CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

ASCOT identifies key regulators of neuronal subtype-specific splicing

(2020) Jonathan P. Ling et al.   Nature Communications

Transcript expression-aware annotation improves rare variant interpretation

(2020) Beryl B. Cummings et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

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

(2019) Pablo Baeza-Centurion et al.   CELL

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing

(2019) Karthik A. Jagadeesh et al.   NATURE GENETICS

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

(2019) Žiga Avsec et al.   NATURE BIOTECHNOLOGY

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

(2019) Pejman Mohammadi et al.   SCIENCE

Personalised analytics for rare disease diagnostics

(2019) Denise Anderson et al.   Nature Communications

GeVIR is a continuous gene-level metric that uses variant distribution patterns to prioritize disease candidate genes

(2019) Nikita Abramovs et al.   NATURE GENETICS

The Expanding Landscape of Alternative Splicing Variation in Human Populations

(2018) Eddie Park et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Splicing mutations in human genetic disorders: examples, detection, and confirmation

(2018) Abramowicz Anna et al.   JOURNAL OF APPLIED GENETICS

The human noncoding genome defined by genetic diversity

(2018) Julia di Iulio et al.   NATURE GENETICS

Large-scale investigation of the reasons why potentially important genes are ignored

(2018) Thomas Stoeger et al.   PLOS BIOLOGY

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

A map of constrained coding regions in the human genome

(2018) James M. Havrilla et al.   NATURE GENETICS

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

The impact of rare variation on gene expression across tissues

(2017) Xin Li et al.   NATURE

Pathogenic variants that alter protein code often disrupt splicing

(2017) Rachel Soemedi et al.   NATURE GENETICS

Alternative splicing as a regulator of development and tissue identity

(2017) Francisco E. Baralle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel

(2016) Cheryl A. Mather et al.   GENETICS IN MEDICINE

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Lessons from non-canonical splicing

(2016) Christopher R. Sibley et al.   NATURE REVIEWS GENETICS

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

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

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

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

(2015) Alexander B. Rosenberg et al.   CELL

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

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

(2014) Martin Kircher et al.   NATURE GENETICS

In silico prediction of splice-altering single nucleotide variants in the human genome

(2014) Xueqiu Jian et al.   NUCLEIC ACIDS RESEARCH

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

(2014) H. Y. Xiong et al.   SCIENCE

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

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

In silico tools for splicing defect prediction: a survey from the viewpoint of end users

(2013) Xueqiu Jian et al.   GENETICS IN MEDICINE

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

Quantitative evaluation of all hexamers as exonic splicing elements

(2011) Shengdong Ke et al.   GENOME RESEARCH

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

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

Detection of nonneutral substitution rates on mammalian phylogenies

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

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS