The functional relevance of somatic synonymous mutations in melanoma and other cancers

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

(2015) Vedrana Bali et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A highly recurrent RPS27 5’UTR mutation in melanoma

(2015) Ken Dutton-Regester et al.   Oncotarget

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Exposing synonymous mutations

(2014) Ryan C. Hunt et al.   TRENDS IN GENETICS

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

(2014) Matthew Mort et al.   GENOME BIOLOGY

The impact of genetic heterogeneity on biomarker development in kidney cancer assessed by multiregional sampling

(2014) Alexander Sankin et al.   Cancer Medicine

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Identification of deleterious synonymous variants in human genomes

(2013) Orion J. Buske et al.   BIOINFORMATICS

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

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

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

A synonymous change, p.Gly16Gly in MECP2 Exon 1, causes a cryptic splice event in a Rett Syndrome patient

(2013) Taimoor I Sheikh et al.   Orphanet Journal of Rare Diseases

MSI2 expression is decreased in grade II of gastric carcinoma

(2013) Modjtaba Emadi-Baygi et al.   PATHOLOGY RESEARCH AND PRACTICE

Human Coding Synonymous Single Nucleotide Polymorphisms at Ramp Regions of mRNA Translation

(2013) Quan Li et al.   PLoS One

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma

(2013) J. J. Gartner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

The evolution, impact and properties of exonic splice enhancers

(2013) Eva Cáceres et al.   GENOME BIOLOGY

Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing

(2012) K. H. Lim et al.   BIOINFORMATICS

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Different mutation profiles associated to P53 accumulation in colorectal cancer

(2012) Ignacio López et al.   GENE

Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene

(2012) Alexandra Scott et al.   Journal of Cystic Fibrosis

Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies

(2012) Paige S. Spencer et al.   JOURNAL OF MOLECULAR BIOLOGY

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

(2012) Michael Krauthammer et al.   NATURE GENETICS

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative Analysis of Somatic Mutations Altering MicroRNA Targeting in Cancer Genomes

(2012) Jesse D. Ziebarth et al.   PLoS One

Prediction of variable translation rate effects on cotranslational protein folding

(2012) Edward P. O'Brien et al.   Nature Communications

Comparative Genomic Analysis of Esophageal Adenocarcinoma and Squamous Cell Carcinoma

(2012) Nishant Agrawal et al.   Cancer Discovery

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

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

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

Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution

(2011) Yedael Y. Waldman et al.   Genome Biology and Evolution

A synonymous polymorphism of the Tristetraprolin (TTP) gene, an AU-rich mRNA-binding protein, affects translation efficiency and response to Herceptin treatment in breast cancer patients

(2011) Paola Griseri et al.   HUMAN MOLECULAR GENETICS

Impact of KRAS Mutations on Clinical Outcomes in Pancreatic Cancer Patients Treated with First-line Gemcitabine-Based Chemotherapy

(2011) S. T. Kim et al.   MOLECULAR CANCER THERAPEUTICS

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing

(2011) Mitchell S Stark et al.   NATURE GENETICS

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma

(2011) Sergey I Nikolaev et al.   NATURE GENETICS

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease

(2011) Patrick Brest et al.   NATURE GENETICS

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

(2011) N. Agrawal et al.   SCIENCE

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

Frequencies of BRAF and NRAS mutations are different in histological types and sites of origin of cutaneous melanoma: a meta-analysis

(2010) J.-H. Lee et al.   BRITISH JOURNAL OF DERMATOLOGY

Using SIFT and PolyPhen to Predict Loss-of-Function and Gain-of-Function Mutations

(2010) Sarah E. Flanagan et al.   Genetic Testing and Molecular Biomarkers

A Synonymous Single Nucleotide Polymorphism in ΔF508CFTRAlters the Secondary Structure of the mRNA and the Expression of the Mutant Protein

(2010) Rafal A. Bartoszewski et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia

(2010) Michael G Kharas et al.   NATURE MEDICINE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Genomic features defining exonic variants that modulate splicing

(2010) Adam Woolfe et al.   GENOME BIOLOGY

A synonymous mutation inTCOF1causes Treacher Collins syndrome due to mis-splicing of a constitutive exon

(2009) D. Macaya et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

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

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

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

IDH1andIDH2Mutations in Gliomas

(2009) Hai Yan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer

(2009) Jens Neumann et al.   PATHOLOGY RESEARCH AND PRACTICE

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct Minima

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease

(2008) Steven A McCarroll et al.   NATURE GENETICS

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE