Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

(2017) Peter D. Stenson et al.   HUMAN GENETICS

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

(2016) Meng Li et al.   HUMAN MUTATION

Variation Interpretation Predictors: Principles, Types, Performance, and Choice

(2016) Abhishek Niroula et al.   HUMAN MUTATION

EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models

(2016) Lukas Folkman et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction

(2016) Yuedong Yang et al.   RNA

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

(2016) Konrad L. M. Rudolph et al.   PLoS Genetics

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

(2015) Lukas Folkman et al.   BIOINFORMATICS

G-quadruplexes: Emerging roles in neurodegenerative diseases and the non-coding transcriptome

(2015) Roberto Simone et al.   FEBS LETTERS

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)

(2015) Christopher Douville et al.   HUMAN MUTATION

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

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

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

G-quadruplexes and their regulatory roles in biology

(2015) Daniela Rhodes et al.   NUCLEIC ACIDS RESEARCH

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i)

(2014) Carlos Bermejo-Das-Neves et al.   BMC BIOINFORMATICS

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation

(2014) X. Zhang et al.   HUMAN MOLECULAR GENETICS

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease

(2014) Sebastian Kirchner et al.   NATURE REVIEWS GENETICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

Identification of deleterious synonymous variants in human genomes

(2013) Orion J. Buske et al.   BIOINFORMATICS

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou 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

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

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   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

Genome-wide survey of interindividual differences of RNA stability in human lymphoblastoid cell lines

(2013) Jubao Duan et al.   Scientific Reports

The evolution, impact and properties of exonic splice enhancers

(2013) Eva Cáceres et al.   GENOME BIOLOGY

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

(2013) Huiying Zhao et al.   GENOME BIOLOGY

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis

(2012) Mauno Vihinen   HUMAN MUTATION

SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

(2012) Tuo Zhang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

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

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

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

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Understanding the contribution of synonymous mutations to human disease

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

WT1 Synonymous Single Nucleotide Polymorphism rs16754 Correlates With Higher mRNA Expression and Predicts Significantly Improved Outcome in Favorable-Risk Pediatric Acute Myeloid Leukemia: A Report From the Children's Oncology Group

(2010) Phoenix A. Ho et al.   JOURNAL OF CLINICAL ONCOLOGY

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

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

Genetic Association Study Identifies HSPB7 as a Risk Gene for Idiopathic Dilated Cardiomyopathy

(2010) Klaus Stark et al.   PLoS Genetics

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

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

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

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics