human transcription factor binding sites

(2013) Leonardo Arbiza et al.   NATURE GENETICS

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

(2013) Chaolin Zhang et al.   NUCLEIC ACIDS RESEARCH

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

(2013) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs

(2013) J. Wan et al.   NUCLEIC ACIDS RESEARCH

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels

(2013) Li Jiang et al.   PLoS Genetics

Strong Purifying Selection at Synonymous Sites in D. melanogaster

(2013) David S. Lawrie et al.   PLoS Genetics

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

The evolution, impact and properties of exonic splice enhancers

(2013) Eva Cáceres et al.   GENOME BIOLOGY

Can ENCODE tell us how much junk DNA we carry in our genome?

(2012) Deng-Ke Niu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

What does our genome encode?

(2012) J. A. Stamatoyannopoulos   GENOME RESEARCH

Observation of dually decoded regions of the human genome using ribosome profiling data

(2012) A. M. Michel et al.   GENOME RESEARCH

Multiple sequence variants ofBRCA2exon 7 alter splicing regulation

(2012) Pascaline Gaildrat et al.   JOURNAL OF MEDICAL GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Connections between chromatin signatures and splicing

(2012) Luciana I. Gómez Acuña et al.   Wiley Interdisciplinary Reviews-RNA

Selected effects and causal role functions in the brain: the case for an etiological approach to neuroscience

(2011) Justin Garson   BIOLOGY & PHILOSOPHY

GC content around splice sites affects splicing through pre-mRNA secondary structures

(2011) Jing Zhang et al.   BMC GENOMICS

RNA structure and the mechanisms of alternative splicing

(2011) C Joel McManus et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes

(2011) Jean Christophe Théry et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Inference of Site Frequency Spectra From High-Throughput Sequence Data: Quantification of Selection on Nonsynonymous and Synonymous Sites in Humans

(2011) Peter D. Keightley et al.   GENETICS

A Method for Inferring the Rate of Occurrence and Fitness Effects of Advantageous Mutations

(2011) Adrian Schneider et al.   GENETICS

Inference of Mutation Parameters and Selective Constraint in Mammalian Coding Sequences by Approximate Bayesian Computation

(2011) P. D. Keightley et al.   GENETICS

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

(2011) M. F. Lin et al.   GENOME RESEARCH

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Loss of exon identity is a common mechanism of human inherited disease

(2011) T. Sterne-Weiler et al.   GENOME RESEARCH

Cancer Risks Associated With Germline Mutations in MLH1, MSH2, and MSH6 Genes in Lynch Syndrome

(2011) Valérie Bonadona   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The Impact of miRNA Target Sites in Coding Sequences and in 3′UTRs

(2011) Zhuo Fang et al.   PLoS One

Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes

(2011) K. H. Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New insights into RNA secondary structure in the alternative splicing of pre-mRNAs

(2011) Yongfeng Jin et al.   RNA Biology

A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences

(2011) Daniel J. Wilson et al.   PLoS Genetics

Regulation of splicing enhancer activities by RNA secondary structures

(2010) Wei Liu et al.   FEBS LETTERS

Overlapping codes within protein-coding sequences

(2010) S. Itzkovitz et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

A Splicing-Independent Function of SF2/ASF in MicroRNA Processing

(2010) Han Wu et al.   MOLECULAR CELL

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

Genomic features defining exonic variants that modulate splicing

(2010) Adam Woolfe et al.   GENOME BIOLOGY

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Distributions of Selectively Constrained Sites and Deleterious Mutation Rates in the Hominid and Murid Genomes

(2009) L. Eory et al.   MOLECULAR BIOLOGY AND EVOLUTION

SR Protein Family Members Display Diverse Activities in the Formation of Nascent and Mature mRNPs In Vivo

(2009) Aparna K. Sapra et al.   MOLECULAR CELL

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

A computational approach for genome-wide mapping of splicing factor binding sites

(2009) Martin Akerman et al.   GENOME BIOLOGY

Overlapping genes in the human and mouse genomes

(2008) Chaitanya R Sanna et al.   BMC GENOMICS

Mid-frequency DFNA8/12 hearing loss caused by a synonymous TECTA mutation that affects an exonic splice enhancer

(2008) Rob W J Collin et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A large fraction of unclassified variants of the mismatch repair genesMLH1andMSH2is associated with splicing defects

(2008) Isabelle Tournier et al.   HUMAN MUTATION

The Splicing Factor SF2/ASF Regulates Translation Initiation by Enhancing Phosphorylation of 4E-BP1

(2008) Gracjan Michlewski et al.   MOLECULAR CELL

The splicing factor SC35 has an active role in transcriptional elongation

(2008) Shengrong Lin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence

(2008) J. J. Forman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved RNA secondary structures promote alternative splicing

(2008) P. J. Shepard et al.   RNA

The Impact of the Nucleosome Code on Protein-Coding Sequence Evolution in Yeast

(2008) Tobias Warnecke et al.   PLoS Genetics

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics

Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes

(2008) Tobias Warnecke et al.   GENOME BIOLOGY