Performance evaluation of differential splicing analysis methods and splicing analytics platform construction

RNA splicing analysis contributes to reclassifying variants of uncertain significance and improves the diagnosis of monogenic disorders

(2022) Wen-Bin He et al.   JOURNAL OF MEDICAL GENETICS

MutSpliceDB: A database of splice sites variants with RNA‐seq based evidence on effects on splicing

(2021) Alida Palmisano et al.   HUMAN MUTATION

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

(2021) Philipp Rentzsch et al.   Genome Medicine

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

(2021) Daniel Danis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bi-allelic variants in DNAH10 cause asthenoteratozoospermia and male infertility

(2021) Kuokuo Li et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA

(2021) Yuan Gao et al.   NUCLEIC ACIDS RESEARCH

Decoding the effects of synonymous variants

(2021) Zishuo Zeng et al.   NUCLEIC ACIDS RESEARCH

VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases

(2021) Dandan Huang et al.   NUCLEIC ACIDS RESEARCH

TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse

(2021) Yuexin Zhang et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Konrad J. Karczewski et al.   NATURE

Clinical impact of splicing in neurodevelopmental disorders

(2020) Stephan J. Sanders et al.   Genome Medicine

LncSEA: a platform for long non-coding RNA related sets and enrichment analysis

(2020) Jiaxin Chen et al.   NUCLEIC ACIDS RESEARCH

dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

(2020) Xiaoming Liu et al.   Genome Medicine

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan 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

regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants

(2019) Shijie Zhang et al.   NUCLEIC ACIDS RESEARCH

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms

(2019) Rebecca L. Walker et al.   CELL

The Expanding Landscape of Alternative Splicing Variation in Human Populations

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

Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort

(2018) Raphaël Leman et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders

(2018) Xinwei Han et al.   Nature Communications

SEdb: a comprehensive human super-enhancer database

(2018) Yong Jiang et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Deep intronic mutations and human disease

(2017) Rita Vaz-Drago et al.   HUMAN GENETICS

Pathogenic variants that alter protein code often disrupt splicing

(2017) Rachel Soemedi et al.   NATURE GENETICS

ASpedia: a comprehensive encyclopedia of human alternative splicing

(2017) Daejin Hyung et al.   NUCLEIC ACIDS RESEARCH

VarCards: an integrated genetic and clinical database for coding variants in the human genome

(2017) Jinchen Li et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Monkol Lek et al.   NATURE

An expanded sequence context model broadly explains variability in polymorphism levels across the human genome

(2016) Varun Aggarwala et al.   NATURE GENETICS

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

TransVar: a multilevel variant annotator for precision genomics

(2015) Wanding Zhou et al.   NATURE METHODS

RNA mis-splicing in disease

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

The human gene damage index as a gene-level approach to prioritizing exome variants

(2015) Yuval Itan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity

(2015) Slavé Petrovski et al.   PLoS Genetics

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

(2014) Xueqiu Jian et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown 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

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

Kaviar: an accessible system for testing SNV novelty

(2011) Gustavo Glusman et al.   BIOINFORMATICS

Quantitative evaluation of all hexamers as exonic splicing elements

(2011) Shengdong Ke et al.   GENOME RESEARCH

Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6

(2011) Michela Raponi et al.   HUMAN MUTATION

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

A G to C transversion at the last nucleotide of exon 25 of the MYH9 gene results in a missense mutation rather than in a splicing defect

(2010) Silvia Vettore et al.   European Journal of Medical Genetics

DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites

(2010) E. Buratti et al.   NUCLEIC ACIDS RESEARCH

Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping

(2009) Petr Divina et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

(2008) Qun Pan et al.   NATURE GENETICS